Daily Papers

Long-horizon agents accumulate trajectories spanning hundreds of interleaved reasoning, action, and observation steps, where answering a query may depend on evidence buried far back in the history. External memory stores such trajectories as structured representations, yet each structure provides a distinct and incomplete view. Existing multi-memory systems either read a fixed set of structures for every query, inflating context and introducing noise, or route each query to a single structure, preventing the composition of complementary evidence. A controlled analysis on AMA-Bench shows that the optimal memory configuration is typically neither a single structure nor the full union, but a tailored composition of multiple structural memories that varies with query and task demands. Motivated by these findings, we formulate structure-level dynamic selection: selecting and fusing a query-adaptive subset from a library of specialized memory structures. We propose MESA (a Multi-structure Evidence Selection framework for long-horizon Agent), which builds five complementary structure views of each trajectory and learns from end-to-end answer-level feedback to select and fuse a query-specific subset for a frozen answer model. To learn under this weak supervision, MESA employs harness optimization with prior-guided search and UCB-guided scheduling to balance exploration and exploitation. On AMA-Bench, MESA outperforms the strongest baseline by 8.5% while using 41% fewer evidence tokens than the all-structure alternative.

Fixed-layout indoor furniture styling requires selecting assets that form a coherent room without changing the prescribed furniture categories, positions, orientations, or scales. Existing approaches typically retrieve each asset independently or rely on static local relations, making them prone to shape, material, and color conflicts after scene composition. We introduce StyleForge, a scene-level structured selection framework built on a dynamic hypergraph style field. A frozen multimodal large language model extracts structured style priors from an open-ended style request and the fixed layout, while StyleForge maintains a learnable candidate distribution for each furniture slot. Conditioned on the target style, the dynamic hypergraph style field adaptively activates and weights layout-induced hyperedges to capture higher-order dependencies among furniture. Counterfactual style preference learning then treats each candidate as a local substitution in the current style field and evaluates its contextual compatibility using Mahalanobis energies. Training alternates between optimizing the style field and the candidate logits. At inference, the model remains frozen and test-time training updates only room-specific candidate logits, progressively correcting cross-slot style conflicts as the global scene context evolves. Experiments on 3D-FRONT demonstrate state-of-the-art furniture retrieval and scene-level style coherence, producing more coherent fixed-layout furniture arrangements than object- and scene-level retrieval baselines.

We derive the tree-level interaction vertices of the linear sigma model with quarks in the presence of global rotation. Starting from the scalar and fermionic field solutions in a rotating background, we construct the corresponding spectral representations and use them to evaluate the mesonic self-interactions and Yukawa couplings of the model. We show that rotation modifies the usual momentum-space structure of the interaction vertices: conservation of longitudinal momentum is accompanied by angular-momentum selection rules, while the transverse dynamics is encoded in rotation-induced radial form factors involving products of Bessel functions. The resulting expressions provide a set of interaction rules adapted to the symmetries and finite geometry of the rotating system. Although derived within the linear sigma model with quarks, the structures obtained for scalar self-interactions and scalar-fermion couplings can be extended to a broader class of quantum field theories under global rotation. These results provide the building blocks for perturbative calculations and contribute toward a microscopic quantum-field-theoretical description of interacting matter in rotating environments.

Contemporary machine learning paradigm excels in statistical data analysis, solving problems that classical AI couldn't. However, it faces key limitations, such as a lack of integration with planning, incomprehensible internal structure, and inability to learn continually. We present the initial design for an AI system, Agential AI (AAI), in principle operating independently or on top of statistical methods, designed to overcome these issues. AAI's core is a learning method that models temporal dynamics with guarantees of completeness, minimality, and continual learning, using component-level variation and selection to learn the structure of the environment. It integrates this with a behavior algorithm that plans on a learned model and encapsulates high-level behavior patterns. Preliminary experiments on a simple environment show AAI's effectiveness and potential.

Dynamic feature selection, where we sequentially query features to make accurate predictions with a minimal budget, is a promising paradigm to reduce feature acquisition costs and provide transparency into a model's predictions. The problem is challenging, however, as it requires both predicting with arbitrary feature sets and learning a policy to identify valuable selections. Here, we take an information-theoretic perspective and prioritize features based on their mutual information with the response variable. The main challenge is implementing this policy, and we design a new approach that estimates the mutual information in a discriminative rather than generative fashion. Building on our approach, we then introduce several further improvements: allowing variable feature budgets across samples, enabling non-uniform feature costs, incorporating prior information, and exploring modern architectures to handle partial inputs. Our experiments show that our method provides consistent gains over recent methods across a variety of datasets.

The human brain processes dynamic visual input through hierarchically organized, functionally specialized regions. While recent in silico brain encoding models can synthesize optimal stimuli to probe selectivity in different brain regions, prior work has been largely limited to static images, leaving dynamic visual processing underexplored. We introduce a novel neural-guided video synthesis framework that generates stimuli optimized for target brain regions across visual cortex. Our method performs evolutionary search over a structured prompt space, guided by a dynamic encoding model that predicts voxel-level responses to video inputs. By maximizing predicted activity for a target ROI, the framework efficiently discovers hyper-activating dynamic stimuli that consistently surpass handcrafted localizer videos. The synthesized videos recover known selectivities across ventral, dorsal, and lateral pathways, and further reveal systematic differences in sensitivity to temporal dynamics. A searchlight analysis provides new insight into the progression toward increasingly complex social-dynamic features along the lateral stream, further supported by probing with synthesized abstract, non-naturalistic stimuli. Taken together, our framework enables in silico exploration of dynamic visual selectivity, with new predictions for in vivo experiments

Although Large Language Models have advanced Automated Heuristic Design, treating algorithm evolution as a monolithic text generation task overlooks the coupling between discrete algorithmic structures and continuous numerical parameters. Consequently, existing methods often discard promising algorithms due to uncalibrated constants and suffer from premature convergence resulting from simple similarity metrics. To address these limitations, we propose TIDE, a Tuning-Integrated Dynamic Evolution framework designed to decouple structural reasoning from parameter optimization. TIDE features a nested architecture where an outer parallel island model utilizes Tree Similarity Edit Distance to drive structural diversity, while an inner loop integrates LLM-based logic generation with a differential mutation operator for parameter tuning. Additionally, a UCB-based scheduler dynamically prioritizes high-yield prompt strategies to optimize resource allocation. Extensive experiments across nine combinatorial optimization problems demonstrate that TIDE discovers heuristics that significantly outperform state-of-the-art baselines in solution quality while achieving improved search efficiency and reduced computational costs.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

RL post-training strategies are dataset-dependent and reveal a recurring empirical pattern: capacity parameters accumulate monotonically across stages, while regularization parameters predominantly oscillate in response to shifting training dynamics. This distinction matters because fixed schedules commit all parameters to fixed trajectories and therefore cannot express the non-stationary exploration-exploitation tradeoffs that regularization must track; the principle provides actionable design rules for multi-stage training. We discover this through LLMZero, a system where LLM agents search over training trajectories via tree search, diagnosing pathologies at each checkpoint and proposing coordinated multi-parameter transitions. Across 4 diverse GRPO tasks, LLMZero discovers strategies that improve over the base model by 9% to 140% relative and over grid search by 6% to 15% relative, consistently outperforming random search and the skill-based agent. The structural principle transfers across tasks, providing an explanation for why discovered strategies take qualitatively different forms yet share similar parameter dynamics.

Feature selection helps reduce data acquisition costs in ML, but the standard approach is to train models with static feature subsets. Here, we consider the dynamic feature selection (DFS) problem where a model sequentially queries features based on the presently available information. DFS is often addressed with reinforcement learning, but we explore a simpler approach of greedily selecting features based on their conditional mutual information. This method is theoretically appealing but requires oracle access to the data distribution, so we develop a learning approach based on amortized optimization. The proposed method is shown to recover the greedy policy when trained to optimality, and it outperforms numerous existing feature selection methods in our experiments, thus validating it as a simple but powerful approach for this problem.

Evolutionary agentic systems intensify the trade-off between computational efficiency and reasoning capability by repeatedly invoking large language models (LLMs) during inference. This setting raises a central question: how can an agent dynamically select an LLM that is sufficiently capable for the current generation step while remaining computationally efficient? While model cascades offer a practical mechanism for balancing this trade-off, existing routing strategies typically rely on static heuristics or external controllers and do not explicitly account for model uncertainty. We introduce AdaptEvolve: Adaptive LLM Selection for Multi-LLM Evolutionary Refinement within an evolutionary sequential refinement framework that leverages intrinsic generation confidence to estimate real-time solvability. Empirical results show that confidence-driven selection yields a favourable Pareto frontier, reducing total inference cost by an average of 37.9% across benchmarks while retaining 97.5% of the upper-bound accuracy of static large-model baselines. Our code is available at https://github.com/raypretam/adaptive_llm_selection.

Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico gold standard, its high computational cost limits scalability. We present DynaProt, a lightweight, SE(3)-invariant framework that predicts rich descriptors of protein dynamics directly from static structures. By casting the problem through the lens of multivariate Gaussians, DynaProt estimates dynamics at two complementary scales: (1) per-residue marginal anisotropy as 3 times 3 covariance matrices capturing local flexibility, and (2) joint scalar covariances encoding pairwise dynamic coupling across residues. From these dynamics outputs, DynaProt achieves high accuracy in predicting residue-level flexibility (RMSF) and, remarkably, enables reasonable reconstruction of the full covariance matrix for fast ensemble generation. Notably, it does so using orders of magnitude fewer parameters than prior methods. Our results highlight the potential of direct protein dynamics prediction as a scalable alternative to existing methods.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

The ever-growing ecosystem of LLMs has posed a challenge in selecting the most appropriate pre-trained model to fine-tune amidst a sea of options. Given constrained resources, fine-tuning all models and making selections afterward is unrealistic. In this work, we formulate this resource-constrained selection task into predicting fine-tuning performance and illustrate its natural connection with scaling laws. Unlike pre-training, We find that the fine-tuning scaling curve includes not just the well-known "power phase" but also the previously unobserved "pre-power phase". We also explain why existing scaling laws fail to capture this phase transition phenomenon both theoretically and empirically. To address this, we introduce the concept of "pre-learned data size" into our rectified scaling law, which overcomes theoretical limitations and fits experimental results much better. By leveraging our law, we propose a novel LLM selection algorithm that selects the near-optimal model with hundreds of times less resource consumption, while other methods may provide negatively correlated selection.

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

Dynamic graph clustering aims to detect and track time-varying clusters in dynamic graphs, revealing the evolutionary mechanisms of complex real-world dynamic systems. Matrix factorization-based methods are promising approaches for this task; however, these methods often struggle with scalability and can be time-consuming when applied to large-scale dynamic graphs. Moreover, they tend to lack robustness and are vulnerable to real-world noisy data. To address these issues, we make three key contributions. First, to improve scalability, we propose temporal separated matrix factorization, where a single matrix is divided into multiple smaller matrices for independent factorization, resulting in faster computation. Second, to improve robustness, we introduce bi-clustering regularization, which jointly optimizes graph embedding and clustering, thereby filtering out noisy features from the graph embeddings. Third, to further enhance effectiveness and efficiency, we propose selective embedding updating, where we update only the embeddings of dynamic nodes while the embeddings of static nodes are fixed among different timestamps. Experimental results on six synthetic and five real-world benchmarks demonstrate the scalability, robustness and effectiveness of our proposed method. Source code is available at https://github.com/Clearloveyuan/DyG-MF.

Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in cases where reward functions are non-differentiable. Some gradient-free guidance methods have been developed, but they often struggle to achieve optimal inference-time alignment. In this work, we newly frame inference-time alignment in diffusion as a search problem and propose Dynamic Search for Diffusion (DSearch), which subsamples from denoising processes and approximates intermediate node rewards. It also dynamically adjusts beam width and tree expansion to efficiently explore high-reward generations. To refine intermediate decisions, DSearch incorporates adaptive scheduling based on noise levels and a lookahead heuristic function. We validate DSearch across multiple domains, including biological sequence design, molecular optimization, and image generation, demonstrating superior reward optimization compared to existing approaches.

Modern Text-to-SQL systems often follow generate-execute-select pipelines, generating multiple candidate queries then selecting the best one. Listwise selection, by jointly comparing multiple candidates, has been widely adopted, but fine-tuning listwise selectors is costly. We thus propose a fine-tuning-free listwise selector. We replace two major fine-tuning objectives with inference-time strategies: (1) learning selection criteria as ordering and (2) mitigating positional bias. First, we build reusable structured memories instead of learning selection behavior as model parameters. Given a question, MaP-SQL retrieves memories distilled from training data that encode how natural language maps to schema elements, SQL operations, and expected outputs. These memories serve as explicit decision criteria for evaluating candidates in a listwise manner. Second, to mitigate ordering bias of listwise selectors, we aggregate rankings across multiple input permutations, with inference cost optimized by execution results and pointwise scoring. Our approach improves selection accuracy while maintaining efficiency and compatibility with existing large language models. Across Text-to-SQL benchmarks, it produces more stable selection without fine-tuning and fewer unnecessary comparisons than existing methods. On BIRD-dev, it outperforms the previous state-of-the-art selector-based method R^3-SQL by 2.02 execution accuracy points on average using the same candidate sets, with 2.92x fewer tokens.

Spatially variant dynamic convolution provides a principled approach of integrating spatial adaptivity into deep neural networks. However, mainstream designs in medical segmentation commonly generate dynamic kernels through average pooling, which implicitly collapses high-frequency spatial details into a coarse, spatially-compressed representation, leading to over-smoothed predictions that degrade the fidelity of fine-grained clinical structures. To address this limitation, we propose a novel Structure-Guided Dynamic Convolution (SGDC) mechanism, which leverages an explicitly supervised structure-extraction branch to guide the generation of dynamic kernels and gating signals for structure-aware feature modulation. Specifically, the high-fidelity boundary information from this auxiliary branch is fused with semantic features to enable spatially-precise feature modulation. By replacing context aggregation with pixel-wise structural guidance, the proposed design effectively prevents the information loss introduced by average pooling. Experimental results show that SGDC achieves state-of-the-art performance on ISIC 2016, PH2, ISIC 2018, and CoNIC datasets, delivering superior boundary fidelity by reducing the Hausdorff Distance (HD95) by 2.05, and providing consistent IoU gains of 0.99\%-1.49\% over pooling-based baselines. Moreover, the mechanism exhibits strong potential for extension to other fine-grained, structure-sensitive vision tasks, such as small-object detection, offering a principled solution for preserving structural integrity in medical image analysis. To facilitate reproducibility and encourage further research, the implementation code for both our SGE and SGDC modules has been is publicly released at https://github.com/solstice0621/SGDC.

Finetuning data selection requires balancing two competing goals: selecting examples that improve the downstream objective, and doing so without repeatedly finetuning models. Train-free selectors are scalable but rely on proxies such as embedding similarity or clustering, which may not match the target objective. Train-based selectors better reflect downstream utility through gradient signals, subset evaluation, or Shapley attribution, but require many costly train--evaluate iterations. We propose Hierarchical Active Region Pruning (HARP), an efficient train-based selector that preserves downstream alignment while reducing selection cost. HARP organizes the training pool into a node--leaf hierarchy, evaluates only representative leaves, and infers unmeasured utilities with empirical Bayes posteriors. It then selects data using two complementary envelopes: HARP-C, which conservatively controls redundancy, and HARP-E, which additively rewards complementary regions. We theoretically show that, under local smoothness and bounded estimation error, HARP controls selection error while reducing train--evaluate cost. We further validate that HARP variants achieve the best result and outperform the strongest baseline by up to +8.9 points, while using roughly 7times fewer training examples.

This paper formalizes threshold-based selection as an evaluation-gating architecture in which each incumbent is tested before variation and a replacement is generated and evaluated only when contextual pressure exceeds intrinsic strength. The mechanism is instantiated as Leaf Abscission Optimization (LAO), using rank-based strength, a phenological seasonal signal, diversity modulation, environmental pressure, and a base regrowth kernel. A blocked two-to-the-fourth-power factorial analysis at dimension 10 on the CEC 2017 suite reduces the original multi-layer design to a parsimonious core: drift is harmful, while the other three auxiliary layers show no robust independent evidence of benefit. The resulting LAO-Core attains the third-best mean Friedman rank among nine optimizers at dimensions 10, 30, and 50 under the equal evaluation budget. A four-budget sweep shows budget-dependent relative performance, with adaptive differential-evolution baselines gaining relative advantage at larger budgets; the nine-cell dimension-budget analysis establishes neither an evaluation-budget-per-dimension-only law nor a statistically significant dimension-budget interaction. A paired intervention shows that diversity modulation changes late-run replacement behaviour without a detectable effect on final error at the tested budget. The evidence supports LAO as a parsimonious evaluation-gating mechanism with regime-qualified competitiveness, rather than as a generally superior optimizer.

Modern machine learning is still largely organized around a single recipe: choose a parameterized model family and optimize its weights. Although highly successful, this paradigm is too narrow for many structured prediction problems, where the main bottleneck is not parameter fitting but discovering what should be computed from the data. Success often depends on identifying the right transformations, statistics, invariances, interaction structures, temporal summaries, gates, or nonlinear compositions, especially when objectives are non-differentiable, evaluation is cross-validation-based, interpretability matters, or continual adaptation is required. We present EvoForest, a hybrid neuro-symbolic system for end-to-end open-ended evolution of computation. Rather than merely generating features, EvoForest jointly evolves reusable computational structure, callable function families, and trainable low-dimensional continuous components inside a shared directed acyclic graph. Intermediate nodes store alternative implementations, callable nodes encode reusable transformation families such as projections, gates, and activations, output nodes define candidate predictive computations, and persistent global parameters can be refined by gradient descent. For each graph configuration, EvoForest evaluates the discovered computation and uses a lightweight Ridge-based readout to score the resulting representation against a non-differentiable cross-validation target. The evaluator also produces structured feedback that guides future LLM-driven mutations. In the 2025 ADIA Lab Structural Break Challenge, EvoForest reached 94.13% ROC-AUC after 600 evolution steps, exceeding the publicly reported winning score of 90.14% under the same evaluation protocol.

We present a Spatially Embedded Evolutionary Algorithm where robot individuals exist in a physically simulated 2D environment, must navigate to encounter potential mates, and compete for survival under various spatially-aware selection pressures. Using HyperNEAT evolved neural controllers for ARIEL gecko-inspired quadrupeds in MuJoCo, we investigate how spatial structure fundamentally alters evolutionary dynamics. Our experiments show a modest 4.9% difference in peak fitness between proximity-based and random pairing possibly within stochastic variation while combining spatial parent selection with stochastic death selection produces unstable population dynamics. We discover a continuous phase transition in energy-based selection experiments, with critical zone count separating extinction-dominated and explosion-dominated regimes. Our density-dependent death selection mechanism achieves 97% completion rates but causes fitness decline, revealing a fundamental dilemma where decoupled mechanisms produce bistable dynamics, positively coupled mechanisms create counter-selection pressures, and only deterministic fitness-based selection maintains stability. These findings provide important constraints for future spatial EA design.

AI for scientific discovery is entering an agentic era, where protein-engineering systems are expected to prioritize future wet-lab experiments rather than merely fit static measurements. We introduce TadA-Bench, a million-variant wet-lab replay benchmark from 31 TadA directed-evolution rounds for future-round discovery toward agentic protein engineering. TadA-Bench preserves the campaign chronology and defines a fixed-data replay task: given earlier experimental rounds, models rank variants that appear only in later rounds. It provides aligned DNA, RNA, and protein views, and uses Seq2Graph, a graph-based label-unification pipeline, to reconcile noisy enrichment measurements into consistent cross-round activity labels. Random-split controls show strong interpolation, but future-round ranking and finite-budget candidate selection are much weaker. Controlled analyses suggest that evolutionary coverage is more informative than local data density, positioning TadA-Bench as a reproducible wet-lab replay substrate for future-round discovery toward agentic protein engineering; the data and code are released on Hugging Face and GitHub.

Dynamic Algorithm Configuration (DAC) aims to dynamically control a target algorithm's hyperparameters in order to improve its performance. Several theoretical and empirical results have demonstrated the benefits of dynamically controlling hyperparameters in domains like evolutionary computation, AI Planning or deep learning. Replicating these results, as well as studying new methods for DAC, however, is difficult since existing benchmarks are often specialized and incompatible with the same interfaces. To facilitate benchmarking and thus research on DAC, we propose DACBench, a benchmark library that seeks to collect and standardize existing DAC benchmarks from different AI domains, as well as provide a template for new ones. For the design of DACBench, we focused on important desiderata, such as (i) flexibility, (ii) reproducibility, (iii) extensibility and (iv) automatic documentation and visualization. To show the potential, broad applicability and challenges of DAC, we explore how a set of six initial benchmarks compare in several dimensions of difficulty.

We investigate the temporal concatenation of sub-policies in Markov Decision Processes (MDP) with time-varying reward functions. We introduce General Dijkstra Search (GDS), and prove that globally optimal goal-reaching policies can be recovered through temporal composition of intermediate optimal sub-policies. Motivated by the "search, select, update" principle underlying GDS, we propose Dynamic Latent Routing (DLR), a language-model post-training method that jointly learns discrete latent codes, routing policies, and model parameters through dynamic search in a single training stage. In low-data fine-tuning settings, DLR matches or outperforms supervised fine-tuning across four datasets and six models, achieving a mean gain of +6.6 percentage points, while prior discrete-latent baselines consistently underperform SFT. Mechanistic analyses and targeted code ablations show that DLR learns structured routing behaviors with distinct causal roles.

Dynamic adaptation has become an essential technique in accelerating distributed machine learning (ML) training. Recent studies have shown that dynamically adjusting model structure (e.g., lottery ticket hypothesis) or hyperparameters (e.g., batch size) can significantly accelerate training without sacrificing accuracy. However, existing ML cluster schedulers are not designed to handle dynamic adaptation. We show that existing schemes fail to provide fairness and degrade system efficiency when the training throughput changes over time under dynamic adaptation. We design Shockwave, a scheduler with future planning that builds on two key ideas. First, Shockwave extends classic market theory from static settings to dynamic settings to co-optimize efficiency and fairness. Second, Shockwave utilizes stochastic dynamic programming to handle dynamic changes. We build a system for Shockwave and validate its performance with both trace-driven simulation and cluster experiments. Results show that for traces of ML jobs with dynamic adaptation, Shockwave improves makespan by 1.3X and fairness by 2X when compared with existing fair scheduling schemes.

Discovering causal structures from multivariate time series is a key problem because interactions span across multiple lags and possibly involve instantaneous dependencies. Additionally, the search space of the dynamic graphs is combinatorial in nature. In this study, we propose Stable Causal Dynamic Differentiable Discovery (SC3D), a two-stage differentiable framework that jointly learns lag-specific adjacency matrices and, if present, an instantaneous directed acyclic graph (DAG). In Stage 1, SC3D performs edge preselection through node-wise prediction to obtain masks for lagged and instantaneous edges, whereas Stage 2 refines these masks by optimizing a likelihood with sparsity along with enforcing acyclicity on the instantaneous block. Numerical results across synthetic SVAR systems, nonlinear and chaotic benchmarks, nonstationary dynamics and real-world datasets demonstrate that SC3D achieves improved stability and more accurate recovery of both lagged and instantaneous causal structures compared to existing baselines.

Recent controllable generation approaches such as FreeControl and Diffusion Self-guidance bring fine-grained spatial and appearance control to text-to-image (T2I) diffusion models without training auxiliary modules. However, these methods optimize the latent embedding for each type of score function with longer diffusion steps, making the generation process time-consuming and limiting their flexibility and use. This work presents Ctrl-X, a simple framework for T2I diffusion controlling structure and appearance without additional training or guidance. Ctrl-X designs feed-forward structure control to enable the structure alignment with a structure image and semantic-aware appearance transfer to facilitate the appearance transfer from a user-input image. Extensive qualitative and quantitative experiments illustrate the superior performance of Ctrl-X on various condition inputs and model checkpoints. In particular, Ctrl-X supports novel structure and appearance control with arbitrary condition images of any modality, exhibits superior image quality and appearance transfer compared to existing works, and provides instant plug-and-play functionality to any T2I and text-to-video (T2V) diffusion model. See our project page for an overview of the results: https://genforce.github.io/ctrl-x

Many biological discovery problems require experiments to be selected sequentially under constrained budgets. CRISPR screening is a prominent example, as exhaustive perturbation testing is often infeasible and candidate perturbations must instead be prioritized over multiple experimental rounds. Despite the importance of this problem, existing benchmarks for adaptive hit discovery remain limited in scale and diversity. Here, we introduce AssayBench-Loop, a large-scale benchmark for adaptive hit discovery comprising 1,389 CRISPR screens across five phenotype categories. Beyond enabling systematic evaluation, its scale makes it possible to learn acquisition strategies across historical experiments. Building on this resource, we introduce AssayLoop, a sequential experimental design framework combining AssayFormer, a transformer-based amortized acquisition policy trained across historical screens to adapt from experimental feedback, with LLM-derived biological priors through an adaptive handoff. In this view, completed experiments become training data for learning how accumulated evidence should guide what to test next, while LLMs provide prior biological knowledge to seed the search. We further introduce AssayLLM, showing that the same principle can be extended directly to an LLM through task-specific post-training. On temporally held-out screens, AssayLoop achieves a 5.67-fold enrichment over random selection and recovers 27.7% of hits after assaying approximately 5% of the candidate library, outperforming existing adaptive-design methods and standalone LLMs, and AssayFormer alone. Performance improves with increasing historical training data and transfers to phenotype categories excluded from training. These results demonstrate the value of learning acquisition policies across historical experiments and combining them with broad biological priors for efficient adaptive hit discovery.

System one models enable direct, low-latency decision-making. Yet recent practice of predicting an answer from serialized text does not, by itself, respect the structure of a decision problem. We argue that current designs underemphasize four important structural requirements. (i) null-aware: Models should distinguish answer absence from uncertainty among candidates; (ii) permutation-invariant: Reordering alternatives should not change the decision; (iii) option-scalable: Growing candidate sets should not require redefining the output space; (iv) cacheable: Request-independent computation over recurring alternatives should be reusable across requests. We introduce Jeva, a decision-native architecture that addresses these requirements jointly. A shared encoder independently represents the request and each option, while a compact decision stack refines only the request state against immutable option memory. Symmetric aggregation yields permutation-equivariant probabilities; shared scoring accommodates variable-size candidate sets. A separate coverage estimate distinguishes answer absence from candidate competition, enabling explicit null outcomes. Request-independent option representations and layer projections support reuse across newly assembled sets. These mechanisms unify Choice, Noul, and Score outputs. Across evaluations, Jeva combines strong typed-decision performance with near-perfect null detection and no decision flips under any tested permutations. It scales to thousands of candidates and substantially reduces latency through cross-request reuse without changing decisions.

We present methodology for using dynamic evaluation to improve neural sequence models. Models are adapted to recent history via a gradient descent based mechanism, causing them to assign higher probabilities to re-occurring sequential patterns. Dynamic evaluation outperforms existing adaptation approaches in our comparisons. Dynamic evaluation improves the state-of-the-art word-level perplexities on the Penn Treebank and WikiText-2 datasets to 51.1 and 44.3 respectively, and the state-of-the-art character-level cross-entropies on the text8 and Hutter Prize datasets to 1.19 bits/char and 1.08 bits/char respectively.

Dynamic multi-objective optimization requires continuous tracking of moving Pareto fronts. Existing methods struggle with irregular mutations and data sparsity, primarily facing three challenges: the non-linear coupling of dynamic modes, negative transfer from outdated historical data, and the cold-start problem during environmental switches. To address these issues, this paper proposes a decoupled basis-vector-driven generative framework (DB-GEN). First, to resolve non-linear coupling, the framework employs the discrete wavelet transform to separate evolutionary trajectories into low-frequency trends and high-frequency details. Second, to mitigate negative transfer, it learns transferable basis vectors via sparse dictionary learning rather than directly memorizing historical instances. Recomposing these bases under a topology-aware contrastive constraint constructs a structured latent manifold. Finally, to overcome the cold-start problem, a surrogate-assisted search paradigm samples initial populations from this manifold. Pre-trained on 120 million solutions, DB-GEN performs direct online inference without retraining or fine-tuning. This zero-shot generation process executes in milliseconds, requiring approximately 0.2 seconds per environmental change. Experimental results demonstrate that DB-GEN improves tracking accuracy across various dynamic benchmarks compared to existing algorithms.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

The integration of Reinforcement Learning (RL) into flow matching models for text-to-image (T2I) generation has driven substantial advances in generation quality. However, these gains often come at the cost of exhaustive exploration and inefficient sampling strategies due to slight variation in the sampling group. Building on this insight, we propose Dynamic-TreeRPO, which implements the sliding-window sampling strategy as a tree-structured search with dynamic noise intensities along depth. We perform GRPO-guided optimization and constrained Stochastic Differential Equation (SDE) sampling within this tree structure. By sharing prefix paths of the tree, our design effectively amortizes the computational overhead of trajectory search. With well-designed noise intensities for each tree layer, Dynamic-TreeRPO can enhance the variation of exploration without any extra computational cost. Furthermore, we seamlessly integrate Supervised Fine-Tuning (SFT) and RL paradigm within Dynamic-TreeRPO to construct our proposed LayerTuning-RL, reformulating the loss function of SFT as a dynamically weighted Progress Reward Model (PRM) rather than a separate pretraining method. By associating this weighted PRM with dynamic-adaptive clipping bounds, the disruption of exploration process in Dynamic-TreeRPO is avoided. Benefiting from the tree-structured sampling and the LayerTuning-RL paradigm, our model dynamically explores a diverse search space along effective directions. Compared to existing baselines, our approach demonstrates significant superiority in terms of semantic consistency, visual fidelity, and human preference alignment on established benchmarks, including HPS-v2.1, PickScore, and ImageReward. In particular, our model outperforms SoTA by 4.9%, 5.91%, and 8.66% on those benchmarks, respectively, while improving the training efficiency by nearly 50%.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

Inference-Time Scaling (ITS) has largely succeeded in verifiable domains like math and coding, where cheap verification enables scalable output selection. However, extending ITS to tasks prone to systematic failure - driven by faulty initial assumptions or unmet multidimensional constraints - typically relies on costly external solvers or brittle, model-based verifiers. Our key insight is that the intrinsic statistics of parallel sample sets, specifically length-adjusted tail entropy, provide a robust discriminative signal for solution quality without access to ground truth. Crucially, these statistics serve as a difficulty gate for adaptive compute allocation, dynamically routing problems across scaling regimes. First, Intrinsic Selection (iS) ranks candidates post-hoc, matching consensus-based algorithms across three domains and improving engineering design selection by 20% over pass@1 baselines. Second, Intrinsic Particle Filtering (iPF) generalizes this to step-level resampling, guiding generation toward high-confidence reasoning trajectories to improve pass@1 by 6.1 points on average on hard math problems. Finally, Particle Distillation (dPF) injects privileged guidance via early logit blending and KL-guided resampling, steering generation past systematic reasoning errors to satisfy expert rubrics, yielding up to 26.5% gains on complex clinical responses. Our pipeline applies seamlessly across broad-purpose, domain-specialized, and multimodal architectures, successfully extending ITS to open-ended domains without requiring trained reward models or exact ground-truth verification.

Diffusion language models (DLMs) have recently emerged as a promising alternative to autoregressive models, primarily due to their ability to enable parallel decoding. Despite this advantage, most existing DLMs rely on a fixed generation length specified prior to decoding, which restricts their flexibility in real-world applications. While a few recent works attempt to support flexible-length generation, they typically suffer from notable limitations: some require costly retraining to accommodate variable-length outputs, while others depend solely on local confidence signals during decoding. Such local criteria fail to capture the evolving structure of the sequence, often resulting in suboptimal generation quality. In this paper, we propose a training-free, Bayesian structured decoding framework that formulates flexible-length generation as a dynamic structural inference problem. Our approach formulates flexible-length generation as a dynamic structural inference problem, jointly computing the expansion length, the block boundaries, and the decoding schedule. At each window expansion step, the method integrates local uncertainty with structural signals via a unified mechanism that supports dynamic structured generation, including both flexible block expansion and block organization, while maintaining coherence. Extensive experiments across multiple benchmarks demonstrate that our approach significantly improves generation quality and flexibility over existing fixed-length and flexible-length baselines. These results highlight the advantage of Bayesian structured decoding for diffusion language model, providing a principled and efficient solution for structured text generation.

From cells to cities, ecosystems to economies, complex networks exhibit peak intensities that define their empirical limit. Estimating these limits traditionally requires domain-specific knowledge. We demonstrate that a wide range of complex networks share a capacity frontier that constrains these maxima. We formalize this regularity by proposing Structural Capacity Theory for Network Substrate Structured Systems. These systems couple a fixed network substrate with an observable dynamical process. The frontier is learned from a vector representation of the network substrate and modulated log-additively by a vector representation of the dynamical process. Frontiers trained on one set of domains reliably bound empirical maxima of entirely different ones without observing their peak intensities or simulating their dynamics. Independent learning paradigms converge on consistent upper bounds. Frontier performance is stable under perturbation, yet degrades under deliberate falsification, with no performance gain under ablation. These findings support the capacity frontier as a generalizable constraint that describes how network structure bounds dynamical processes across otherwise unrelated systems.

This article summarizes principles and ideas from the emerging area of applying conditional computation methods to the design of neural networks. In particular, we focus on neural networks that can dynamically activate or de-activate parts of their computational graph conditionally on their input. Examples include the dynamic selection of, e.g., input tokens, layers (or sets of layers), and sub-modules inside each layer (e.g., channels in a convolutional filter). We first provide a general formalism to describe these techniques in an uniform way. Then, we introduce three notable implementations of these principles: mixture-of-experts (MoEs) networks, token selection mechanisms, and early-exit neural networks. The paper aims to provide a tutorial-like introduction to this growing field. To this end, we analyze the benefits of these modular designs in terms of efficiency, explainability, and transfer learning, with a focus on emerging applicative areas ranging from automated scientific discovery to semantic communication.

Recent works exploring deep learning application to dynamical systems modeling have demonstrated that embedding physical priors into neural networks can yield more effective, physically-realistic, and data-efficient models. However, in the absence of complete prior knowledge of a dynamical system's physical characteristics, determining the optimal structure and optimization strategy for these models can be difficult. In this work, we explore methods for discovering neural state space dynamics models for system identification. Starting with a design space of block-oriented state space models and structured linear maps with strong physical priors, we encode these components into a model genome alongside network structure, penalty constraints, and optimization hyperparameters. Demonstrating the overall utility of the design space, we employ an asynchronous genetic search algorithm that alternates between model selection and optimization and obtains accurate physically consistent models of three physical systems: an aerodynamics body, a continuous stirred tank reactor, and a two tank interacting system.

Dynamic Data selection aims to accelerate training by prioritizing informative samples during online training. However, existing methods typically rely on task-specific handcrafted metrics or static/snapshot-based criteria to estimate sample importance, limiting scalability across learning paradigms and making it difficult to capture the evolving utility of data throughout training. To address this challenge, we propose Data Agent, an end-to-end dynamic data selection framework that formulates data selection as a training-aware sequential decision-making problem. The agent learns a sample-wise selection policy that co-evolves with model optimization, guided by a composite reward that integrates loss-based difficulty and confidence-based uncertainty signals. The reward signals capture complementary objectives of optimization impact and information gain, together with a tuning-free adaptive weighting mechanism that balances these signals over training. Extensive experiments across a wide range of datasets and architectures demonstrate that Data Agent consistently accelerates training while preserving or improving performance, e.g., reducing costs by over 50\% on ImageNet-1k and MMLU with lossless performance. Moreover, its dataset-agnostic formulation and modular reward make it plug-and-play across tasks and scenarios, e.g., robustness to noisy datasets, highlighting its potential in real-world scenarios. Code is available at https://github.com/Jackbrocp/Data-Agent.

Large language models (LLMs) are increasingly used to evolve programs and multi-agent systems, yet most existing approaches rely on overwrite-based mutations that maintain only a single candidate at a time. Such methods discard useful variants, suffer from destructive edits, and explore a brittle search space prone to structural failure. We introduce EvoLattice, a framework that represents an entire population of candidate programs or agent behaviors within a single directed acyclic graph. Each node stores multiple persistent alternatives, and every valid path through the graph defines a distinct executable candidate, yielding a large combinatorial search space without duplicating structure. EvoLattice enables fine-grained alternative-level evaluation by scoring each alternative across all paths in which it appears, producing statistics that reveal how local design choices affect global performance. These statistics provide a dense, data-driven feedback signal for LLM-guided mutation, recombination, and pruning, while preserving successful components. Structural correctness is guaranteed by a deterministic self-repair mechanism that enforces acyclicity and dependency consistency independently of the LLM. EvoLattice naturally extends to agent evolution by interpreting alternatives as prompt fragments or sub-agent behaviors. Across program synthesis (proxy and optimizer meta-learning), EvoLattice yields more stable evolution, greater expressivity, and stronger improvement trajectories than prior LLM-guided methods. The resulting dynamics resemble quality-diversity optimization, emerging implicitly from EvoLattice's internal multi-alternative representation rather than an explicit external archive.

The study of hardest and easiest fitness landscapes is an active area of research. Recently, Kaufmann, Larcher, Lengler and Zou conjectured that for the self-adjusting (1,lambda)-EA, Adversarial Dynamic BinVal (ADBV) is the hardest dynamic monotone function to optimize. We introduce the function Switching Dynamic BinVal (SDBV) which coincides with ADBV whenever the number of remaining zeros in the search point is strictly less than n/2, where n denotes the dimension of the search space. We show, using a combinatorial argument, that for the (1+1)-EA with any mutation rate p in [0,1], SDBV is drift-minimizing among the class of dynamic monotone functions. Our construction provides the first explicit example of an instance of the partially-ordered evolutionary algorithm (PO-EA) model with parameterized pessimism introduced by Colin, Doerr and F\'erey, building on work of Jansen. We further show that the (1+1)-EA optimizes SDBV in Theta(n^{3/2}) generations. Our simulations demonstrate matching runtimes for both static and self-adjusting (1,lambda) and (1+lambda)-EA. We further show, using an example of fixed dimension, that drift-minimization does not equal maximal runtime.

If autoresearch is itself a form of research, then autoresearch can be applied to research itself. We present Bilevel Autoresearch, a bilevel framework in which an outer autoresearch loop improves an inner autoresearch loop by reading its code and traces, identifying bottlenecks, and generating injectable Python search mechanisms at runtime. The inner loop optimizes task performance; the outer loop optimizes how the inner loop searches. Both loops use the same LLM, so improvements come from the bilevel architecture rather than a stronger meta-level model, although the outer loop consumes additional inference and wall-clock budget. On Karpathy's GPT pretraining benchmark, the meta-autoresearch outer loop achieves a 5x improvement over the standard inner loop alone (-0.045 vs. -0.009 val_bpb), while parameter-level adjustment without mechanism change yields no reliable gain. The outer loop instantiates mechanisms from adjacent search domains, including combinatorial optimization, multi-armed bandits, and design of experiments, without human specification of the final mechanism design. Trace analysis suggests that these mechanisms break deterministic search patterns and force exploration of directions the LLM's priors avoid. The experiments demonstrate, on this benchmark, a first bilevel step: an outer loop improves the search behavior of an inner loop. Code is the mechanism carrier in this implementation, but skills, prompts, workflows, evaluators, domain principles, world-model assumptions, and memory schemas can also encode mechanisms that shape future agent behavior. This suggests a path toward recursive bootstrapping, where mechanisms discovered for the inner loop can be fed back to improve the meta-level loop itself.

Predicting the behavior of complex systems is critical in many scientific and engineering domains, and hinges on the model's ability to capture their underlying dynamics. Existing methods encode the intrinsic dynamics of high-dimensional observations through latent representations and predict autoregressively. However, these latent representations lose the inherent spatial structure of spatiotemporal dynamics, leading to the predictor's inability to effectively model spatial interactions and neglect emerging dynamics during long-term prediction. In this work, we propose SparseDiff, introducing a test-time adaptation strategy to dynamically update the encoding scheme to accommodate emergent spatiotemporal structures during the long-term evolution of the system. Specifically, we first design a codebook-based sparse encoder, which coarsens the continuous spatial domain into a sparse graph topology. Then, we employ a graph neural ordinary differential equation to model the dynamics and guide a diffusion decoder for reconstruction. SparseDiff autoregressively predicts the spatiotemporal evolution and adjust the sparse topological structure to adapt to emergent spatiotemporal patterns by adaptive re-encoding. Extensive evaluations on representative systems demonstrate that SparseDiff achieves an average prediction error reduction of 49.99\% compared to baselines, requiring only 1\% of the spatial resolution.

Networks have become indispensable and ubiquitous structures in many fields to model the interactions among different entities, such as friendship in social networks or protein interactions in biological graphs. A major challenge is to understand the structure and dynamics of these systems. Although networks evolve through time, most existing graph representation learning methods target only static networks. Whereas approaches have been developed for the modeling of dynamic networks, there is a lack of efficient continuous time dynamic graph representation learning methods that can provide accurate network characterization and visualization in low dimensions while explicitly accounting for prominent network characteristics such as homophily and transitivity. In this paper, we propose the Piecewise-Velocity Model (PiVeM) for the representation of continuous-time dynamic networks. It learns dynamic embeddings in which the temporal evolution of nodes is approximated by piecewise linear interpolations based on a latent distance model with piecewise constant node-specific velocities. The model allows for analytically tractable expressions of the associated Poisson process likelihood with scalable inference invariant to the number of events. We further impose a scalable Kronecker structured Gaussian Process prior to the dynamics accounting for community structure, temporal smoothness, and disentangled (uncorrelated) latent embedding dimensions optimally learned to characterize the network dynamics. We show that PiVeM can successfully represent network structure and dynamics in ultra-low two-dimensional spaces. It outperforms relevant state-of-art methods in downstream tasks such as link prediction. In summary, PiVeM enables easily interpretable dynamic network visualizations and characterizations that can further improve our understanding of the intrinsic dynamics of time-evolving networks.

Fine-tuning large-scale pre-trained models is inherently a resource-intensive task. While it can enhance the capabilities of the model, it also incurs substantial computational costs, posing challenges to the practical application of downstream tasks. Existing parameter-efficient fine-tuning (PEFT) methods such as Low-Rank Adaptation (LoRA) rely on a bypass framework that ignores the differential parameter budget requirements across weight matrices, which may lead to suboptimal fine-tuning outcomes. To address this issue, we introduce the Dynamic Low-Rank Adaptation (DoRA) method. DoRA decomposes high-rank LoRA layers into structured single-rank components, allowing for dynamic pruning of parameter budget based on their importance to specific tasks during training, which makes the most of the limited parameter budget. Experimental results demonstrate that DoRA can achieve competitive performance compared with LoRA and full model fine-tuning, and outperform various strong baselines with the same storage parameter budget. Our code is available at https://github.com/MIkumikumi0116/DoRA

Large language models (LLMs) have achieved remarkable success across various domains, driving significant technological advancements and innovations. Despite the rapid growth in model scale and capability, systematic, data-driven research on how structural configurations affect performance remains scarce. To address this gap, we present a large-scale dataset encompassing diverse open-source LLM structures and their performance across multiple benchmarks. Leveraging this dataset, we conduct a systematic, data mining-driven analysis to validate and quantify the relationship between structural configurations and performance. Our study begins with a review of the historical development of LLMs and an exploration of potential future trends. We then analyze how various structural choices impact performance across benchmarks and further corroborate our findings using mechanistic interpretability techniques. By providing data-driven insights into LLM optimization, our work aims to guide the targeted development and application of future models. We will release our dataset at https://huggingface.co/datasets/DX0369/LLM-Structure-Performance-Dataset

We introduce Tadpole, a novel foundation model for three-dimensional partial differential equations (PDEs) that addresses key challenges in transferability, scalability to high dimensionality, and multi-functionality. Tadpole is pre-trained as an autoencoder on synthetic 3D PDE data generated by an efficient online data-generation framework. This enables large-scale, diverse training without storage or I/O overhead, demonstrated by scaling to an equivalent of hundreds of terabytes of training data. By autoencoding single-channel spatial crops, Tadpole learns rich and transferable representations across heterogeneous physical systems with varying numbers of state variables and spatial resolutions. Although pre-trained solely as an autoencoder, Tadpole can be efficiently applied for multiple downstream tasks beyond reconstruction, including dynamics learning and generative modeling. For dynamics learning, we propose a novel parameter-efficient fine-tuning strategy that integrates low-rank adaptation, latent-space transformations, and reintroduced skip connections, achieving accurate temporal modeling with a minimal number of trainable parameters. Tadpole demonstrates strong fine-tuning performance across various downstream tasks, highlighting its versatility and effectiveness as a foundation model for 3D PDE learning. Source code and pre-trained weights of Tadpole are available at https://github.com/tum-pbs/tadpole

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

In this paper, we investigate dynamic feature selection within multivariate time-series scenario, a common occurrence in clinical prediction monitoring where each feature corresponds to a bio-test result. Many existing feature selection methods fall short in effectively leveraging time-series information, primarily because they are designed for static data. Our approach addresses this limitation by enabling the selection of time-varying feature subsets for each patient. Specifically, we employ reinforcement learning to optimize a policy under maximum cost restrictions. The prediction model is subsequently updated using synthetic data generated by trained policy. Our method can seamlessly integrate with non-differentiable prediction models. We conducted experiments on a sizable clinical dataset encompassing regression and classification tasks. The results demonstrate that our approach outperforms strong feature selection baselines, particularly when subjected to stringent cost limitations. Code will be released once paper is accepted.

Compound AI systems that combine multiple LLM calls, such as self-refine and multi-agent-debate, achieve strong performance on many AI tasks. We address a core question in optimizing compound systems: for each LLM call or module in the system, how should one decide which LLM to use? We show that these LLM choices have a large effect on quality, but the search space is exponential. We propose LLMSelector, an efficient framework for model selection in compound systems, which leverages two key empirical insights: (i) end-to-end performance is often monotonic in how well each module performs, with all other modules held fixed, and (ii) per-module performance can be estimated accurately by an LLM. Building upon these insights, LLMSelector iteratively selects one module and allocates to it the model with the highest module-wise performance, as estimated by an LLM, until no further gain is possible. LLMSelector is applicable to any compound system with a bounded number of modules, and its number of API calls scales linearly with the number of modules, achieving high-quality model allocation both empirically and theoretically. Experiments with popular compound systems such as multi-agent debate and self-refine using LLMs such as GPT-4o, Claude 3.5 Sonnet and Gemini 1.5 show that LLMSelector confers 5%-70% accuracy gains compared to using the same LLM for all modules.

We introduce IntFold, a controllable foundation model for both general and specialized biomolecular structure prediction. IntFold demonstrates predictive accuracy comparable to the state-of-the-art AlphaFold3, while utilizing a superior customized attention kernel. Beyond standard structure prediction, IntFold can be adapted to predict allosteric states, constrained structures, and binding affinity through the use of individual adapters. Furthermore, we introduce a novel confidence head to estimate docking quality, offering a more nuanced assessment for challenging targets such as antibody-antigen complexes. Finally, we share insights gained during the training process of this computationally intensive model.

We establish a fundamental connection between optimal structure learning and optimal conditional independence testing by showing that the minimax optimal rate for structure learning problems is determined by the minimax rate for conditional independence testing in these problems. This is accomplished by establishing a general reduction between these two problems in the case of poly-forests, and demonstrated by deriving optimal rates for several examples, including Bernoulli, Gaussian and nonparametric models. Furthermore, we show that the optimal algorithm in these settings is a suitable modification of the PC algorithm. This theoretical finding provides a unified framework for analyzing the statistical complexity of structure learning through the lens of minimax testing.

Supervised fine-tuning (SFT) data selection is commonly formulated as instance ranking: score each example and retain a top-k subset. However, effective SFT training subsets are often produced through ordered curation recipes, where filtering, mixing, and deduplication operators jointly shape the final data distribution. We formulate this problem as fixed-pool data recipe search: given a raw instruction pool and a library of grounded operators, the goal is to discover an executable recipe that constructs a high-quality selected subset under a limited budget of full SFT evaluations, without generating, rewriting, or augmenting training samples. We introduce AutoSelection, a two-layer solver that decouples fixed-pool materialization based on cached task-, data-, and model-side signals from expensive full evaluation, using warmup probes, realized subset states, local recipe edits, Gaussian-process-assisted ranking, and stagnation-triggered reseeding. Experiments on a 90K instruction pool show that AutoSelection achieves the strongest in-distribution reasoning average across three base models, outperforming full-data training, random recipe search, random top-k, and single-operator selectors. Additional Out-of-distribution graph-reasoning results, search-stability analyses, structural ablations, and 1.5B-to-7B transfer checks further show that recipe structure matters beyond individual selection operators. Code is available at https://github.com/w253/AutoSelection.

Differentiable matching layers and residual connection paradigms, often implemented via entropy-regularized Optimal Transport (OT), serve as critical mechanisms in structural prediction and architectural scaling. However, recovering discrete permutations or maintaining identity mappings via annealing εto 0 is notoriously unstable. In this work, we identify a fundamental mechanism for this failure: Premature Mode Collapse. By analyzing the non-normal dynamics of the Sinkhorn fixed-point map, we reveal a theoretical thermodynamic speed limit: standard exponential cooling outpaces the contraction rate of the inference operator, which degrades as O(1/ε). To address this, we propose Efficient Piecewise Hybrid Adaptive Stability Control (EPH-ASC), an adaptive scheduling algorithm that monitors the stability of the inference process. We demonstrate that EPH-ASC is essential for stabilizing Manifold-Constrained Hyper-Connections (mHC) during large-scale training on the FineWeb-Edu dataset, effectively preventing late-stage gradient explosions by enforcing a linear stability law.

Intrinsically disordered protein regions (IDRs) play central roles in cellular processes such as transcriptional regulation, signal transduction, and subcellular localization, yet their functional design remains challenging. Structure-based design methods do not readily apply to IDRs, and existing protein language models are trained on full-length protein sequences, thus learning a prior that is biased towards folded domains. Here, we present IDiom, an autoregressive protein language model trained on IDiom-DB, a dataset of 54 million predicted IDRs curated from the AlphaFold Database. IDiom generates diverse sequences that recapitulate the composition, patterning, motifs, and predicted disorder of natural IDRs. To control function-associated sequence patterns, we also introduce reinforcement learning with sparse autoencoder features (RL-SAE), a post-training method that rewards the generation of sequences that activate specified feature sets. Across eight IDR design tasks, RL-SAE sequences activate, on average, 90% of 30 targeted features, compared to 24% for activation steering. We demonstrate that RL-SAE improves the predicted subcellular localization and transcriptional activity of generated IDRs compared to steering and supervised fine-tuning, and enables features associated with distinct biological functions to be combined within individual sequences. Thus, IDiom and RL-SAE enable interpretable and composable IDR design through explicit control of function-associated sequence features. More broadly, RL-SAE could extend to other protein design settings where interpretable features provide useful design targets. Code is available at https://github.com/rotskoff-group/idiom.

Benchmarks of machine learning models often include many datasets, making evaluation expensive. For efficiency, it is preferable to perform evaluations on small, representative datasets instead. The selection of such subsets typically relies on heuristics and is rarely analyzed for the robustness of the resulting model rankings. We introduce a framework to perform the task of selecting datasets subsets with an evaluation of how different selection strategies preserve the global model rankings. Our framework includes bootstrap aggregation, which provides valid confidence intervals, allowing a principled comparison of selection strategies. We consider clustering, design criteria (A/D-optimality), random baselines, and greedy farthest-first (FAFI). For the latter, we derive upper bounds on selection quality in terms of ranking errors as a function of the number of selected datasets. Empirically, in time series classification (TSC, 112 datasets) and in a supplementary natural language processing benchmark derived from MTEB (57 tasks), several selection strategies improve rank preservation compared with random subsets, including simple FAFI. In contrast, in recommender systems (30 datasets), the improvement of strategies over random selection is small and typically statistically insignificant. For TSC, our best-performing strategy achieves a Spearman correlation of 0.95 with the full benchmark model rankings using only five selected datasets. Additional experiments indicate that the effectiveness of selection approaches depends on both the quality of dataset representations and the scale of the benchmarking regime.

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

While large-scale training data is fundamental for developing capable large language models (LLMs), strategically selecting high-quality data has emerged as a critical approach to enhance training efficiency and reduce computational costs. Current data selection methodologies predominantly rely on static, training-agnostic criteria, failing to account for the dynamic model training and data interactions. In this paper, we propose a new Data Weighting Model (DWM) to adjust the weight of selected data within each batch to achieve a dynamic data utilization during LLM training. Specially, to better capture the dynamic data preference of the trained model, a bi-level optimization framework is implemented to update the weighting model. Our experiments demonstrate that DWM enhances the performance of models trained with randomly-selected data, and the learned weighting model can be transferred to enhance other data selection methods and models of different sizes. Moreover, we further analyze how a model's data preferences evolve throughout training, providing new insights into the data preference of the model during training.

Large Language Model (LLM)-based automated algorithm design typically evolves algorithms as complete, indivisible programs. While this whole-program perspective simplifies the search space, it fundamentally couples the useful local logic to its host program. Consequently, valuable code snippets vanish when the overall program is discarded, making it highly difficult to assess the contribution of individual algorithmic components.To address this, we propose Primitive-Aware Code Evolution (PACE), which decouples local logic from complete programs by representing it as persistent units called Executable Algorithmic Primitives (EAPs). To enable code-level transfer, PACE maintains a dynamic set of EAPs. Algorithm evolution is driven by primitive-aware operators that structurally guarantee the retention and cross-program transfer of these components. To evaluate them effectively, PACE leverages Thompson sampling based on parent-relative performance improvements, guiding primitive selection from the set without requiring extra evaluation datasets. Experiments on four tasks demonstrate that PACE effectively discovers competitive algorithms while structurally preserving valuable algorithmic components.

Projection maintenance is one of the core data structure tasks. Efficient data structures for projection maintenance have led to recent breakthroughs in many convex programming algorithms. In this work, we further extend this framework to the Kronecker product structure. Given a constraint matrix {sf A} and a positive semi-definite matrix Win R^{ntimes n} with a sparse eigenbasis, we consider the task of maintaining the projection in the form of {sf B}^top({sf B}{sf B}^top)^{-1}{sf B}, where {sf B}={sf A}(Wotimes I) or {sf B}={sf A}(W^{1/2}otimes W^{1/2}). At each iteration, the weight matrix W receives a low rank change and we receive a new vector h. The goal is to maintain the projection matrix and answer the query {sf B}^top({sf B}{sf B}^top)^{-1}{sf B}h with good approximation guarantees. We design a fast dynamic data structure for this task and it is robust against an adaptive adversary. Following the beautiful and pioneering work of [Beimel, Kaplan, Mansour, Nissim, Saranurak and Stemmer, STOC'22], we use tools from differential privacy to reduce the randomness required by the data structure and further improve the running time.

We revisit the structure learning problem for dynamic Bayesian networks and propose a method that simultaneously estimates contemporaneous (intra-slice) and time-lagged (inter-slice) relationships between variables in a time-series. Our approach is score-based, and revolves around minimizing a penalized loss subject to an acyclicity constraint. To solve this problem, we leverage a recent algebraic result characterizing the acyclicity constraint as a smooth equality constraint. The resulting algorithm, which we call DYNOTEARS, outperforms other methods on simulated data, especially in high-dimensions as the number of variables increases. We also apply this algorithm on real datasets from two different domains, finance and molecular biology, and analyze the resulting output. Compared to state-of-the-art methods for learning dynamic Bayesian networks, our method is both scalable and accurate on real data. The simple formulation and competitive performance of our method make it suitable for a variety of problems where one seeks to learn connections between variables across time.

Self-evolution methods enhance code generation through iterative "generate-verify-refine" cycles, yet existing approaches suffer from low exploration efficiency, failing to discover solutions with superior complexity within limited budgets. This inefficiency stems from initialization bias trapping evolution in poor solution regions, uncontrolled stochastic operations lacking feedback guidance, and insufficient experience utilization across tasks. To address these bottlenecks, we propose Controlled Self-Evolution (CSE), which consists of three key components. Diversified Planning Initialization generates structurally distinct algorithmic strategies for broad solution space coverage. Genetic Evolution replaces stochastic operations with feedback-guided mechanisms, enabling targeted mutation and compositional crossover. Hierarchical Evolution Memory captures both successful and failed experiences at inter-task and intra-task levels. Experiments on EffiBench-X demonstrate that CSE consistently outperforms all baselines across various LLM backbones. Furthermore, CSE achieves higher efficiency from early generations and maintains continuous improvement throughout evolution. Our code is publicly available at https://github.com/QuantaAlpha/EvoControl.

The paradigm of automated program generation is shifting from one-shot generation to inference-time search, where Large Language Models (LLMs) function as semantic mutation operators within evolutionary loops. While effective, these systems are currently governed by static schedules that fail to account for the non-stationary dynamics of the search process. This rigidity results in substantial computational waste, as resources are indiscriminately allocated to stagnating populations while promising frontiers remain under-exploited. We introduce AdaEvolve, a framework that reformulates LLM-driven evolution as a hierarchical adaptive optimization problem. AdaEvolve uses an "accumulated improvement signal" to unify decisions across three levels: Local Adaptation, which dynamically modulates the exploration intensity within a population of solution candidates; Global Adaptation, which routes the global resource budget via bandit-based scheduling across different solution candidate populations; and Meta-Guidance which generates novel solution tactics based on the previously generated solutions and their corresponding improvements when the progress stalls. We demonstrate that AdaEvolve consistently outperforms the open-sourced baselines across 185 different open-ended optimization problems including combinatorial, systems optimization and algorithm design problems.

Heuristic algorithms play a vital role in solving combinatorial optimization (CO) problems, yet traditional designs depend heavily on manual expertise and struggle to generalize across diverse instances. We introduce HeurAgenix, a two-stage hyper-heuristic framework powered by large language models (LLMs) that first evolves heuristics and then selects among them automatically. In the heuristic evolution phase, HeurAgenix leverages an LLM to compare seed heuristic solutions with higher-quality solutions and extract reusable evolution strategies. During problem solving, it dynamically picks the most promising heuristic for each problem state, guided by the LLM's perception ability. For flexibility, this selector can be either a state-of-the-art LLM or a fine-tuned lightweight model with lower inference cost. To mitigate the scarcity of reliable supervision caused by CO complexity, we fine-tune the lightweight heuristic selector with a dual-reward mechanism that jointly exploits singals from selection preferences and state perception, enabling robust selection under noisy annotations. Extensive experiments on canonical benchmarks show that HeurAgenix not only outperforms existing LLM-based hyper-heuristics but also matches or exceeds specialized solvers. Code is available at https://github.com/microsoft/HeurAgenix.

Structured state-space models (SSMs) such as S4, stemming from the seminal work of Gu et al., are gaining popularity as effective approaches for modeling sequential data. Deep SSMs demonstrate outstanding performance across a diverse set of domains, at a reduced training and inference cost compared to attention-based transformers. Recent developments show that if the linear recurrence powering SSMs allows for multiplicative interactions between inputs and hidden states (e.g. GateLoop, Mamba, GLA), then the resulting architecture can surpass in both in accuracy and efficiency attention-powered foundation models trained on text, at scales of billion parameters. In this paper, we give theoretical grounding to this recent finding using tools from Rough Path Theory: we show that when random linear recurrences are equipped with simple input-controlled transitions (selectivity mechanism), then the hidden state is provably a low-dimensional projection of a powerful mathematical object called the signature of the input -- capturing non-linear interactions between tokens at distinct timescales. Our theory not only motivates the success of modern selective state-space models such as Mamba but also provides a solid framework to understand the expressive power of future SSM variants.

The success of generative molecular design hinges on a model's steerability toward high-reward samples. Because many molecular properties are intrinsically linked to molecular size, accurately capturing the joint distribution of properties and the number of atoms is essential. However, current diffusion and flow-based models fix the number of atoms, which ultimately limits their ability to navigate this complex relationship. To address this, we introduce Morph, a flexible-size generative model for conditional and unconditional 3D molecular design based on geometric graphs. By dynamically adapting size, Morph can seamlessly integrate existing structural priors, like scaffolds, and significantly enhances property steering. We show that Morph matches current fixed-size state-of-the-art models while offering the benefit of unparalleled sampling flexibility. We demonstrate out-of-distribution generation in regimes where previous models fail, paving the way for enhanced generative modeling for molecular design.

Structure-based drug design (SBDD) aims to efficiently discover high-affinity ligands within vast chemical spaces. However, current generative models struggle with objective misalignment and rigid sampling budgets. We present MolFORM, a fast multi-modal flow matching framework for discrete atom types and continuous coordinates. Crucially, to bridge the gap between generative capability and biochemical objectives, we introduce two distinct post-training strategies: (1) Direct Preference Optimization (DPO), which performs offline alignment using ranked preference pairs; and (2) an online reinforcement learning paradigm that optimizes the generative flow directly on the forward process. Both strategies effectively navigate the chemical space toward high-affinity regions. MolFORM achieves state-of-the-art results on the CrossDocked2020 benchmark (Vina Score -7.60, Diversity 0.75), demonstrating that incorporating preference alignment mechanisms-whether via offline optimization or online reinforcement-is crucial for steering generative models toward high-affinity binding regions. The source code for MolFORM is publicly available at https://github.com/daiheng-zhang/SBDD-MolFORM.

Reinforcement learning fine-tuning has proven effective for steering generative diffusion models toward desired properties in image and molecular domains. Graph diffusion models have similarly been applied to combinatorial structure generation, including neural architecture search (NAS). However, neural architectures are directed acyclic graphs (DAGs) where edge direction encodes functional semantics such as data flow-information that existing graph diffusion methods, designed for undirected structures, discard. We propose Directed Graph Policy Optimization (DGPO), which extends reinforcement learning fine-tuning of discrete graph diffusion models to DAGs via topological node ordering and positional encoding. Validated on NAS-Bench-101 and NAS-Bench-201, DGPO matches the benchmark optimum on all three NAS-Bench-201 tasks (91.61%, 73.49%, 46.77%). The central finding is that the model learns transferable structural priors: pretrained on only 7% of the search space, it generates near-oracle architectures after fine-tuning, within 0.32 percentage points of the full-data model and extrapolating 7.3 percentage points beyond its training ceiling. Bidirectional control experiments confirm genuine reward-driven steering, with inverse optimization reaching near random-chance accuracy (9.5%). These results demonstrate that reinforcement learning-steered discrete diffusion, once extended to handle directionality, provides a controllable generative framework for directed combinatorial structures.

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

Instruction tuning relies on large instruction-response corpora whose quality and composition strongly affect downstream performance. We propose Answer Divergence-Guided Selection (ADG), which selects instruction data based on the geometric structure of multi-sample outputs. ADG draws several high-temperature generations per instruction, maps responses into an embedding space, and computes an output divergence score that jointly encodes dispersion magnitude and shape anisotropy. High scores correspond to instructions whose answers are both far apart and multi-modal, rather than clustered paraphrases along a single direction. Across two backbones and three public instruction pools, fine-tuning on only 10K ADG-selected examples consistently outperforms strong selectors on six benchmarks spanning reasoning, knowledge, and coding. Analyses further show that both dispersion magnitude and shape anisotropy are necessary, supporting answer divergence as a practical signal for instruction data selection. Code and appendix are included in the supplementary materials.

Transfer learning has become crucial in computer vision tasks due to the vast availability of pre-trained deep learning models. However, selecting the optimal pre-trained model from a diverse pool for a specific downstream task remains a challenge. Existing methods for measuring the transferability of pre-trained models rely on statistical correlations between encoded static features and task labels, but they overlook the impact of underlying representation dynamics during fine-tuning, leading to unreliable results, especially for self-supervised models. In this paper, we present an insightful physics-inspired approach named PED to address these challenges. We reframe the challenge of model selection through the lens of potential energy and directly model the interaction forces that influence fine-tuning dynamics. By capturing the motion of dynamic representations to decline the potential energy within a force-driven physical model, we can acquire an enhanced and more stable observation for estimating transferability. The experimental results on 10 downstream tasks and 12 self-supervised models demonstrate that our approach can seamlessly integrate into existing ranking techniques and enhance their performances, revealing its effectiveness for the model selection task and its potential for understanding the mechanism in transfer learning. Code will be available at https://github.com/lixiaotong97/PED.

Not a day goes by without hearing about the impressive feats of large language models (LLMs), and equally, not a day passes without hearing about their challenges. LLMs are notoriously vulnerable to biases in their dataset, leading to issues such as toxicity. While domain-adaptive training has been employed to mitigate these issues, these techniques often address all model parameters indiscriminately during the repair process, resulting in poor repair quality and reduced model versatility. In this paper, we introduce a novel dynamic slicing-based intent-aware LLM repair strategy, IRepair. This approach selectively targets the most error-prone sections of the model for repair. Specifically, we propose dynamically slicing the model's most sensitive layers that require immediate attention, concentrating repair efforts on those areas. This method enables more effective repairs with potentially less impact on the model's overall performance by altering a smaller portion of the model. We evaluated our technique on three models from the GPT2 and GPT-Neo families, with parameters ranging from 800M to 1.6B, in a toxicity mitigation setup. Our results show that IRepair repairs errors 43.6% more effectively while causing 46% less disruption to general performance compared to the closest baseline, direct preference optimization. Our empirical analysis also reveals that errors are more concentrated in a smaller section of the model, with the top 20% of layers exhibiting 773% more error density than the remaining 80\%. This highlights the need for selective repair. Additionally, we demonstrate that a dynamic selection approach is essential for addressing errors dispersed throughout the model, ensuring a robust and efficient repair.

Estimating the structure of directed acyclic graphs (DAGs) of features (variables) plays a vital role in revealing the latent data generation process and providing causal insights in various applications. Although there have been many studies on structure learning with various types of data, the structure learning on the dynamic graph has not been explored yet, and thus we study the learning problem of node feature generation mechanism on such ubiquitous dynamic graph data. In a dynamic graph, we propose to simultaneously estimate contemporaneous relationships and time-lagged interaction relationships between the node features. These two kinds of relationships form a DAG, which could effectively characterize the feature generation process in a concise way. To learn such a DAG, we cast the learning problem as a continuous score-based optimization problem, which consists of a differentiable score function to measure the validity of the learned DAGs and a smooth acyclicity constraint to ensure the acyclicity of the learned DAGs. These two components are translated into an unconstraint augmented Lagrangian objective which could be minimized by mature continuous optimization techniques. The resulting algorithm, named GraphNOTEARS, outperforms baselines on simulated data across a wide range of settings that may encounter in real-world applications. We also apply the proposed approach on two dynamic graphs constructed from the real-world Yelp dataset, demonstrating our method could learn the connections between node features, which conforms with the domain knowledge.

Recent work such as AlphaEvolve has shown that combining LLM-driven optimization with evolutionary search can effectively improve programs, prompts, and algorithms across domains. In this paradigm, previously evaluated solutions are reused to guide the model toward new candidate solutions. Crucially, the effectiveness of this evolution process depends on the search strategy: how prior solutions are selected and varied to generate new candidates. However, most existing methods rely on fixed search strategies with predefined knobs (e.g., explore-exploit ratios) that remain static throughout execution. While effective in some settings, these approaches often fail to adapt across tasks, or even within the same task as the search space changes over time. We introduce EvoX, an adaptive evolution method that optimizes its own evolution process. EvoX jointly evolves candidate solutions and the search strategies used to generate them, continuously updating how prior solutions are selected and varied based on progress. This enables the system to dynamically shift between different search strategies during the optimization process. Across nearly 200 real-world optimization tasks, EvoX outperforms existing AI-driven evolutionary methods including AlphaEvolve, OpenEvolve, GEPA, and ShinkaEvolve on the majority of tasks.

Protein-molecule virtual screening is increasingly cast as a problem of representation learning in a shared embedding space. Existing methods rely on dense holistic alignment, entangling invariant binding determinants with nuisance correlations and limiting transfer to new targets. It has been noted that binding in protein-molecule systems involves sparse cross-modality interactions: binding is governed by a small contact interface and a few decisive local interactions (e.g., hydrogen bonds, hydrophobic contacts, and salt bridges) rather than the global structures of the protein and molecule. We hypothesize that uncovering and leveraging sparse interaction patterns is critical for generalization beyond the training data, as these patterns are reusable and expected to improve performance across different scenarios. In this paper, we aim to identify and leverage sparse interaction patterns, and verify our hypothesis. Since the training data contain only observed binding pairs, we formalize this prior via a V-structure causal model under Heckman-style selection, and establish three theoretical results: (i) the latent concepts of interacting proteins and molecules are not identifiable without appropriate sparsity constraints; (ii) these concepts and their sparse interactions are component-wise identifiable under structural sparsity conditions; and (iii) a low-rank relaxation of these conditions yields subspace identifiability of the concepts and interactions. Inspired by these principles, we propose CausalBind with three implementation variants. Extensive experiments on DUD-E and LIT-PCBA benchmarks show that all variants consistently outperform strong retrieval baselines, with the largest gains on LIT-PCBA early enrichment, and further generalize to target- and scaffold-level out-of-distribution splits. Code is available at https://github.com/lokali/CausalBind.

Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying deep generative models for three-dimensional (3D) molecular design conditioned on protein pockets to solve SBDD has attracted much attention, but their formulation as probabilistic modeling often leads to unsatisfactory optimization performance. On the other hand, traditional combinatorial optimization methods such as genetic algorithms (GA) have demonstrated state-of-the-art performance in various molecular optimization tasks. However, they do not utilize protein target structure to inform design steps but rely on a random-walk-like exploration, which leads to unstable performance and no knowledge transfer between different tasks despite the similar binding physics. To achieve a more stable and efficient SBDD, we propose Reinforced Genetic Algorithm (RGA) that uses neural models to prioritize the profitable design steps and suppress random-walk behavior. The neural models take the 3D structure of the targets and ligands as inputs and are pre-trained using native complex structures to utilize the knowledge of the shared binding physics from different targets and then fine-tuned during optimization. We conduct thorough empirical studies on optimizing binding affinity to various disease targets and show that RGA outperforms the baselines in terms of docking scores and is more robust to random initializations. The ablation study also indicates that the training on different targets helps improve performance by leveraging the shared underlying physics of the binding processes. The code is available at https://github.com/futianfan/reinforced-genetic-algorithm.

In real-world applications of reinforcement learning, it is often challenging to obtain a state representation that is parsimonious and satisfies the Markov property without prior knowledge. Consequently, it is common practice to construct a state larger than necessary, e.g., by concatenating measurements over contiguous time points. However, needlessly increasing the dimension of the state may slow learning and obfuscate the learned policy. We introduce the notion of a minimal sufficient state in a Markov decision process (MDP) as the subvector of the original state under which the process remains an MDP and shares the same reward function as the original process. We propose a novel SEquEntial Knockoffs (SEEK) algorithm that estimates the minimal sufficient state in a system with high-dimensional complex nonlinear dynamics. In large samples, the proposed method achieves selection consistency. As the method is agnostic to the reinforcement learning algorithm being applied, it benefits downstream tasks such as policy learning. Empirical experiments verify theoretical results and show the proposed approach outperforms several competing methods regarding variable selection accuracy and regret.

Classical continual learning (CL) has primarily focused on enabling models to update and retain knowledge through parameter-centric mechanisms, e.g., training strategies, architectural designs, and weight adaptation. However, emerging paradigms are reshaping the scope of CL beyond this traditional model adaptation view. For instance, on-policy learning broadens the space of update mechanisms; test-time training extends CL from the training phase to inference; and external harness components such as memory, skill libraries, and interaction protocols extend the evolutionary boundaries of model capabilities far beyond the static parameter space. Collectively, these developments indicate a transition from parameter-centric learning toward system-level adaptation. To characterize this transition, we examine the evolution of continual learning through three dimensions: When, How, and Where learning occurs. The How dimension encompasses off-policy, on-policy, and beyond-gradient optimization mechanics. The When dimension captures evolution across pre-training, post-training, and inference-time stages. The Where dimension delineates updates occurring within internal parameters versus external structural constraints. Anchored by this tri-axial framework, we systematically survey representative methods, trace the ongoing transition of continual learning, and discuss the key challenges, broader implications, and future directions arising from this paradigm shift.

Symbolic world modeling requires inferring and representing an environment's transitional dynamics as an executable program. Prior work has focused on largely deterministic environments with abundant interaction data, simple mechanics, and human guidance. We address a more realistic and challenging setting, learning in a complex, stochastic environment where the agent has only "one life" to explore a hostile environment without human guidance. We introduce OneLife, a framework that models world dynamics through conditionally-activated programmatic laws within a probabilistic programming framework. Each law operates through a precondition-effect structure, activating in relevant world states. This creates a dynamic computation graph that routes inference and optimization only through relevant laws, avoiding scaling challenges when all laws contribute to predictions about a complex, hierarchical state, and enabling the learning of stochastic dynamics even with sparse rule activation. To evaluate our approach under these demanding constraints, we introduce a new evaluation protocol that measures (a) state ranking, the ability to distinguish plausible future states from implausible ones, and (b) state fidelity, the ability to generate future states that closely resemble reality. We develop and evaluate our framework on Crafter-OO, our reimplementation of the Crafter environment that exposes a structured, object-oriented symbolic state and a pure transition function that operates on that state alone. OneLife can successfully learn key environment dynamics from minimal, unguided interaction, outperforming a strong baseline on 16 out of 23 scenarios tested. We also test OneLife's planning ability, with simulated rollouts successfully identifying superior strategies. Our work establishes a foundation for autonomously constructing programmatic world models of unknown, complex environments.

The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing empirically derived force fields, MC or MD simulations explore the conformational space through numerically evolving the system via Markov chain or Newtonian mechanics. However, the high-energy barrier of the force fields can hamper the exploration of both methods by the rare event, resulting in inadequately sampled ensemble without exhaustive running. Existing learning-based approaches perform direct sampling yet heavily rely on target-specific simulation data for training, which suffers from high data acquisition cost and poor generalizability. Inspired by simulated annealing, we propose Str2Str, a novel structure-to-structure translation framework capable of zero-shot conformation sampling with roto-translation equivariant property. Our method leverages an amortized denoising score matching objective trained on general crystal structures and has no reliance on simulation data during both training and inference. Experimental results across several benchmarking protein systems demonstrate that Str2Str outperforms previous state-of-the-art generative structure prediction models and can be orders of magnitude faster compared to long MD simulations. Our open-source implementation is available at https://github.com/lujiarui/Str2Str

Instruction fine-tuning of large language models (LLMs) often involves selecting a subset of instruction training data from a large candidate pool, using a small query set from the target task. Despite growing interest, the literature on targeted instruction selection remains fragmented and opaque: methods vary widely in selection budgets, often omit zero-shot baselines, and frequently entangle the contributions of key components. As a result, practitioners lack actionable guidance on selecting instructions for their target tasks. In this work, we aim to bring clarity to this landscape by disentangling and systematically analyzing the two core ingredients: data representation and selection algorithms. Our framework enables controlled comparisons across models, tasks, and budgets. We find that only gradient-based data representations choose subsets whose similarity to the query consistently predicts performance across datasets and models. While no single method dominates, gradient-based representations paired with a greedy round-robin selection algorithm tend to perform best on average at low budgets, but these benefits diminish at larger budgets. Finally, we unify several existing selection algorithms as forms of approximate distance minimization between the selected subset and the query set, and support this view with new generalization bounds. More broadly, our findings provide critical insights and a foundation for more principled data selection in LLM fine-tuning. The code is available at https://github.com/dcml-lab/targeted-instruction-selection.

Protein sequence design has seen significant advances through discrete diffusion and autoregressive approaches, yet the potential of continuous diffusion remains underexplored. Here, we present DiMA, a latent diffusion framework that operates on protein language model representations. Through systematic exploration of architectural choices and diffusion components, we develop a robust methodology that generalizes across multiple protein encoders ranging from 8M to 3B parameters. We demonstrate that our framework achieves consistently high performance across sequence-only (ESM-2, ESMc), dual-decodable (CHEAP), and multimodal (SaProt) representations using the same architecture and training approach. We extensively evaluate existing methods alongside DiMA using multiple metrics across two protein modalities, covering quality, diversity, novelty, and distribution matching of generated proteins. DiMA consistently produces novel, high-quality and diverse protein sequences and achieves strong results compared to baselines such as autoregressive, discrete diffusion and flow matching language models. The model demonstrates versatile functionality, supporting conditional generation tasks including protein family-generation, motif scaffolding and infilling, and fold-specific sequence design. This work provides a universal continuous diffusion framework for protein sequence generation, offering both architectural insights and practical applicability across various protein design scenarios. Code is released at https://github.com/MeshchaninovViacheslav/DiMA{GitHub}.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.

Coreset selection picks a representative subset of the labeled training set to make training cheaper. However, it is usually evaluated by downstream accuracy at a fixed subset size, ignoring both the time spent selecting the subset and the training recipe behind each reported number. We introduce an end-to-end benchmark that standardizes downstream training and charges selection and training to the same auditable wall-clock budget, spanning 4 datasets from CIFAR-10 to ImageNet-1K, 11 selectors, 5 fractions, and 3 seeds, with over 1,500 released runs. Repeated-sampling work has shown that budget-aware evaluation already favors random strategies. Our two budget studies test whether that verdict survives when every selector is granted its most favorable operating point. Across eight wall-clock budget anchors on each of CIFAR-10 and Tiny ImageNet, no anchor is won by a sophisticated selector: every winner is class-balanced random sampling, repeated random sampling, or full-data training. In fixed-budget duels on ImageNet-1K, training on all data for fewer epochs beats every selection strategy we probe while also costing the least. A per-dataset cost audit shows that selection cost is dominated at every scale by a fixed full-dataset scan, so it cannot be amortized away by selecting a smaller fraction, and its absolute size does not extrapolate from one dataset to another. We further quantify when selection does pay back through subset reuse, and document 9 correctness fixes to a widely used codebase, one of which shifts a standard Herding baseline by nearly 6 points. Selection time is not free preprocessing, and an evaluation that ignores it measures the wrong quantity.

The performance of an algorithm often critically depends on its parameter configuration. While a variety of automated algorithm configuration methods have been proposed to relieve users from the tedious and error-prone task of manually tuning parameters, there is still a lot of untapped potential as the learned configuration is static, i.e., parameter settings remain fixed throughout the run. However, it has been shown that some algorithm parameters are best adjusted dynamically during execution, e.g., to adapt to the current part of the optimization landscape. Thus far, this is most commonly achieved through hand-crafted heuristics. A promising recent alternative is to automatically learn such dynamic parameter adaptation policies from data. In this article, we give the first comprehensive account of this new field of automated dynamic algorithm configuration (DAC), present a series of recent advances, and provide a solid foundation for future research in this field. Specifically, we (i) situate DAC in the broader historical context of AI research; (ii) formalize DAC as a computational problem; (iii) identify the methods used in prior-art to tackle this problem; (iv) conduct empirical case studies for using DAC in evolutionary optimization, AI planning, and machine learning.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

High-frequency trading (HFT) represents a pivotal and intensely competitive domain within the financial markets. The velocity and accuracy of data processing exert a direct influence on profitability, underscoring the significance of this field. The objective of this work is to optimise the real-time processing of data in high-frequency trading algorithms. The dynamic feature selection mechanism is responsible for monitoring and analysing market data in real time through clustering and feature weight analysis, with the objective of automatically selecting the most relevant features. This process employs an adaptive feature extraction method, which enables the system to respond and adjust its feature set in a timely manner when the data input changes, thus ensuring the efficient utilisation of data. The lightweight neural networks are designed in a modular fashion, comprising fast convolutional layers and pruning techniques that facilitate the expeditious completion of data processing and output prediction. In contrast to conventional deep learning models, the neural network architecture has been specifically designed to minimise the number of parameters and computational complexity, thereby markedly reducing the inference time. The experimental results demonstrate that the model is capable of maintaining consistent performance in the context of varying market conditions, thereby illustrating its advantages in terms of processing speed and revenue enhancement.

We apply preference learning to the task of language model-guided design of novel structural alloys. In contrast to prior work that focuses on generating stable inorganic crystals, our approach targets the synthesizeability of a specific structural class: BCC/B2 superalloys, an underexplored family of materials with potential applications in extreme environments. Using three open-weight models (LLaMA-3.1, Gemma-2, and OLMo-2), we demonstrate that language models can be optimized for multiple design objectives using a single, unified reward signal through Direct Preference Optimization (DPO). Unlike prior approaches that rely on heuristic or human-in-the-loop feedback (costly), our reward signal is derived from thermodynamic phase calculations, offering a scientifically grounded criterion for model tuning. To our knowledge, this is the first demonstration of preference-tuning a language model using physics-grounded feedback for structural alloy design. The resulting framework is general and extensible, providing a path forward for intelligent design-space exploration across a range of physical science domains.

Task allocation is a key combinatorial optimization problem, crucial for modern applications such as multi-robot cooperation and resource scheduling. Decision makers must allocate entities to tasks reasonably across different scenarios. However, traditional methods assume static attributes and numbers of tasks and entities, often relying on dynamic programming and heuristic algorithms for solutions. In reality, task allocation resembles Markov decision processes, with dynamically changing task and entity attributes. Thus, algorithms must dynamically allocate tasks based on their states. To address this issue, we propose a two-stage task allocation algorithm based on similarity, utilizing reinforcement learning to learn allocation strategies. The proposed pre-assign strategy allows entities to preselect appropriate tasks, effectively avoiding local optima and thereby better finding the optimal allocation. We also introduce an attention mechanism and a hyperparameter network structure to adapt to the changing number and attributes of entities and tasks, enabling our network structure to generalize to new tasks. Experimental results across multiple environments demonstrate that our algorithm effectively addresses the challenges of dynamic task allocation in practical applications. Compared to heuristic algorithms like genetic algorithms, our reinforcement learning approach better solves dynamic allocation problems and achieves zero-shot generalization to new tasks with good performance. The code is available at https://github.com/yk7333/TaskAllocation.

Morphology-control co-design concerns the coupled optimization of an agent's body structure and control policy. This problem exhibits a bi-level structure, where the control dynamically adapts to the morphology to maximize performance. Existing methods typically neglect the control's adaptation dynamics by adopting a single-level formulation that treats the control policy as fixed when optimizing morphology. This can lead to inefficient optimization, as morphology updates may be misaligned with control adaptation. In this paper, we revisit the co-design problem from a game-theoretic perspective, modeling the intrinsic coupling between morphology and control as a novel variant of a Stackelberg game. We propose Stackelberg Proximal Policy Optimization (Stackelberg PPO), which explicitly incorporates the control's adaptation dynamics into morphology optimization. By modeling this intrinsic coupling, our method aligns morphology updates with control adaptation, thereby stabilizing training and improving learning efficiency. Experiments across diverse co-design tasks demonstrate that Stackelberg PPO outperforms standard PPO in both stability and final performance, opening the way for dramatically more efficient robotics designs.

The rapid growth of large language models (LLMs) with diverse capabilities, costs, and domains has created a critical need for intelligent model selection at inference time. While smaller models suffice for routine queries, complex tasks demand more capable models. However, static model deployment does not account for the complexity and domain of incoming queries, leading to suboptimal performance and increased costs. Dynamic routing systems that adaptively select models based on query characteristics have emerged as a solution to this challenge. This survey provides a systematic analysis of multi-LLM routing and cascading approaches, focusing on systems that route queries across a pool of independently trained LLMs at inference time. We cover diverse routing paradigms, including query difficulty, human preferences, clustering, uncertainty quantification, reinforcement learning, multimodality, and cascading. For each paradigm, we analyze representative methods and examine key trade-offs. Beyond taxonomy, we introduce a conceptual framework that characterizes routing systems along three dimensions: when decisions are made, what information is used, and how they are computed. This perspective highlights that practical systems are often compositional, integrating multiple paradigms under operational constraints. Our analysis demonstrates that effective multi-LLM routing requires balancing competing objectives. Choosing the optimal routing strategy depends on deployment and computational constraints. Well-designed routing systems can outperform even the most powerful individual models by strategically leveraging specialized capabilities across models while maximizing efficiency gains. Meanwhile, open challenges remain in developing and evaluating routing mechanisms that generalize across diverse architectures, modalities, and applications.

In evolutionary algorithms powered by language models, the LLM acts as a single operator that simultaneously updates structural components (like control flow) and continuous parameters. While LLMs can be good at the first, they are not efficient at the second, wasting tokens taking discrete jumps inside a trial and error loop. We resolve this by formalizing a hybrid nested search, in which an outer loop has the LLM propose a structural sketch, with numeric gaps, and an inner numerical optimizer tunes the sketch. Both the outer and inner solvers are pluggable: any text-based optimizer can be combined with a zero-order optimizer (CMA-ES), gradient-based routines, or MCMC samplers. We validate our framework across three scientific domains: (i) meta-optimizers on closed-form test functions, (ii) code-based policies for systems research and social dilemmas; and (iii) approximate Bayesian inference tasks. Across all three, the hybrid optimizer is superior to both vanilla LLM-driven search and pure numerical optimization baselines. Code at: https://github.com/vicgalle/hybrid-nested-search

Modern optimization in experimental chemistry employs algorithmic search through black-box parameter spaces. Here we demonstrate that pre-trained knowledge in large language models (LLMs) fundamentally changes this paradigm. Using six fully enumerated categorical reaction datasets (768 - 5,684 experiments), we benchmark LLM-guided optimization (LLM-GO) against Bayesian optimization (BO) and random sampling. Frontier LLMs consistently match or exceed BO performance across five single-objective datasets, with advantages growing as parameter complexity increases and high-performing conditions become scarce (<5% of space). BO retains superiority only for explicit multi-objective trade-offs. To understand these contrasting behaviors, we introduce a topology-agnostic information theory framework quantifying sampling diversity throughout optimization campaigns. This analysis reveals that LLMs maintain systematically higher exploration entropy than BO across all datasets while achieving superior performance, with advantages most pronounced in solution-scarce parameter spaces where high-entropy exploration typically fails - suggesting that pre-trained domain knowledge enables more effective navigation of chemical parameter space rather than replacing structured exploration strategies. To enable transparent benchmarking and community validation, we release Iron Mind (https://gomes.andrew.cmu.edu/iron-mind), a no-code platform for side-by-side evaluation of human, algorithmic, and LLM optimization campaigns with public leaderboards and complete trajectories. Our findings establish that LLM-GO excels precisely where traditional methods struggle: complex categorical spaces requiring domain understanding rather than mathematical optimization.

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In this work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings because easy negative edges are often used in the current evaluation setting. To evaluate against more difficult negative edges, we introduce two more challenging negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.

Self-evolving skill systems promise to improve agents by turning execution feedback into persistent skill updates without changing the underlying model. Yet it remains unclear when further evolution helps, how successful and failed trajectories shape revision, and whether extra test-time computation can recover the same gains. To address these questions, we present a controlled evaluation framework across five benchmarks and three models. Our primary study contains 42 feedback runs across 14 supported model-benchmark settings. Within each setting, we hold the executor and optimizer configuration, revision procedure, validation rule, and round budget fixed, while varying only the feedback shown to the optimizer: successes and failures (Normal), failures only, or successes only. Evolution is sparse: only 55 of 388 candidates establish byte-distinct validation bests. Validation-based selection chooses an evolved skill in 11 of 14 settings, nine of which improve released-test performance. All 11 selections come from feedback conditions that include failed trajectories, although the relative ranking of Normal and Fail-only varies across settings. Validation and downstream evaluations on test, robustness, and transfer sometimes favor different feedback views. A broader SearchQA analysis covering eight models shows similarly sparse, feedback-dependent dynamics. In the GPT-5.5 test-time-scaling controls, oracle Parallel Sampling comes within 0.43 points of the evolved SearchQA skill but remains 30.96 points behind on SpreadsheetBench; Sequential Refinement recovers neither gain. Overall, persistent skill self-evolution is better understood as sparse, validation-filtered search with model- and benchmark-dependent returns, rather than steady improvement from additional rounds. The implementation is available at https://github.com/HKUST-KnowComp/rethinkskill.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

High-dimensional, underdetermined and highly correlated systems are common in data science practice, especially when analyzing physical measurements. In such settings, feature selection poses a fundamental challenge because multiple distinct sparse subsets may explain the response equally well. Their identification is crucial not only for predictive modeling but also for generating domain-specific insights into the underlying mechanisms. Yet, conventional methods typically isolate a single solution, obscuring the full spectrum of plausible explanations. This work introduces GEMSS (Gaussian Ensemble for Multiple Sparse Solutions), a variational algorithm designed to simultaneously discover multiple, diverse sparse feature combinations. The method employs a structured spike-and-slab prior for sparsity, a mixture of Gaussians to approximate the intractable multimodal posterior, and a Jaccard-based penalty to further control solution diversity. A single objective function is optimized via stochastic gradient descent. The method is tested on 128 comprehensive experiments by a novel benchmarking framework designed to generate artificial problems with multiple sparse solutions of equal predictive properties. This allows us to measure the retrieval of ground truth features rather than only evaluating predictive performance -- characteristics more fitting to our practical needs. A comparative analysis shows that GEMSS consistently outperforms five prominent feature selection methods adapted through the ALFESE framework. Finally, we demonstrate practical usability through 3 challenging real-world datasets from metabolomics and physical chemistry: GEMSS successfully isolates multiple distinct yet quality solutions. GEMSS is available as a PyPI package 'gemss'. The corresponding repository github.com/kat-er-ina/gemss/ includes the full codebase and a free, no-code application GEMSS Explorer.

Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.

Reinforcement fine-tuning (RFT) is increasingly used to strengthen the reasoning abilities of large models, yet its effectiveness is bound by how training data are selected and used. Most data-centric RFT methods rely on static or heuristic sample selection, implicitly assuming a sample's value is fixed over training. This overlooks the non-stationary dynamics of policy learning and can lead to suboptimal updates. We propose Dynamic Important Example Mining (DIEM), a principled and fully automated framework that makes data utilization adaptive throughout RFT. DIEM integrates two components into each optimization step: (i) a gradient-alignment importance estimator that efficiently approximates each sample's marginal contribution to policy improvement; and (ii) a constrained batch reweighting scheme that maximizes aggregate utility while preserving the update's gradient magnitude to stabilize optimization. Across several reasoning benchmarks, DIEM consistently outperforms strong static and dynamic baselines. The code will be released via https://github.com/hrtan/DIEM.

Predicting cellular responses to genetic perturbations is a central capability for virtual cells and a key step toward computational modeling of biological interventions. Most existing models directly map an unperturbed molecular profile and perturba- tion to the resulting observation without explicitly representing the latent cellular transition induced by the intervention. We introduce a mechanism-centric virtual cell world model that represents cellular state as a set of Latent Mechanism Units (LMUs) and treats genetic perturbations as actions on these latent states. Each LMU combines a reusable identity grounded in multimodal biological evidence with an observation-specific state, allowing a perturbation to induce mechanism- specific stochastic transitions before decoding the resulting transcriptional response. We train VCLMU through two-stage pretraining, first on around 200K pseudo-bulk perturbation profiles and then on gene-aligned single-cell perturbation data. Across six perturbation-disjoint benchmarks, VCLMU consistently improves perturbation- specific response recovery over strong baselines while maintaining competitive global response accuracy. We further analyze learned LMUs through enrichment between perturbation responses and LMU gene sets and show that they capture structured biological response programs. These results support mechanism-level latent state transition as a useful formulation for virtual cell models that aim to predict and interpret cellular responses to biological interventions.

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

Heterogeneous tabular data poses unique challenges in generative modelling due to its fundamentally different underlying data structure compared to homogeneous modalities, such as images and text. Although previous research has sought to adapt the successes of generative modelling in homogeneous modalities to the tabular domain, defining an effective generator for tabular data remains an open problem. One major reason is that the evaluation criteria inherited from other modalities often fail to adequately assess whether tabular generative models effectively capture or utilise the unique structural information encoded in tabular data. In this paper, we carefully examine the limitations of the prevailing evaluation framework and introduce TabStruct, a novel evaluation benchmark that positions structural fidelity as a core evaluation dimension. Specifically, TabStruct evaluates the alignment of causal structures in real and synthetic data, providing a direct measure of how effectively tabular generative models learn the structure of tabular data. Through extensive experiments using generators from eight categories on seven datasets with expert-validated causal graphical structures, we show that structural fidelity offers a task-independent, domain-agnostic evaluation dimension. Our findings highlight the importance of tabular data structure and offer practical guidance for developing more effective and robust tabular generative models. Code is available at https://github.com/SilenceX12138/TabStruct.

Network Architecture Search and specifically Regularized Evolution is a common way to refine the structure of a deep learning model.However, little is known about how models empirically evolve over time which has design implications for designing caching policies, refining the search algorithm for particular applications, and other important use cases.In this work, we algorithmically analyze and quantitatively characterize the patterns of model evolution for a set of models from the Candle project and the Nasbench-201 search space.We show how the evolution of the model structure is influenced by the regularized evolution algorithm. We describe how evolutionary patterns appear in distributed settings and opportunities for caching and improved scheduling. Lastly, we describe the conditions that affect when particular model architectures rise and fall in popularity based on their frequency of acting as a donor in a sliding window.

Scientific discovery is a closed-loop process in which hypotheses guide data acquisition and observations refine the hypothesis space. Yet most approaches reduce discovery to supervised learning over fixed datasets, where limited observations can support multiple plausible mechanisms that fit locally but fail to generalize. Thus, the key challenge is selecting informative observations to resolve uncertainty, shifting the focus from static inference to adaptive data acquisition. To address this, we propose LLM-AutoSciLab, a closed-loop framework that couples hypothesis generation with hypothesis-conditioned experiment selection and mechanism refinement. Rather than fitting models to passively collected data, LLM-AutoSciLab iteratively proposes plausible hypotheses, selects informative experiments to distinguish or refine them, and updates its state using the resulting evidence. To evaluate dynamic, closed-loop scientific discovery with active data acquisition, we introduce ActiveSciBench, comprising two datasets: ActiveSciBench-Chem with 57 enzyme-kinetics tasks and ActiveSciBench-GRN with 45 gene-regulatory-network tasks. These datasets model discovery as a budget-constrained process requiring adaptive experiment design, variable selection, and recovery of true mechanisms. Across NewtonBench, ActiveSciBench-Chem, and ActiveSciBench-GRN, LLM-AutoSciLab outperforms prior methods, achieving 67.6% and 35.1% symbolic accuracy on NewtonBench and ActiveSciBench-Chem, respectively, and 31.1% exact graph recovery on ActiveSciBench-GRN. Moreover, hypothesis-guided experimentation is 2-5x more sample-efficient than the strongest competing baselines. Code and data are available at: https://github.com/scientific-discovery/LLM-AutoSciLab

Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called CAPSUL, a Comprehensive humAn Protein benchmark for SUbcellular Localization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern α-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.

Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation. However, these achievements have primarily depended on task-specific conditional training or error-prone heuristic approximations. Ideally, a conditional generation method should provide exact samples for a broad range of conditional distributions without requiring task-specific training. To this end, we introduce the Twisted Diffusion Sampler, or TDS. TDS is a sequential Monte Carlo (SMC) algorithm that targets the conditional distributions of diffusion models through simulating a set of weighted particles. The main idea is to use twisting, an SMC technique that enjoys good computational efficiency, to incorporate heuristic approximations without compromising asymptotic exactness. We first find in simulation and in conditional image generation tasks that TDS provides a computational statistical trade-off, yielding more accurate approximations with many particles but with empirical improvements over heuristics with as few as two particles. We then turn to motif-scaffolding, a core task in protein design, using a TDS extension to Riemannian diffusion models. On benchmark test cases, TDS allows flexible conditioning criteria and often outperforms the state of the art.

Budget-constrained agentic search arises when an LLM agent must refine candidates under a small evaluation budget, because validation is expensive, generation requires multiple model calls, or both. In this regime, standard MCTS allocates budget poorly: exploration bonuses dominate at low visit counts, unpromising siblings are expanded before promising chains can deepen, and branching is independent of node quality. We introduce ExTS, a tree-search policy that treats expansion itself as a value-of-information decision. ExTS combines three mechanisms: discriminative reward shaping to separate candidates under narrow score distributions, a stochastic virtual child that estimates the value of creating a new branch from the parent's reward history, and quality-conditioned branching that expands only when a node's score justifies the budget cost. Across prompt optimization, code generation, molecular structure elucidation, and agentic workflow optimization, ExTS is competitive with or improves over task-specific tree-search baselines, with an average relative gain of +5.5% using a single fixed configuration. We further introduce pilot-run diagnostics that characterize what makes budget-constrained agentic search problems structurally different from one another, providing both understanding of the problem space and practical guidance for adaptation.

Complex agentic AI systems, powered by a coordinated ensemble of Large Language Models (LLMs), tool and memory modules, have demonstrated remarkable capabilities on intricate, multi-turn tasks. However, this success is shadowed by prohibitive economic costs and severe latency, exposing a critical, yet underexplored, trade-off. We formalize this challenge as the Agent System Trilemma: the inherent tension among achieving state-of-the-art performance, minimizing monetary cost, and ensuring rapid task completion. To dismantle this trilemma, we introduce EvoRoute, a self-evolving model routing paradigm that transcends static, pre-defined model assignments. Leveraging an ever-expanding knowledge base of prior experience, EvoRoute dynamically selects Pareto-optimal LLM backbones at each step, balancing accuracy, efficiency, and resource use, while continually refining its own selection policy through environment feedback. Experiments on challenging agentic benchmarks such as GAIA and BrowseComp+ demonstrate that EvoRoute, when integrated into off-the-shelf agentic systems, not only sustains or enhances system performance but also reduces execution cost by up to 80% and latency by over 70%.

Automated analysis for engineering structures offers considerable potential for boosting efficiency by minimizing repetitive tasks. Although AI-driven methods are increasingly common, no systematic framework yet leverages Large Language Models (LLMs) for automatic structural analysis. To address this gap, we propose a novel framework that integrates LLMs with structural analysis software. LLMs serve as the core engine: they parse structural descriptions from text and translate them into executable Python scripts. Moreover, the framework integrates the generative capabilities of LLMs with code-based finite element (FE) tools like OpenSeesPy. It employs domain-specific prompt design and in-context learning strategies to enhance the LLM's problem-solving capabilities and generative stability, enabling fully automated structural analysis from descriptive text to model outputs. In our experiments, we introduce a well-curated small-scale benchmark dataset of 20 structural analysis word problems (SAWPs) with ground-truth solutions and evaluate the performance of different LLMs within our framework in solving these SAWPs. The role of system instructions, crafted by structural engineers, is also investigated to understand their impact on LLM-driven structural analysis. Additionally, the generative stability of our framework is examined. Through multiple validation experiments on the benchmark, our results demonstrate that the proposed framework can substantially increase the level of automation in solving SAWPs compared to traditional methods. Quantitatively, the framework, built on GPT-4o, achieved 100% accuracy, surpassing GPT-4 (85%), Gemini 1.5 Pro (80%), and Llama-3.3 (30%) on the test examples. Furthermore, integrating domain-specific instructions enhanced performance by 30% on problems with asymmetrical structural configurations.

Timestep sampling p(t) is a central design choice in Flow Matching models, yet common practice increasingly favors static middle-biased distributions (e.g., Logit-Normal). We show that this choice induces a speed--quality trade-off: middle-biased sampling accelerates early convergence but yields worse asymptotic fidelity than Uniform sampling. By analyzing per-timestep training losses, we identify a U-shaped difficulty profile with persistent errors near the boundary regimes, implying that under-sampling the endpoints leaves fine details unresolved. Guided by this insight, we propose Curriculum Sampling, a two-phase schedule that begins with middle-biased sampling for rapid structure learning and then switches to Uniform sampling for boundary refinement. On CIFAR-10, Curriculum Sampling improves the best FID from 3.85 (Uniform) to 3.22 while reaching peak performance at 100k rather than 150k training steps. Our results highlight that timestep sampling should be treated as an evolving curriculum rather than a fixed hyperparameter.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Selective state space models (SSM), such as Mamba, have gained prominence for their effectiveness in modeling sequential data. Despite their outstanding empirical performance, a comprehensive theoretical understanding of deep selective SSM remains elusive, hindering their further development and adoption for applications that need high fidelity. In this paper, we investigate the dynamical properties of tokens in a pre-trained Mamba model. In particular, we derive the dynamical system governing the continuous-time limit of the Mamba model and characterize the asymptotic behavior of its solutions. In the one-dimensional case, we prove that only one of the following two scenarios happens: either all tokens converge to zero, or all tokens diverge to infinity. We provide criteria based on model parameters to determine when each scenario occurs. For the convergent scenario, we empirically verify that this scenario negatively impacts the model's performance. For the divergent scenario, we prove that different tokens will diverge to infinity at different rates, thereby contributing unequally to the updates during model training. Based on these investigations, we propose two refinements for the model: excluding the convergent scenario and reordering tokens based on their importance scores, both aimed at improving practical performance. Our experimental results validate these refinements, offering insights into enhancing Mamba's effectiveness in real-world applications.

Current pre-trained large language models typically need instruction tuning to align with human preferences. However, instruction tuning data is often quantity-saturated due to the large volume of data collection and fast model iteration, leaving coreset data selection important but underexplored. On the other hand, existing quality-driven data selection methods such as LIMA (NeurIPS 2023 (Zhou et al., 2024)) and AlpaGasus (ICLR 2024 (Chen et al.)) generally ignore the equal importance of data diversity and complexity. In this work, we aim to design a diversity-aware data selection strategy and creatively propose using sparse autoencoders to tackle the challenge of data diversity measure. In addition, sparse autoencoders can also provide more interpretability of model behavior and explain, e.g., the surprising effectiveness of selecting the longest response (ICML 2024 (Zhao et al.)). Using effective data selection, we experimentally prove that models trained on our selected data can outperform other methods in terms of model capabilities, reduce training cost, and potentially gain more control over model behaviors.

Test-time scaling has become a dominant paradigm for improving LLM agent reliability, yet current approaches treat compute as an abundant resource, allowing agents to exhaust token and tool budgets on redundant steps or dead-end trajectories. Existing budget-aware methods either require expensive fine-tuning or rely on coarse, trajectory-level heuristics that cannot intervene mid-execution. We propose the Budget-Aware Value Tree (BAVT), a training-free inference-time framework that models multi-hop reasoning as a dynamic search tree guided by step-level value estimation within a single LLM backbone. Another key innovation is a budget-conditioned node selection mechanism that uses the remaining resource ratio as a natural scaling exponent over node values, providing a principled, parameter-free transition from broad exploration to greedy exploitation as the budget depletes. To combat the well-known overconfidence of LLM self-evaluation, BAVT employs a residual value predictor that scores relative progress rather than absolute state quality, enabling reliable pruning of uninformative or redundant tool calls. We further provide a theoretical convergence guarantee, proving that BAVT reaches a terminal answer with probability at least 1-ε under an explicit finite budget bound. Extensive evaluations on four multi-hop QA benchmarks across two model families demonstrate that BAVT consistently outperforms parallel sampling baselines. Most notably, BAVT under strict low-budget constraints surpasses baseline performance at 4times the resource allocation, establishing that intelligent budget management fundamentally outperforms brute-force compute scaling.

Dynamics models learned from visual observations have shown to be effective in various robotic manipulation tasks. One of the key questions for learning such dynamics models is what scene representation to use. Prior works typically assume representation at a fixed dimension or resolution, which may be inefficient for simple tasks and ineffective for more complicated tasks. In this work, we investigate how to learn dynamic and adaptive representations at different levels of abstraction to achieve the optimal trade-off between efficiency and effectiveness. Specifically, we construct dynamic-resolution particle representations of the environment and learn a unified dynamics model using graph neural networks (GNNs) that allows continuous selection of the abstraction level. During test time, the agent can adaptively determine the optimal resolution at each model-predictive control (MPC) step. We evaluate our method in object pile manipulation, a task we commonly encounter in cooking, agriculture, manufacturing, and pharmaceutical applications. Through comprehensive evaluations both in the simulation and the real world, we show that our method achieves significantly better performance than state-of-the-art fixed-resolution baselines at the gathering, sorting, and redistribution of granular object piles made with various instances like coffee beans, almonds, corn, etc.

Large pre-trained models achieve remarkable performance in vision tasks but are impractical for fine-tuning due to high computational and storage costs. Parameter-Efficient Fine-Tuning (PEFT) methods mitigate this issue by updating only a subset of parameters; however, most existing approaches are task-agnostic, failing to fully exploit task-specific adaptations, which leads to suboptimal efficiency and performance. To address this limitation, we propose Task-Relevant Parameter and Token Selection (TR-PTS), a task-driven framework that enhances both computational efficiency and accuracy. Specifically, we introduce Task-Relevant Parameter Selection, which utilizes the Fisher Information Matrix (FIM) to identify and fine-tune only the most informative parameters in a layer-wise manner, while keeping the remaining parameters frozen. Simultaneously, Task-Relevant Token Selection dynamically preserves the most informative tokens and merges redundant ones, reducing computational overhead. By jointly optimizing parameters and tokens, TR-PTS enables the model to concentrate on task-discriminative information. We evaluate TR-PTS on benchmark, including FGVC and VTAB-1k, where it achieves state-of-the-art performance, surpassing full fine-tuning by 3.40% and 10.35%, respectively. The code are available at https://github.com/synbol/TR-PTS.