Daily Papers

Text-to-optimization requires two separable capabilities: modeling -- choosing the right optimization structure -- and binding -- grounding every coefficient, index, and parameter in the concrete problem data. We study this via Text2Opt-Bench, a scalable benchmark of solver-verified optimization problems spanning 12 categories, from textbook linear programs to stochastic and multi-objective formulations with up to thousands of variables. Across 10+ models, we find that accuracy collapses as instance data grows, even when the formulation itself is simple. We call this the effective binding limit. We address this via a simple inference-time approach, BIND, which externalizes numeric data to structured files so the model binds data programmatically rather than transcribing from the prompt. BIND improves GPT-5-Nano from 59.1% to 82.4% accuracy, matching pass@5 (82.0%) at lower token cost than pass@1, and GPT-5 from 86.2% to 95.8%. Furthermore, we validate our hypothesis by finetuning a model exclusively on binding and show that it outperforms end-to-end SFT and RL across three structurally distinct optimization categories, with a 1.5B binding specialist alone matching a 7B end-to-end baseline.

Computational design of protein-binding proteins is a fundamental capability with broad utility in biomedical research and biotechnology. Recent methods have made strides against some target proteins, but on-demand creation of high-affinity binders without multiple rounds of experimental testing remains an unsolved challenge. This technical report introduces AlphaProteo, a family of machine learning models for protein design, and details its performance on the de novo binder design problem. With AlphaProteo, we achieve 3- to 300-fold better binding affinities and higher experimental success rates than the best existing methods on seven target proteins. Our results suggest that AlphaProteo can generate binders "ready-to-use" for many research applications using only one round of medium-throughput screening and no further optimization.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

Large language model (LLM) providers boast big numbers for maximum context window sizes. To test the real world use of context windows, we 1) define a concept of maximum effective context window, 2) formulate a testing method of a context window's effectiveness over various sizes and problem types, and 3) create a standardized way to compare model efficacy for increasingly larger context window sizes to find the point of failure. We collected hundreds of thousands of data points across several models and found significant differences between reported Maximum Context Window (MCW) size and Maximum Effective Context Window (MECW) size. Our findings show that the MECW is, not only, drastically different from the MCW but also shifts based on the problem type. A few top of the line models in our test group failed with as little as 100 tokens in context; most had severe degradation in accuracy by 1000 tokens in context. All models fell far short of their Maximum Context Window by as much as 99 percent. Our data reveals the Maximum Effective Context Window shifts based on the type of problem provided, offering clear and actionable insights into how to improve model accuracy and decrease model hallucination rates.

Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we validate relative binding free energy (RBFE) accuracy using neural network potentials (NNPs) for the ligands. We utilize a novel NNP model, AceForce 1.0, based on the TensorNet architecture for small molecules that broadens the applicability to diverse drug-like compounds, including all important chemical elements and supporting charged molecules. Using established benchmarks, we show overall improved accuracy and correlation in binding affinity predictions compared with GAFF2 for molecular mechanics and ANI2-x for NNPs. Slightly less accuracy but comparable correlations with OPLS4. We also show that we can run the NNP simulations at 2 fs timestep, at least two times larger than previous NNP models, providing significant speed gains. The results show promise for further evolutions of free energy calculations using NNPs while demonstrating its practical use already with the current generation. The code and NNP model are publicly available for research use.

For a real quadratic field Q(d), we study the norm-form energy N = S_ζ^2 - d cdot S_L^2, where S_ζ and S_L are Lorentzian-weighted zero sums with w(ρ) = 2/(1/4 + γ^2). We prove three main results. (1) Spacelike spectral data: N < 0 unconditionally for all squarefree d > 1, as a consequence of a low-lying zero dominance theorem proved via explicit zero-counting. (2) Effective density bound: at each verified truncation level M, dens{N > 0} leq 2|f_{S_L^{(M)}}|_infty cdot (W_1(ζ)/d + ε_M), established unconditionally via Jacobi--Anger resonance analysis. (3) Exact asymptotic: under the computationally verified hypothesis that the infinite resonance lattice Λ_infty has finite rank (verified for M leq 20, where rank = 0), the sharp asymptotic dens{N > 0} = C(d)/d + o(1/d) holds. For d = 5, C(5) = 2,f_{S_L}(0)cdotE[|S_ζ|] = 0.1191; the constant depends on d through the zeros of L(s,χ_d), and C(d) = O(1/log d) as d to infty.

Protein-ligand binding affinity prediction is essential for drug discovery and toxicity assessment. While machine learning (ML) promises fast and accurate predictions, its progress is constrained by the availability of reliable data. In contrast, physics-based methods such as absolute binding free energy perturbation (AB-FEP) deliver high accuracy but are computationally prohibitive for high-throughput applications. To bridge this gap, we introduce ToxBench, the first large-scale AB-FEP dataset designed for ML development and focused on a single pharmaceutically critical target, Human Estrogen Receptor Alpha (ERalpha). ToxBench contains 8,770 ERalpha-ligand complex structures with binding free energies computed via AB-FEP with a subset validated against experimental affinities at 1.75 kcal/mol RMSE, along with non-overlapping ligand splits to assess model generalizability. Using ToxBench, we further benchmark state-of-the-art ML methods, and notably, our proposed DualBind model, which employs a dual-loss framework to effectively learn the binding energy function. The benchmark results demonstrate the superior performance of DualBind and the potential of ML to approximate AB-FEP at a fraction of the computational cost.

Effective LLM training depends on predictable scaling of key quantities -- such as final loss and optimal hyperparameters -- with model and dataset size. Qiu et al. (2025) recently showed that this predictability can extend beyond scalars: whole training loss curves can *collapse* onto a universal trajectory after a simple normalization. What remains unclear is whether this phenomenon persists for LLM families trained under *practical scaling recipes*, where width, depth, learning rate, batch size, and weight decay are scaled jointly. We show that it does: loss curves collapse across scales precisely when optimization hyperparameters are set optimally for the given data budget, in accordance with recent empirical scaling laws. Collapse therefore emerges as a signature of compute-efficient training. We demonstrate two applications at scale: (1) deviation-from-collapse provides a sensitive, early diagnostic of training pathologies, and (2) predictability of collapsed curves enables early stopping in large-scale hyperparameter tuning. Finally, we train a competitive LLM family, *Celerity*, using these insights, establishing collapse as an effective tool for developing efficient LLMs.

Large Language Models (LLMs) have emerged as a milestone in artificial intelligence, and their performance can improve as the model size increases. However, this scaling brings great challenges to training and inference efficiency, particularly for deploying LLMs in resource-constrained environments, and the scaling trend is becoming increasingly unsustainable. This paper introduces the concept of ``capacity density'' as a new metric to evaluate the quality of the LLMs across different scales and describes the trend of LLMs in terms of both effectiveness and efficiency. To calculate the capacity density of a given target LLM, we first introduce a set of reference models and develop a scaling law to predict the downstream performance of these reference models based on their parameter sizes. We then define the effective parameter size of the target LLM as the parameter size required by a reference model to achieve equivalent performance, and formalize the capacity density as the ratio of the effective parameter size to the actual parameter size of the target LLM. Capacity density provides a unified framework for assessing both model effectiveness and efficiency. Our further analysis of recent open-source base LLMs reveals an empirical law (the densing law)that the capacity density of LLMs grows exponentially over time. More specifically, using some widely used benchmarks for evaluation, the capacity density of LLMs doubles approximately every three months. The law provides new perspectives to guide future LLM development, emphasizing the importance of improving capacity density to achieve optimal results with minimal computational overhead.

Instruction-tuned large language models produce helpful, structured responses, but how robust is this helpfulness under trivial constraints? We show that simple lexical constraints (banning a single punctuation character or common word) cause instruction-tuned LLMs to collapse their responses, losing 14--48\% of comprehensiveness across seven models spanning five families (7B--70B, open- and closed-weight). A blinded human evaluation with 10 STEM-trained evaluators confirms genuine content loss, with information criteria degrading 1.5--2.3times more than surface criteria, a finding corroborated by over 4,100 automated pairwise comparisons (77--100\% baseline preference) across three LLM judges from two model families. Diagnostic analysis identifies this as a planning failure: two-pass generation recovers 59--96\% of response length, and linear probes on prompt representations predict response length with R^2 = 0.51--0.94 before generation begins. The same probes yield negative R^2 on base models, confirming that instruction tuning introduces the representational structure underlying the collapse. Base models show no systematic degradation under identical constraints, demonstrating that instruction tuning couples task competence to narrow surface-form templates. The effect extends to realistic deployment constraints (preamble suppression, corporate tone guidelines, legal compliance hedging, accessibility requirements) causing comparable degradation (-22\% to -34\%), with suppressing the conversational opener alone (``Certainly!'') causing 40\% collapse on our most fragile model despite restricting only the opening tokens. We further show that standard independent LLM-as-judge evaluation detects only a 3.5\% quality drop where pairwise evaluation reveals 23\%, exposing a methodological blind spot in current evaluation practice.

Training compute is increasingly outpacing the availability of high-quality data. This shifts the central challenge from optimal compute allocation to extracting maximum value from limited data. The widely adopted Chinchilla scaling law assumes every training token is unique. This limits its ability to guide pretraining decisions in data-constrained regimes. We model the excess loss under repetition with a simple additive overfitting penalty and find that it accurately describes model behavior. Our scaling law yields qualitatively new compute-optimal allocation advice. Beyond a point, further repetition is counterproductive and compute is better spent on model capacity. We show that following our law's recommended configuration improves performance in data-constrained regimes. Finally, because our one-parameter form isolates overfitting in a single coefficient, it enables direct comparison across training configurations. As a case study, we show that strong weight decay (λ=1.0) reduces this coefficient by approximately 70%, providing a scaling-law explanation for recent findings that optimal weight decay in data-constrained regimes is an order of magnitude larger than standard practice.

This paper explores the relationship between the condition number of a neural network's weight tensor and the extent of information encoded by the associated processing unit, viewed through the lens of information theory. It argues that a high condition number, though not sufficient for effective knowledge encoding, may indicate that the unit has learned to selectively amplify and compress information. This intuition is formalized for linear units with Gaussian inputs, linking the condition number and the transformation's log-volume scaling factor to the characteristics of the output entropy and the geometric properties of the learned transformation. The analysis demonstrates that for a fixed weight norm, a concentrated distribution of singular values (high condition number) corresponds to reduced overall information transfer, indicating a specialized and efficient encoding strategy. Furthermore, the linear stage entropy bound provides an upper limit on post-activation information for contractive, element-wise nonlinearities, supporting the condition number as a scale-invariant proxy for encoding capacity in practical neural networks. An empirical case study applies these principles to guide selective fine-tuning of Large Language Models for both a new task and a new input modality. The experiments show that the proposed method, named KappaTune, effectively mitigates catastrophic forgetting. Unlike many existing catastrophic forgetting mitigation methods that rely on access to pre-training statistics, which are often unavailable, this selective fine-tuning approach offers a way to bypass this common requirement.

Emerging large-scale text-to-image generative models, e.g., Stable Diffusion (SD), have exhibited overwhelming results with high fidelity. Despite the magnificent progress, current state-of-the-art models still struggle to generate images fully adhering to the input prompt. Prior work, Attend & Excite, has introduced the concept of Generative Semantic Nursing (GSN), aiming to optimize cross-attention during inference time to better incorporate the semantics. It demonstrates promising results in generating simple prompts, e.g., ``a cat and a dog''. However, its efficacy declines when dealing with more complex prompts, and it does not explicitly address the problem of improper attribute binding. To address the challenges posed by complex prompts or scenarios involving multiple entities and to achieve improved attribute binding, we propose Divide & Bind. We introduce two novel loss objectives for GSN: a novel attendance loss and a binding loss. Our approach stands out in its ability to faithfully synthesize desired objects with improved attribute alignment from complex prompts and exhibits superior performance across multiple evaluation benchmarks. More videos and updates can be found on the project page https://sites.google.com/view/divide-and-bind.

Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision and fail to predict binding fitness, limiting translational impact. We present AuroBind, a scalable virtual screening framework that fine-tunes a custom atomic-level structural model on million-scale chemogenomic data. AuroBind integrates direct preference optimization, self-distillation from high-confidence complexes, and a teacher-student acceleration strategy to jointly predict ligand-bound structures and binding fitness. The proposed models outperform state-of-the-art models on structural and functional benchmarks while enabling 100,000-fold faster screening across ultra-large compound libraries. In a prospective screen across ten disease-relevant targets, AuroBind achieved experimental hit rates of 7-69%, with top compounds reaching sub-nanomolar to picomolar potency. For the orphan GPCRs GPR151 and GPR160, AuroBind identified both agonists and antagonists with success rates of 16-30%, and functional assays confirmed GPR160 modulation in liver and prostate cancer models. AuroBind offers a generalizable framework for structure-function learning and high-throughput molecular screening, bridging the gap between structure prediction and therapeutic discovery.

Peer review is fundamental to scientific research, but the growing volume of publications has intensified the challenges of this expertise-intensive process. While LLMs show promise in various scientific tasks, their potential to assist with peer review, particularly in identifying paper limitations, remains understudied. We first present a comprehensive taxonomy of limitation types in scientific research, with a focus on AI. Guided by this taxonomy, for studying limitations, we present LimitGen, the first comprehensive benchmark for evaluating LLMs' capability to support early-stage feedback and complement human peer review. Our benchmark consists of two subsets: LimitGen-Syn, a synthetic dataset carefully created through controlled perturbations of high-quality papers, and LimitGen-Human, a collection of real human-written limitations. To improve the ability of LLM systems to identify limitations, we augment them with literature retrieval, which is essential for grounding identifying limitations in prior scientific findings. Our approach enhances the capabilities of LLM systems to generate limitations in research papers, enabling them to provide more concrete and constructive feedback.

The ``LLM-as-a-judge'' paradigm has become a standard method for evaluating open-ended generation. To address the quadratic scalability costs of pairwise comparisons, popular benchmarks like Arena-Hard and AlpacaEval compare all models against a single anchor. However, despite its widespread use, the impact of anchor selection on the reliability of the results remains largely unexplored. In this work, we systematically investigate the effect of anchor selection by evaluating 22 different anchors on the Arena-Hard-v2.0 dataset. We find that the choice of anchor is critical: a poor anchor can dramatically reduce correlation with human rankings. We identify that common anchor choices (best-performing and worst-performing models) make poor anchors. Because these extreme anchors are consistently better or worse than all other models, they are seldom indicative of the relative ranking of the models. We further quantify the effect size of anchor selection, showing it is comparable to the selection of a judge model. We conclude with actionable recommendations. First, we conduct a power analysis, and compute sufficient benchmark sizes for anchor-based evaluation, finding that standard benchmark sizes are insufficient for pairwise evaluation and fail to distinguish between competitive models reliably. Second, we provide guidelines for selecting informative anchors to ensure reliable and efficient evaluation practices.

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

As the context limits of Large Language Models (LLMs) increase, the range of possible applications and downstream functions broadens. In many real-world tasks, decisions depend on details scattered across collections of often disparate documents containing mostly irrelevant information. Long-context LLMs appear well-suited to this form of complex information retrieval and reasoning, which has traditionally proven costly and time-consuming. However, although the development of longer context models has seen rapid gains in recent years, our understanding of how effectively LLMs use their context has not kept pace. To address this, we conduct a set of retrieval experiments designed to evaluate the capabilities of 17 leading LLMs, such as their ability to follow threads of information through the context window. Strikingly, we find that many models are remarkably threadsafe: capable of simultaneously following multiple threads without significant loss in performance. Still, for many models, we find the effective context limit is significantly shorter than the supported context length, with accuracy decreasing as the context window grows. Our study also highlights the important point that token counts from different tokenizers should not be directly compared -- they often correspond to substantially different numbers of written characters. We release our code and long-context experimental data.

Scaling limits, such as infinite-width limits, serve as promising theoretical tools to study large-scale models. However, it is widely believed that existing infinite-width theory does not faithfully explain the behavior of practical networks, especially those trained in standard parameterization (SP) meaning He initialization with a global learning rate. For instance, existing theory for SP predicts instability at large learning rates and vanishing feature learning at stable ones. In practice, however, optimal learning rates decay slower than theoretically predicted and networks exhibit both stable training and non-trivial feature learning, even at very large widths. Here, we show that this discrepancy is not fully explained by finite-width phenomena. Instead, we find a resolution through a finer-grained analysis of the regime previously considered unstable and therefore uninteresting. In particular, we show that, under cross-entropy (CE) loss, the unstable regime comprises two distinct sub-regimes: a catastrophically unstable regime and a more benign controlled divergence regime, where logits diverge but gradients and activations remain stable. Moreover, under large learning rates at the edge of the controlled divergence regime, there exists a well-defined infinite width limit where features continue to evolve in all the hidden layers. In experiments across optimizers, architectures, and data modalities, we validate that neural networks operate in this controlled divergence regime under CE loss but not under MSE loss. Our empirical evidence suggests that width-scaling considerations are surprisingly useful for predicting empirically maximal stable learning rate exponents which provide useful guidance on optimal learning rate exponents. Finally, our analysis clarifies the effectiveness and limitations of recently proposed layerwise learning rate scaling for standard initialization.

Making statements about the performance of trained models on tasks involving new data is one of the primary goals of machine learning, i.e., to understand the generalization power of a model. Various capacity measures try to capture this ability, but usually fall short in explaining important characteristics of models that we observe in practice. In this study, we propose the local effective dimension as a capacity measure which seems to correlate well with generalization error on standard data sets. Importantly, we prove that the local effective dimension bounds the generalization error and discuss the aptness of this capacity measure for machine learning models.

Prior work has shown that fine-tuning models on a narrow domain with misaligned data can lead to broad misalignment - a phenomenon termed "emergent misalignment" (Betley et al. 2025). While all tested models were susceptible to emergent misalignment, some models showed more resistance than others. Specifically the Qwen-2.5 family proved to be relatively resistant, while GPT-4o exhibited the strongest misalignment. In this paper we evaluate if current-generation open-weights models exhibit similar resistance to the Qwen-2.5 family and measure misalignment robustness over a range of model architectures and scales. We replicate the effect across nine modern open-weights models (Gemma 3 and Qwen 3 families, 1B-32B parameters). Models fine-tuned on insecure code generation show a 0.68% misalignment rate (compared to 0.07% for base models), matching the lower end of prior open-model results but dramatically lower than GPT-4o's 20%. We identify a critical format-dependent vulnerability: requiring JSON output doubles misalignment rates compared to natural language prompts (0.96% vs 0.42%). This suggests that structural constraints may bypass safety training by reducing the model's 'degrees of freedom' to refuse. These findings confirm emergent misalignment as a reproducible phenomenon in modern open-weights models, with rates substantially lower than observed in proprietary systems.

Machine learning force fields (MLFFs) have revolutionized molecular simulations by providing quantum mechanical accuracy at the speed of molecular mechanical computations. However, a fundamental reliance of these models on fixed-cutoff architectures limits their applicability to macromolecular systems where long-range interactions dominate. We demonstrate that this locality constraint causes force prediction errors to scale monotonically with system size, revealing a critical architectural bottleneck. To overcome this, we establish the systematically designed MolLR25 ({Mol}ecules with {L}ong-{R}ange effect) benchmark up to 1200 atoms, generated using high-fidelity DFT, and introduce E2Former-LSR, an equivariant transformer that explicitly integrates long-range attention blocks. E2Former-LSR exhibits stable error scaling, achieves superior fidelity in capturing non-covalent decay, and maintains precision on complex protein conformations. Crucially, its efficient design provides up to 30% speedup compared to purely local models. This work validates the necessity of non-local architectures for generalizable MLFFs, enabling high-fidelity molecular dynamics for large-scale chemical and biological systems.

We carry out an information-theoretical analysis of a two-layer neural network trained from input-output pairs generated by a teacher network with matching architecture, in overparametrized regimes. Our results come in the form of bounds relating i) the mutual information between training data and network weights, or ii) the Bayes-optimal generalization error, to the same quantities but for a simpler (generalized) linear model for which explicit expressions are rigorously known. Our bounds, which are expressed in terms of the number of training samples, input dimension and number of hidden units, thus yield fundamental performance limits for any neural network (and actually any learning procedure) trained from limited data generated according to our two-layer teacher neural network model. The proof relies on rigorous tools from spin glasses and is guided by ``Gaussian equivalence principles'' lying at the core of numerous recent analyses of neural networks. With respect to the existing literature, which is either non-rigorous or restricted to the case of the learning of the readout weights only, our results are information-theoretic (i.e. are not specific to any learning algorithm) and, importantly, cover a setting where all the network parameters are trained.

On-policy distillation (OPD) is widely used for LLM post-training. When pushed with a reward-extrapolation coefficient lambda > 1, the student can lift past the teacher in domain, but past a threshold lambda* the same step violates the output contract on structured-output tasks. In a single-position Bernoulli reduction, we derive a closed-form base-relative clip-safety threshold lambda*(p,b,c) determined by three measurable quantities: the teacher modal probability, the warm-start mass, and the importance-sampling clip strength. Above lambda*, the extrapolated fixed point exits the clip-safe region, changing training from format-preserving to format-collapsing. We extend the rule to calibrated K-ary listwise JSON tasks where a single binding equivalence class dominates the output contract and SFT retains parse headroom. On Amazon Fashion, three pre-registered tests--a fine-grid cliff interval, a budget-extension test, and a small-clip cross-prediction--fall within their locked prediction windows, with the small-clip value matching the closed-form prediction below grid resolution. Operating just below lambda*, ListOPD brings a 1.7B Qwen3 student to in-domain parity with an 8B-SFT baseline at one-fifth the parameters. The gain is driven primarily by format adherence: NDCG@1 on parsed outputs remains flat across lambda, while parse validity sharply changes at the predicted boundary. The cliff diagnostic is rubric-independent, whereas the parity claim uses a Gemini-graded rubric and inherits that evaluator's exposure.

Predicting peptide--major histocompatibility complex I (pMHC-I) binding affinity remains challenging due to extreme allelic diversity (sim30,000 HLA alleles), severe data scarcity for most alleles, and noisy experimental measurements. Current methods particularly struggle with underrepresented alleles and quantitative binding prediction. We test whether domain-specific continued pre-training of protein language models is beneficial for their application to pMHC-I binding affinity prediction. Starting from ESM Cambrian (300M parameters), we perform masked-language modeling (MLM)-based continued pre-training on HLA-associated peptides (epitopes), testing two input formats: epitope sequences alone versus epitopes concatenated with HLA heavy chain sequences. We then fine-tune for functional IC_{50} binding affinity prediction using only high-quality quantitative data, avoiding mass spectrometry biases that are inherited by existing methods.

Current long context large language models (LLMs) can process inputs up to 100,000 tokens, yet struggle to generate outputs exceeding even a modest length of 2,000 words. Through controlled experiments, we find that the model's effective generation length is inherently bounded by the sample it has seen during supervised fine-tuning (SFT). In other words, their output limitation is due to the scarcity of long-output examples in existing SFT datasets. To address this, we introduce AgentWrite, an agent-based pipeline that decomposes ultra-long generation tasks into subtasks, enabling off-the-shelf LLMs to generate coherent outputs exceeding 20,000 words. Leveraging AgentWrite, we construct LongWriter-6k, a dataset containing 6,000 SFT data with output lengths ranging from 2k to 32k words. By incorporating this dataset into model training, we successfully scale the output length of existing models to over 10,000 words while maintaining output quality. We also develop LongBench-Write, a comprehensive benchmark for evaluating ultra-long generation capabilities. Our 9B parameter model, further improved through DPO, achieves state-of-the-art performance on this benchmark, surpassing even much larger proprietary models. In general, our work demonstrates that existing long context LLM already possesses the potential for a larger output window--all you need is data with extended output during model alignment to unlock this capability. Our code & models are at: https://github.com/THUDM/LongWriter.

We introduce Aligner, a novel Parameter-Efficient Fine-Tuning (PEFT) method for aligning multi-billion-parameter-sized Large Language Models (LLMs). Aligner employs a unique design that constructs a globally shared set of tunable tokens that modify the attention of every layer. Remarkably with this method, even when using one token accounting for a mere 5,000 parameters, Aligner can still perform comparably well to state-of-the-art LLM adaptation methods like LoRA that require millions of parameters. This capacity is substantiated in both instruction following and value alignment tasks. Besides the multiple order-of-magnitude improvement in parameter efficiency, the insight Aligner provides into the internal mechanisms of LLMs is also valuable. The architectural features and efficacy of our method, in addition to our experiments demonstrate that an LLM separates its internal handling of "form" and "knowledge" in a somewhat orthogonal manner. This finding promises to motivate new research into LLM mechanism understanding and value alignment.

We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate predictions for a range of affinity values associated with ligand-protein interactions on out-of-sample data in a zero-shot setting. Only the SMILES string of the ligand and the amino acid sequence of the protein were used as the model inputs. Our results demonstrate a clear improvement over machine learning (ML) and free-energy perturbation (FEP+) based methods in accurately predicting a range of ligand-protein interaction affinities, which can be leveraged to further accelerate drug discovery campaigns against challenging therapeutic targets.

The dynamic range of activations is a first-order constraint for low-bit quantization, activation scaling, and stable LLM inference. Prior work characterized outlier features and massive activations on pre-2024 LLaMA-style models, and the downstream activation-quantization stack inherits that picture without revisiting it for the post-LLaMA open-model boom. We ask the deployment-oriented question: how large can activations get in modern open LLMs, and how does this magnitude vary across families, generations, and training stages? Under a unified pipeline (5,000-sample multi-domain corpus, family-specific tokenization, identical hooks across embeddings, hidden states, attention, MLP/MoE, SwiGLU gates, and final norm), we measure global and layerwise maxima on 27 checkpoints from 8 open families spanning dense, MoE, vision-language, intermediate-training, and instruction-tuned variants. We find that (i) global maxima span over nearly four orders of magnitude at comparable parameter counts, with Qwen3.5 and MoE checkpoints in the 10^2 to 10^3 range and Gemma3-27B-it reaching ~7 x 10^5; (ii) cross-family and cross-generation comparisons break simple monotonic scaling; and (iii) MoE checkpoints exhibit 14.0-23.4x lower peaks than matched-scale dense counterparts, while the residual stream carries the global maximum in 22/24 checkpoints. A lightweight INT-8 sanity check shows that measured maxima co-vary with low-bit reconstruction error via activation-scale selection. We conclude that maximum activation magnitude is a model property tied to family, architecture, and training stage - not a simple byproduct of size - and should be measured and reported alongside any open-weight release before low-bit deployment. The code is publicly available at https://github.com/clx1415926/Max_act_llm.

Although text-to-image (T2I) models exhibit remarkable generation capabilities, they frequently fail to accurately bind semantically related objects or attributes in the input prompts; a challenge termed semantic binding. Previous approaches either involve intensive fine-tuning of the entire T2I model or require users or large language models to specify generation layouts, adding complexity. In this paper, we define semantic binding as the task of associating a given object with its attribute, termed attribute binding, or linking it to other related sub-objects, referred to as object binding. We introduce a novel method called Token Merging (ToMe), which enhances semantic binding by aggregating relevant tokens into a single composite token. This ensures that the object, its attributes and sub-objects all share the same cross-attention map. Additionally, to address potential confusion among main objects with complex textual prompts, we propose end token substitution as a complementary strategy. To further refine our approach in the initial stages of T2I generation, where layouts are determined, we incorporate two auxiliary losses, an entropy loss and a semantic binding loss, to iteratively update the composite token to improve the generation integrity. We conducted extensive experiments to validate the effectiveness of ToMe, comparing it against various existing methods on the T2I-CompBench and our proposed GPT-4o object binding benchmark. Our method is particularly effective in complex scenarios that involve multiple objects and attributes, which previous methods often fail to address. The code will be publicly available at https://github.com/hutaihang/ToMe.

Safety aligned Large Language Models (LLMs) are vulnerable to harmful fine-tuning attacks qi2023fine-- a few harmful data mixed in the fine-tuning dataset can break the LLMs's safety alignment. Existing mitigation strategies include alignment stage solutions huang2024vaccine, rosati2024representation and fine-tuning stage solutions huang2024lazy,mukhoti2023fine. However, our evaluation shows that both categories of defenses fail when some specific training hyper-parameters are chosen -- a large learning rate or a large number of training epochs in the fine-tuning stage can easily invalidate the defense, which however, is necessary to guarantee finetune performance. To this end, we propose Antidote, a post-fine-tuning stage solution, which remains \textit{agnostic to the training hyper-parameters in the fine-tuning stage}. Antidote relies on the philosophy that by removing the harmful parameters, the harmful model can be recovered from the harmful behaviors, regardless of how those harmful parameters are formed in the fine-tuning stage. With this philosophy, we introduce a one-shot pruning stage after harmful fine-tuning to remove the harmful weights that are responsible for the generation of harmful content. Despite its embarrassing simplicity, empirical results show that Antidote can reduce harmful score while maintaining accuracy on downstream tasks.Our project page is at https://huangtiansheng.github.io/Antidote_gh_page/

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Deployed language models must produce outputs that are both correct and format-compliant. We study this structured-output reliability gap using two mathematical benchmarks -- GSM8K and MATH -- as a controlled testbed: ground truth is unambiguous and the output contract is strict (JSON with required fields). We evaluate three 7-9B models under five prompting strategies and report output accuracy -- the joint event of mathematical correctness and valid JSON structure -- as the primary metric. A systematic format failure emerges: NAIVE prompting (no system prompt) achieves up to 85% task accuracy on GSM8K but 0% output accuracy across all models and datasets. REFERENCE prompting (a minimal hand-written JSON format prompt) fares little better, yielding 0% output accuracy for two of four models tested. Constrained decoding enforces syntactic validity but incurs 3.6x-8.2x latency overhead and in several settings degrades task performance substantially. To overcome this limitation, we developed AloLab, an iterative system-prompt optimizer (meta-agent: Claude Sonnet 4.5) requiring only black-box API access to the target model; it reaches 84-87% output accuracy on GSM8K and 34-40% on MATH across five independent runs per model, with 29/30 paired McNemar comparisons against the best static prompt significant at p < 0.05, at near-NAIVE inference latency and without model fine-tuning. The same format failure extends to GPT-4o (OpenAI, 2024), a proprietary closed-source model: REFERENCE achieves 0% output accuracy due to systematic markdown-fence wrapping, while AloLab reaches 95.2% [94.8, 95.6]. An ablation replacing the Sonnet 4.5 meta-agent with Claude 3 Haiku reduces mean output accuracy to 61.0% and increases run-to-run standard deviation from <1 pp to 21.8 pp, confirming that meta-agent capability is a primary driver of optimization quality.

We introduce AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for antibody binding affinity maturation and design. Unlike previous strategies that evaluate antibodies in isolation, typically by comparing them to natural sequences with metrics such as amino acid recovery rate or structural RMSD, AbBiBench instead treats the antibody-antigen (Ab-Ag) complex as the fundamental unit. It evaluates an antibody design's binding potential by measuring how well a protein model scores the full Ab-Ag complex. We first curate, standardize, and share more than 184,500 experimental measurements of antibody mutants across 14 antibodies and 9 antigens-including influenza, lysozyme, HER2, VEGF, integrin, Ang2, and SARS-CoV-2-covering both heavy-chain and light-chain mutations. Using these datasets, we systematically compare 15 protein models including masked language models, autoregressive language models, inverse folding models, diffusion-based generative models, and geometric graph models by comparing the correlation between model likelihood and experimental affinity values. Additionally, to demonstrate AbBiBench's generative utility, we apply it to antibody F045-092 in order to introduce binding to influenza H1N1. We sample new antibody variants with the top-performing models, rank them by the structural integrity and biophysical properties of the Ab-Ag complex, and assess them with in vitro ELISA binding assays. Our findings show that structure-conditioned inverse folding models outperform others in both affinity correlation and generation tasks. Overall, AbBiBench provides a unified, biologically grounded evaluation framework to facilitate the development of more effective, function-aware antibody design models.

Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.

Large Language Models (LLMs) are advancing at an amazing speed and have become indispensable across academia, industry, and daily applications. To keep pace with the status quo, this survey probes the core challenges that the rise of LLMs poses for evaluation. We identify and analyze two pivotal transitions: (i) from task-specific to capability-based evaluation, which reorganizes benchmarks around core competencies such as knowledge, reasoning, instruction following, multi-modal understanding, and safety; and (ii) from manual to automated evaluation, encompassing dynamic dataset curation and "LLM-as-a-judge" scoring. Yet, even with these transitions, a crucial obstacle persists: the evaluation generalization issue. Bounded test sets cannot scale alongside models whose abilities grow seemingly without limit. We will dissect this issue, along with the core challenges of the above two transitions, from the perspectives of methods, datasets, evaluators, and metrics. Due to the fast evolving of this field, we will maintain a living GitHub repository (links are in each section) to crowd-source updates and corrections, and warmly invite contributors and collaborators.

Measurements of Higgs boson production cross-sections are carried out in the diphoton decay channel using 139 fb^{-1} of pp collision data at s = 13 TeV collected by the ATLAS experiment at the LHC. The analysis is based on the definition of 101 distinct signal regions using machine-learning techniques. The inclusive Higgs boson signal strength in the diphoton channel is measured to be 1.04^{+0.10}_{-0.09}. Cross-sections for gluon-gluon fusion, vector-boson fusion, associated production with a W or Z boson, and top associated production processes are reported. An upper limit of 10 times the Standard Model prediction is set for the associated production process of a Higgs boson with a single top quark, which has a unique sensitivity to the sign of the top quark Yukawa coupling. Higgs boson production is further characterized through measurements of Simplified Template Cross-Sections (STXS). In total, cross-sections of 28 STXS regions are measured. The measured STXS cross-sections are compatible with their Standard Model predictions, with a p-value of 93%. The measurements are also used to set constraints on Higgs boson coupling strengths, as well as on new interactions beyond the Standard Model in an effective field theory approach. No significant deviations from the Standard Model predictions are observed in these measurements, which provide significant sensitivity improvements compared to the previous ATLAS results.

Supervised learning is often affected by a covariate shift in which the marginal distributions of instances (covariates x) of training and testing samples p_tr(x) and p_te(x) are different but the label conditionals coincide. Existing approaches address such covariate shift by either using the ratio p_te(x)/p_tr(x) to weight training samples (reweighted methods) or using the ratio p_tr(x)/p_te(x) to weight testing samples (robust methods). However, the performance of such approaches can be poor under support mismatch or when the above ratios take large values. We propose a minimax risk classification (MRC) approach for covariate shift adaptation that avoids such limitations by weighting both training and testing samples. In addition, we develop effective techniques that obtain both sets of weights and generalize the conventional kernel mean matching method. We provide novel generalization bounds for our method that show a significant increase in the effective sample size compared with reweighted methods. The proposed method also achieves enhanced classification performance in both synthetic and empirical experiments.

In nonstationary bandit learning problems, the decision-maker must continually gather information and adapt their action selection as the latent state of the environment evolves. In each time period, some latent optimal action maximizes expected reward under the environment state. We view the optimal action sequence as a stochastic process, and take an information-theoretic approach to analyze attainable performance. We bound limiting per-period regret in terms of the entropy rate of the optimal action process. The bound applies to a wide array of problems studied in the literature and reflects the problem's information structure through its information-ratio.

We study the notion of a generalization bound being uniformly tight, meaning that the difference between the bound and the population loss is small for all learning algorithms and all population distributions. Numerous generalization bounds have been proposed in the literature as potential explanations for the ability of neural networks to generalize in the overparameterized setting. However, in their paper ``Fantastic Generalization Measures and Where to Find Them,'' Jiang et al. (2020) examine more than a dozen generalization bounds, and show empirically that none of them are uniformly tight. This raises the question of whether uniformly-tight generalization bounds are at all possible in the overparameterized setting. We consider two types of generalization bounds: (1) bounds that may depend on the training set and the learned hypothesis (e.g., margin bounds). We prove mathematically that no such bound can be uniformly tight in the overparameterized setting; (2) bounds that may in addition also depend on the learning algorithm (e.g., stability bounds). For these bounds, we show a trade-off between the algorithm's performance and the bound's tightness. Namely, if the algorithm achieves good accuracy on certain distributions, then no generalization bound can be uniformly tight for it in the overparameterized setting. We explain how these formal results can, in our view, inform research on generalization bounds for neural networks, while stressing that other interpretations of these results are also possible.

Emergent misalignment can arise when a language model is fine-tuned on a narrowly scoped supervised objective: the model learns the target behavior, yet also develops undesirable out-of-domain behaviors. We investigate a mechanistic approach to preventing emergent misalignment by identifying a small set of internal features that reliably control the misaligned behavior and then discouraging the model from strengthening these features during fine-tuning. Across six fine-tuning domains, blocking (i.e., constraining) a fixed set of features achieves up to 95\% relative reduction in emergent misalignment with no degradation in model quality or target-task performance. We strengthen validity with disjoint selection/evaluation splits, multiple independent judges, multiple random seeds for key settings, quality metrics, and extensive ablations demonstrating that the reduction in misalignment is specific to the identified mechanism. We also characterize a limiting regime in which misalignment re-emerges under prolonged fine-tuning, present evidence consistent with rerouting through alternative features or layers, and evaluate modifications that partially restore the misalignment-blocking effect. Overall, our results show that targeted training-time constraints on internal mechanisms can mitigate emergent misalignment without degrading target-task performance.

We study the accuracy of differentially private mechanisms in the continual release model. A continual release mechanism receives a sensitive dataset as a stream of T inputs and produces, after receiving each input, an accurate output on the obtained inputs. In contrast, a batch algorithm receives the data as one batch and produces a single output. We provide the first strong lower bounds on the error of continual release mechanisms. In particular, for two fundamental problems that are widely studied and used in the batch model, we show that the worst case error of every continual release algorithm is tilde Omega(T^{1/3}) times larger than that of the best batch algorithm. Previous work shows only a polylogarithimic (in T) gap between the worst case error achievable in these two models; further, for many problems, including the summation of binary attributes, the polylogarithmic gap is tight (Dwork et al., 2010; Chan et al., 2010). Our results show that problems closely related to summation -- specifically, those that require selecting the largest of a set of sums -- are fundamentally harder in the continual release model than in the batch model. Our lower bounds assume only that privacy holds for streams fixed in advance (the "nonadaptive" setting). However, we provide matching upper bounds that hold in a model where privacy is required even for adaptively selected streams. This model may be of independent interest.

Instruction tuning is critical to improve LLMs but usually suffers from low-quality and redundant data. Data filtering for instruction tuning has proved important in improving both the efficiency and performance of the tuning process. But it also leads to extra cost and computation due to the involvement of LLMs in this process. To reduce the filtering cost, we study Superfiltering: Can we use a smaller and weaker model to select data for finetuning a larger and stronger model? Despite the performance gap between weak and strong language models, we find their highly consistent capability to perceive instruction difficulty and data selection results. This enables us to use a much smaller and more efficient model to filter the instruction data used to train a larger language model. Not only does it largely speed up the data filtering, but the filtered-data-finetuned LLM achieves even better performance on standard benchmarks. Extensive experiments validate the efficacy and efficiency of our approach.

Unlimited, or so-called helpful-only language models are trained without safety alignment constraints and never refuse user queries. They are widely used by leading AI companies as internal tools for red teaming and alignment evaluation. For example, if a safety-aligned model produces harmful outputs similar to an unlimited model, this indicates alignment failures that require further attention. Despite their essential role in assessing alignment, such models are not available to the research community. We introduce Jinx, a helpful-only variant of popular open-weight LLMs. Jinx responds to all queries without refusals or safety filtering, while preserving the base model's capabilities in reasoning and instruction following. It provides researchers with an accessible tool for probing alignment failures, evaluating safety boundaries, and systematically studying failure modes in language model safety.

More transformer blocks with residual connections have recently achieved impressive results on various tasks. To achieve better performance with fewer trainable parameters, recent methods are proposed to go shallower by parameter sharing or model compressing along with the depth. However, weak modeling capacity limits their performance. Contrastively, going wider by inducing more trainable matrixes and parameters would produce a huge model requiring advanced parallelism to train and inference. In this paper, we propose a parameter-efficient framework, going wider instead of deeper. Specially, following existing works, we adapt parameter sharing to compress along depth. But, such deployment would limit the performance. To maximize modeling capacity, we scale along model width by replacing feed-forward network (FFN) with mixture-of-experts (MoE). Across transformer blocks, instead of sharing normalization layers, we propose to use individual layernorms to transform various semantic representations in a more parameter-efficient way. To evaluate our plug-and-run framework, we design WideNet and conduct comprehensive experiments on popular computer vision and natural language processing benchmarks. On ImageNet-1K, our best model outperforms Vision Transformer (ViT) by 1.5% with 0.72 times trainable parameters. Using 0.46 times and 0.13 times parameters, our WideNet can still surpass ViT and ViT-MoE by 0.8% and 2.1%, respectively. On four natural language processing datasets, WideNet outperforms ALBERT by 1.8% on average and surpass BERT using factorized embedding parameterization by 0.8% with fewer parameters.

The recent breakthrough successes in machine learning are mainly attributed to scale: namely large-scale attention-based architectures and datasets of unprecedented scale. This paper investigates the impact of training at scale for chess. Unlike traditional chess engines that rely on complex heuristics, explicit search, or a combination of both, we train a 270M parameter transformer model with supervised learning on a dataset of 10 million chess games. We annotate each board in the dataset with action-values provided by the powerful Stockfish 16 engine, leading to roughly 15 billion data points. Our largest model reaches a Lichess blitz Elo of 2895 against humans, and successfully solves a series of challenging chess puzzles, without any domain-specific tweaks or explicit search algorithms. We also show that our model outperforms AlphaZero's policy and value networks (without MCTS) and GPT-3.5-turbo-instruct. A systematic investigation of model and dataset size shows that strong chess performance only arises at sufficient scale. To validate our results, we perform an extensive series of ablations of design choices and hyperparameters.

In scientific research, limitations refer to the shortcomings, constraints, or weaknesses within a study. Transparent reporting of such limitations can enhance the quality and reproducibility of research and improve public trust in science. However, authors often a) underreport them in the paper text and b) use hedging strategies to satisfy editorial requirements at the cost of readers' clarity and confidence. This underreporting behavior, along with an explosion in the number of publications, has created a pressing need to automatically extract or generate such limitations from scholarly papers. In this direction, we present a complete architecture for the computational analysis of research limitations. Specifically, we create a dataset of limitations in ACL, NeurIPS, and PeerJ papers by extracting them from papers' text and integrating them with external reviews; we propose methods to automatically generate them using a novel Retrieval Augmented Generation (RAG) technique; we create a fine-grained evaluation framework for generated limitations; and we provide a meta-evaluation for the proposed evaluation techniques.

Large language models (LLMs) have attracted significant attention due to their impressive general capabilities across diverse downstream tasks. However, without domain-specific optimization, they often underperform on specialized knowledge benchmarks and even produce hallucination. Recent studies show that strategically infusing domain knowledge during pretraining can substantially improve downstream performance. A critical challenge lies in balancing this infusion trade-off: injecting too little domain-specific data yields insufficient specialization, whereas excessive infusion triggers catastrophic forgetting of previously acquired knowledge. In this work, we focus on the phenomenon of memory collapse induced by over-infusion. Through systematic experiments, we make two key observations, i.e. 1) Critical collapse point: each model exhibits a threshold beyond which its knowledge retention capabilities sharply degrade. 2) Scale correlation: these collapse points scale consistently with the model's size. Building on these insights, we propose a knowledge infusion scaling law that predicts the optimal amount of domain knowledge to inject into large LLMs by analyzing their smaller counterparts. Extensive experiments across different model sizes and pertaining token budgets validate both the effectiveness and generalizability of our scaling law.

The scaling of large language models (LLMs) emphasizes increasing depth, yet performance gains diminish with added layers. Prior work introduces the concept of "effective depth", arguing that deeper models fail to fully utilize their layers for meaningful computation. Building on this, we systematically study how effective depth varies with model scale, training type, and task difficulty. First, we analyze the model behavior of Qwen-2.5 family (1.5B-32B) and find that while the number of effective layers grows with model size, the effective depth ratio remains stable. Besides, comparisons between base and corresponding long-CoT models show no increase in effective depth, suggesting that improved reasoning stems from longer context rather than deeper per-token computation. Furthermore, evaluations across tasks of varying difficulty indicate that models do not dynamically use more layers for harder problems. Our results suggest that current LLMs underuse available depth across scales, training paradigms and tasks of varying difficulties, pointing out research opportunities on increasing the layer utilization rate of LLMs, model pruning, and early exiting. Our code is released at https://github.com/AheadOFpotato/what_affects_effective_depth.

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSA-annotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motif-scaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13\% in designability and 13\% in catalytic efficiency compared to the baseline models. The code is released at https://github.com/Vecteur-libre/EnzyControl.

Motivated by the need to efficiently identify multiple candidates in high trial-and-error cost tasks such as drug discovery, we propose a near-optimal algorithm to identify all ε-best arms (i.e., those at most ε worse than the optimum). Specifically, we introduce LinFACT, an algorithm designed to optimize the identification of all ε-best arms in linear bandits. We establish a novel information-theoretic lower bound on the sample complexity of this problem and demonstrate that LinFACT achieves instance optimality by matching this lower bound up to a logarithmic factor. A key ingredient of our proof is to integrate the lower bound directly into the scaling process for upper bound derivation, determining the termination round and thus the sample complexity. We also extend our analysis to settings with model misspecification and generalized linear models. Numerical experiments, including synthetic and real drug discovery data, demonstrate that LinFACT identifies more promising candidates with reduced sample complexity, offering significant computational efficiency and accelerating early-stage exploratory experiments.

Training Large Language Models (LLMs) with Group Relative Policy Optimization (GRPO) encounters a significant challenge: models often fail to produce accurate responses, particularly in small-scale architectures. This limitation not only diminishes performance improvements and undermines the potential of GRPO but also frequently leads to mid-training collapse, adversely affecting stability and final efficacy. To address these issues, we propose ToolExpander, a novel framework that advances tool-oriented reinforcement learning for resource-constrained LLMs through two key innovations:(1) Dynamic Multi-Round Hard Sampling, which dynamically substitutes challenging samples(those without correct outputs over 10 rollouts) with high-quality few-shot demonstrations during training, coupled with an exponential learning rate decay strategy to mitigate oscillations;(2) Self-Exemplifying Thinking, an enhanced GRPO framework that eliminates KL divergence and incorporates adjusted clipping coefficients, encouraging models to autonomously generate and analyze few-shot examples via a minimal additional reward (0.01).Experimental results demonstrate that ToolExpander significantly enhances tool-using capabilities in LLMs, especially in weaker small-scale models, improving both training stability and overall performance.

LongRoPE2 is a novel approach that extends the effective context window of pre-trained large language models (LLMs) to the target length, while preserving the performance on the original shorter context window. This is achieved by three contributions: (1) a hypothesis that insufficient training in higher RoPE dimensions contributes to the persistent out-of-distribution (OOD) issues observed in existing methods; (2) an effective RoPE rescaling algorithm that adopts evolutionary search guided by "needle-driven" perplexity to address the insufficient training problem; (3) a mixed context window training approach that fine-tunes model weights to adopt rescaled RoPE for long-context sequences while preserving the short-context performance with the original RoPE. Extensive experiments on LLaMA3-8B and Phi3-mini-3.8B across various benchmarks validate the hypothesis and demonstrate the effectiveness of LongRoPE2. Remarkably, LongRoPE2 extends LLaMA3-8B to achieve a 128K effective context length while retaining over 98.5% of short-context performance, using only 10B tokens -- 80x fewer than Meta's approach, which fails to reach the target effective context length. Code will be available at https://github.com/microsoft/LongRoPE.

Multi-controlled single-target (MC) gates are some of the most crucial building blocks for varied quantum algorithms. How to implement them optimally is thus a pivotal question. To answer this question in an architecture-independent manner, and to get a worst-case estimate, we should look at a linear nearest-neighbor (LNN) architecture, as this can be embedded in almost any qubit connectivity. Motivated by the above, here we describe a method which implements MC gates using no more than sim 4k+8n CNOT gates -- up-to 60% reduction over state-of-the-art -- while allowing for complete flexibility to choose the locations of n controls, the target, and a dirty ancilla out of k qubits. More strikingly, in case k approx n, our upper bound is sim 12n -- the best known for unrestricted connectivity -- and if n = 1, our upper bound is sim 4k -- the best known for a single long-range CNOT gate over k qubits -- therefore, if our upper bound can be reduced, then the cost of one or both of these simpler versions of MC gates will be immediately reduced accordingly. In practice, our method provides circuits that tend to require fewer CNOT gates than our upper bound for almost any given instance of MC gates.

Since compute grows much faster than web text available for language model pre-training, we ask how one should approach pre-training under fixed data and no compute constraints. We first show that existing data-constrained approaches of increasing epoch count and parameter count eventually overfit, and we significantly improve upon such recipes by properly tuning regularization, finding that the optimal weight decay is 30times larger than standard practice. Since our regularized recipe monotonically decreases loss following a simple power law in parameter count, we estimate its best possible performance via the asymptote of its scaling law rather than the performance at a fixed compute budget. We then identify that ensembling independently trained models achieves a significantly lower loss asymptote than the regularized recipe. Our best intervention combining epoching, regularization, parameter scaling, and ensemble scaling achieves an asymptote at 200M tokens using 5.17times less data than our baseline, and our data scaling laws predict that this improvement persists at higher token budgets. We find that our data efficiency gains can be realized at much smaller parameter counts as we can distill an ensemble into a student model that is 8times smaller and retains 83% of the ensembling benefit. Finally, our interventions designed for validation loss generalize to downstream benchmarks, achieving a 9% improvement for pre-training evals and a 17.5times data efficiency improvement over continued pre-training on math mid-training data. Our results show that simple algorithmic improvements can enable significantly more data-efficient pre-training in a compute-rich future.

Distilling knowledge from a large teacher model to a lightweight one is a widely successful approach for generating compact, powerful models in the semi-supervised learning setting where a limited amount of labeled data is available. In large-scale applications, however, the teacher tends to provide a large number of incorrect soft-labels that impairs student performance. The sheer size of the teacher additionally constrains the number of soft-labels that can be queried due to prohibitive computational and/or financial costs. The difficulty in achieving simultaneous efficiency (i.e., minimizing soft-label queries) and robustness (i.e., avoiding student inaccuracies due to incorrect labels) hurts the widespread application of knowledge distillation to many modern tasks. In this paper, we present a parameter-free approach with provable guarantees to query the soft-labels of points that are simultaneously informative and correctly labeled by the teacher. At the core of our work lies a game-theoretic formulation that explicitly considers the inherent trade-off between the informativeness and correctness of input instances. We establish bounds on the expected performance of our approach that hold even in worst-case distillation instances. We present empirical evaluations on popular benchmarks that demonstrate the improved distillation performance enabled by our work relative to that of state-of-the-art active learning and active distillation methods.

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

Accurate prediction of protein-ligand binding poses is crucial for structure-based drug design, yet existing methods struggle to balance speed, accuracy, and physical plausibility. We introduce Matcha, a novel molecular docking pipeline that combines multi-stage flow matching with learned scoring and physical validity filtering. Our approach consists of three sequential stages applied consecutively to refine docking predictions, each implemented as a flow matching model operating on appropriate geometric spaces (R^3, SO(3), and SO(2)). We enhance the prediction quality through a dedicated scoring model and apply unsupervised physical validity filters to eliminate unrealistic poses. Compared to various approaches, Matcha demonstrates superior performance on Astex and PDBbind test sets in terms of docking success rate and physical plausibility. Moreover, our method works approximately 25 times faster than modern large-scale co-folding models. The model weights and inference code to reproduce our results are available at https://github.com/LigandPro/Matcha.

Large language models (LLMs) exhibit degraded performance under prompt compression, but the mechanisms remain poorly understood. We introduce the Compression-Decay Comprehension Test (CDCT), a benchmark that independently measures constraint compliance (CC) and semantic accuracy (SA) across compression levels. We evaluate 9 frontier LLMs across 8 concepts using 5 compression levels from extreme (c=0.0, ~2 words) to none (c=1.0, ~135 words). A three-judge LLM jury achieves almost perfect inter-rater agreement on CC (Fleiss' appa=0.90). We observe a universal U-curve pattern in constraint compliance (97.2% prevalence), with violations peaking at medium compression (c=0.5, ~27 words). Counterintuitively, models perform better at extreme compression than medium lengths. The dimensions are statistically orthogonal (r=0.193, p=0.084), with constraint effects 2.9x larger than semantic effects. Experimental validation via RLHF ablation confirms our constraint salience hypothesis: removing "helpfulness" signals improves CC by 598% on average (71/72 trials, p<0.001), with 79% achieving perfect compliance. This demonstrates that RLHF-trained helpfulness behaviors are the dominant cause of constraint violations at medium compression. Reasoning models outperform efficient models by 27.5% (Cohen's d=0.96). Our findings reveal a fundamental tension between RLHF alignment and instruction-following, providing actionable guidelines for improving deployed systems.

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 pm 0.043, 0.914 pm 0.004, and 0.8132 pm 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

Vector embeddings have been tasked with an ever-increasing set of retrieval tasks over the years, with a nascent rise in using them for reasoning, instruction-following, coding, and more. These new benchmarks push embeddings to work for any query and any notion of relevance that could be given. While prior works have pointed out theoretical limitations of vector embeddings, there is a common assumption that these difficulties are exclusively due to unrealistic queries, and those that are not can be overcome with better training data and larger models. In this work, we demonstrate that we may encounter these theoretical limitations in realistic settings with extremely simple queries. We connect known results in learning theory, showing that the number of top-k subsets of documents capable of being returned as the result of some query is limited by the dimension of the embedding. We empirically show that this holds true even if we restrict to k=2, and directly optimize on the test set with free parameterized embeddings. We then create a realistic dataset called LIMIT that stress tests models based on these theoretical results, and observe that even state-of-the-art models fail on this dataset despite the simple nature of the task. Our work shows the limits of embedding models under the existing single vector paradigm and calls for future research to develop methods that can resolve this fundamental limitation.

The Universal Approximation Theorem posits that neural networks can theoretically possess unlimited approximation capacity with a suitable activation function and a freely chosen or trained set of parameters. However, a more practical scenario arises when these neural parameters, especially the nonlinear weights and biases, are bounded. This leads us to question: Does the approximation capacity of a neural network remain universal, or does it have a limit when the parameters are practically bounded? And if it has a limit, how can it be measured? Our theoretical study indicates that while universal approximation is theoretically feasible, in practical numerical scenarios, Deep Neural Networks (DNNs) with any analytic activation functions (such as Tanh and Sigmoid) can only be approximated by a finite-dimensional vector space under a bounded nonlinear parameter space (NP space), whether in a continuous or discrete sense. Based on this study, we introduce the concepts of ε outer measure and Numerical Span Dimension (NSdim) to quantify the approximation capacity limit of a family of networks both theoretically and practically. Furthermore, drawing on our new theoretical study and adopting a fresh perspective, we strive to understand the relationship between back-propagation neural networks and random parameter networks (such as the Extreme Learning Machine (ELM)) with both finite and infinite width. We also aim to provide fresh insights into regularization, the trade-off between width and depth, parameter space, width redundancy, condensation, and other related important issues.

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

To deploy language models safely, it is crucial that they abstain from responding to inappropriate requests. Several prior studies test the safety promises of models based on their effectiveness in blocking malicious requests. In this work, we focus on evaluating the underlying techniques that cause models to abstain. We create SELECT, a benchmark derived from a set of benign concepts (e.g., "rivers") from a knowledge graph. Focusing on benign concepts isolates the effect of safety training, and grounding these concepts in a knowledge graph allows us to study the generalization and specificity of abstention techniques. Using SELECT, we benchmark different abstention techniques over six open-weight and closed-source models. We find that the examined techniques indeed cause models to abstain with over 80% abstention rates. However, these techniques are not as effective for descendants of the target concepts, where abstention rates drop by 19%. We also characterize the generalization-specificity trade-offs for different techniques. Overall, no single technique is invariably better than others, and our findings inform practitioners of the various trade-offs involved.

We investigate the relationship between representation geometry and neural network performance. Analyzing 52 pretrained ImageNet models across 13 architecture families, we show that effective dimension -- an unsupervised geometric metric -- strongly predicts accuracy. Output effective dimension achieves partial r=0.75 (p < 10^(-10)) after controlling for model capacity, while total compression achieves partial r=-0.72. These findings replicate across ImageNet and CIFAR-10, and generalize to NLP: effective dimension predicts performance for 8 encoder models on SST-2/MNLI and 15 decoder-only LLMs on AG News (r=0.69, p=0.004), while model size does not (r=0.07). We establish bidirectional causality: degrading geometry via noise causes accuracy loss (r=-0.94, p < 10^(-9)), while improving geometry via PCA maintains accuracy across architectures (-0.03pp at 95% variance). This relationship is noise-type agnostic -- Gaussian, Uniform, Dropout, and Salt-and-pepper noise all show |r| > 0.90. These results establish that effective dimension provides domain-agnostic predictive and causal information about neural network performance, computed entirely without labels.

Dynamic Tanh (DyT) removes LayerNorm by bounding activations with a learned tanh(alpha x). We show that this bounding is a regime-dependent implicit regularizer, not a uniformly beneficial replacement. Across GPT-2-family models spanning 64M to 3.78B parameters and 1M to 118M tokens, with Llama and ViT cross-checks, DyT improves validation loss by 27.3% at 64M/1M but worsens it by 18.8% at 64M/118M; the 1M benefit vanishes with capacity (+1.7% at 3.78B), while the 118M penalty reaches +27.9%. The mechanism is measurable: 49% of DyT activations saturate at 1M versus 23% at 118M, and a 500-step saturation heuristic classifies DyT's sign with 75% raw in-sample accuracy on the 12-cell GPT-2 calibration set (AUC 0.75; 64% when adding Scale 5 stress cells), correctly labels 3/3 Llama checks, but only reaches 50% raw leave-one-scale-out accuracy. Three interventions support the bounding explanation: HardTanh reproduces the regime pattern, increasing alpha at 118M monotonically reduces DyT's penalty, and vanilla+dropout(p=0.5) matches DyT's data-rich loss. We also localize Llama-DyT collapse to SwiGLU gating, where saturation separates collapse from convergence in a 3-seed component ablation (r=0.94). Scope: all experiments are compute-limited (T/P < 1.84), below Chinchilla-optimal training.

Standard evaluation protocols reveal a counterintuitive phenomenon: on 7.7% of benchmark problems spanning five datasets, larger language models underperform smaller ones by 28.4 percentage points despite 10-100x more parameters. Through systematic evaluation of 31 models (0.5B-405B parameters) across 1,485 problems, we identify the mechanism as spontaneous scale-dependent verbosity that introduces errors through overelaboration. Causal intervention experiments demonstrate this reflects correctable prompt design rather than fundamental capability limitations. Constraining large models to produce brief responses improves accuracy by 26 percentage points and reduces performance gaps by up to two-thirds. Most critically, brevity constraints completely reverse performance hierarchies on mathematical reasoning and scientific knowledge benchmarks, with large models achieving 7.7-15.9 percentage point advantages over small models -- direct inversions of the original gaps. These reversals prove large models possess superior latent capabilities that universal prompting masks. We validate findings through three independent contamination tests and demonstrate inverse scaling operates continuously across the full parameter spectrum, with dataset-specific optimal scales ranging from 0.5B to 3.0B parameters. Our results establish that maximizing large model performance requires scale-aware prompt engineering rather than universal evaluation protocols, with immediate implications for deployment: prompt adaptation simultaneously improves accuracy and reduces computational costs.

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

We propose an approach to estimate the number of samples required for a model to reach a target performance. We find that the power law, the de facto principle to estimate model performance, leads to large error when using a small dataset (e.g., 5 samples per class) for extrapolation. This is because the log-performance error against the log-dataset size follows a nonlinear progression in the few-shot regime followed by a linear progression in the high-shot regime. We introduce a novel piecewise power law (PPL) that handles the two data regimes differently. To estimate the parameters of the PPL, we introduce a random forest regressor trained via meta learning that generalizes across classification/detection tasks, ResNet/ViT based architectures, and random/pre-trained initializations. The PPL improves the performance estimation on average by 37% across 16 classification and 33% across 10 detection datasets, compared to the power law. We further extend the PPL to provide a confidence bound and use it to limit the prediction horizon that reduces over-estimation of data by 76% on classification and 91% on detection datasets.

Safety alignment in Large Language Models is critical for healthcare; however, reliance on binary refusal boundaries often results in over-refusal of benign queries or unsafe compliance with harmful ones. While existing benchmarks measure these extremes, they fail to evaluate Safe Completion: the model's ability to maximise helpfulness on dual-use or borderline queries by providing safe, high-level guidance without crossing into actionable harm. We introduce Health-ORSC-Bench, the first large-scale benchmark designed to systematically measure Over-Refusal and Safe Completion quality in healthcare. Comprising 31,920 benign boundary prompts across seven health categories (e.g., self-harm, medical misinformation), our framework uses an automated pipeline with human validation to test models at varying levels of intent ambiguity. We evaluate 30 state-of-the-art LLMs, including GPT-5 and Claude-4, revealing a significant tension: safety-optimised models frequently refuse up to 80\% of "Hard" benign prompts, while domain-specific models often sacrifice safety for utility. Our findings demonstrate that model family and size significantly influence calibration: larger frontier models (e.g., GPT-5, Llama-4) exhibit "safety-pessimism" and higher over-refusal than smaller or MoE-based counterparts (e.g., Qwen-3-Next), highlighting that current LLMs struggle to balance refusal and compliance. Health-ORSC-Bench provides a rigorous standard for calibrating the next generation of medical AI assistants toward nuanced, safe, and helpful completions. The code and data will be released upon acceptance. red{Warning: Some contents may include toxic or undesired contents.}

As model finetuning is central to the modern NLP, we set to maximize its efficiency. Motivated by redundancy in training examples and the sheer sizes of pretrained models, we exploit a key opportunity: training only on important data. To this end, we set to filter training examples in a streaming fashion, in tandem with training the target model. Our key techniques are two: (1) automatically determine a training loss threshold for skipping backward training passes; (2) run a meta predictor for further skipping forward training passes. We integrate the above techniques in a holistic, three-stage training process. On a diverse set of benchmarks, our method reduces the required training examples by up to 5.3times and training time by up to 6.8times, while only seeing minor accuracy degradation. Our method is effective even when training one epoch, where each training example is encountered only once. It is simple to implement and is compatible with the existing finetuning techniques. Code is available at: https://github.com/xo28/efficient- NLP-multistage-training

Pre-training foundation models on large-scale datasets demonstrates exceptional performance. However, recent research questions this traditional notion, exploring whether an increase in pre-training data always leads to enhanced model performance. To address this issue, data-effective learning approaches have been introduced. However, current methods in this area lack a clear standard for sample selection. Our experiments reveal that by maximizing V-information, sample selection can be framed as an optimization problem, enabling effective improvement in model performance even with fewer samples. Under this guidance, we develop an optimal data-effective learning method (OptiDEL) to maximize V-information. The OptiDEL method generates hard samples to achieve or even exceed the performance of models trained on the full dataset while using substantially less data. We compare the OptiDEL method with state-of-the-art approaches finding that OptiDEL consistently outperforms existing approaches across different datasets, with foundation models trained on only 5% of the pre-training data surpassing the performance of those trained on the full dataset.

Low precision training and inference affect both the quality and cost of language models, but current scaling laws do not account for this. In this work, we devise "precision-aware" scaling laws for both training and inference. We propose that training in lower precision reduces the model's "effective parameter count," allowing us to predict the additional loss incurred from training in low precision and post-train quantization. For inference, we find that the degradation introduced by post-training quantization increases as models are trained on more data, eventually making additional pretraining data actively harmful. For training, our scaling laws allow us to predict the loss of a model with different parts in different precisions, and suggest that training larger models in lower precision may be compute optimal. We unify the scaling laws for post and pretraining quantization to arrive at a single functional form that predicts degradation from training and inference in varied precisions. We fit on over 465 pretraining runs and validate our predictions on model sizes up to 1.7B parameters trained on up to 26B tokens.

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

Solving complex or long-horizon problems often requires large language models (LLMs) to use external tools and operate over a significantly longer context window. New LLMs enable longer context windows and support tool calling capabilities. Prior works have focused mainly on evaluation of LLMs on long-context prompts, leaving agentic setup relatively unexplored, both from capability and safety perspectives. Our work addresses this gap. We find that LLM agents could be sensitive to length, type, and placement of the context, exhibiting unexpected and inconsistent shifts in task performance and in refusals to execute harmful requests. Models with 1M-2M token context windows show severe degradation already at 100K tokens, with performance drops exceeding 50\% for both benign and harmful tasks. Refusal rates shift unpredictably: GPT-4.1-nano increases from sim5\% to sim40\% while Grok 4 Fast decreases from sim80\% to sim10\% at 200K tokens. Our work shows potential safety issues with agents operating on longer context and opens additional questions on the current metrics and paradigm for evaluating LLM agent safety on long multi-step tasks. In particular, our results on LLM agents reveal a notable divergence in both capability and safety performance compared to prior evaluations of LLMs on similar criteria.

Because large language models are expensive to pretrain on different datasets, using smaller-scale experiments to decide on data is crucial for reducing costs. Which benchmarks and methods of making decisions from observed performance at small scale most accurately predict the datasets that yield the best large models? To empower open exploration of this question, we release models, data, and evaluations in DataDecide -- the most extensive open suite of models over differences in data and scale. We conduct controlled pretraining experiments across 25 corpora with differing sources, deduplication, and filtering up to 100B tokens, model sizes up to 1B parameters, and 3 random seeds. We find that the ranking of models at a single, small size (e.g., 150M parameters) is a strong baseline for predicting best models at our larger target scale (1B) (~80% of com parisons correct). No scaling law methods among 8 baselines exceed the compute-decision frontier of single-scale predictions, but DataDecide can measure improvement in future scaling laws. We also identify that using continuous likelihood metrics as proxies in small experiments makes benchmarks including MMLU, ARC, HellaSwag, MBPP, and HumanEval >80% predictable at the target 1B scale with just 0.01% of the compute.

Recent work has shown that small distilled language models are strong competitors to models that are orders of magnitude larger and slower in a wide range of information retrieval tasks. This has made distilled and dense models, due to latency constraints, the go-to choice for deployment in real-world retrieval applications. In this work, we question this practice by showing that the number of parameters and early query-document interaction play a significant role in the generalization ability of retrieval models. Our experiments show that increasing model size results in marginal gains on in-domain test sets, but much larger gains in new domains never seen during fine-tuning. Furthermore, we show that rerankers largely outperform dense ones of similar size in several tasks. Our largest reranker reaches the state of the art in 12 of the 18 datasets of the Benchmark-IR (BEIR) and surpasses the previous state of the art by 3 average points. Finally, we confirm that in-domain effectiveness is not a good indicator of zero-shot effectiveness. Code is available at https://github.com/guilhermemr04/scaling-zero-shot-retrieval.git

With infinitely many high-quality data points, infinite computational power, an infinitely large foundation model with a perfect training algorithm and guaranteed zero generalization error on the pretext task, can the model be used for everything? This question cannot be answered by the existing theory of representation, optimization or generalization, because the issues they mainly investigate are assumed to be nonexistent here. In this paper, we show that category theory provides powerful machinery to answer this question. We have proved three results. The first one limits the power of prompt-based learning, saying that the model can solve a downstream task with prompts if and only if the task is representable. The second one says fine tuning does not have this limit, as a foundation model with the minimum required power (up to symmetry) can theoretically solve downstream tasks for the category defined by pretext task, with fine tuning and enough resources. Our final result can be seen as a new type of generalization theorem, showing that the foundation model can generate unseen objects from the target category (e.g., images) using the structural information from the source category (e.g., texts). Along the way, we provide a categorical framework for supervised and self-supervised learning, which might be of independent interest.

High-quality data plays a critical role in the pretraining and fine-tuning of large language models (LLMs), even determining their performance ceiling to some degree. Consequently, numerous data selection methods have been proposed to identify subsets of data that can effectively and efficiently enhance model performance. However, most of these methods focus on general data selection and tend to overlook the specific nuances of domain-related data. In this paper, we introduce MASS, a MAthematical data Selection framework using the Skill graph for pretraining LLMs in the mathematical reasoning domain. By taking into account the unique characteristics of mathematics and reasoning, we construct a skill graph that captures the mathematical skills and their interrelations from a reference dataset. This skill graph guides us in assigning quality scores to the target dataset, enabling us to select the top-ranked subset which is further used to pretrain LLMs. Experimental results demonstrate the efficiency and effectiveness of MASS across different model sizes (1B and 7B) and pretraining datasets (web data and synthetic data). Specifically, in terms of efficiency, models trained on subsets selected by MASS can achieve similar performance to models trained on the original datasets, with a significant reduction in the number of trained tokens - ranging from 50\% to 70\% fewer tokens. In terms of effectiveness, when trained on the same amount of tokens, models trained on the data selected by MASS outperform those trained on the original datasets by 3.3\% to 5.9\%. These results underscore the potential of MASS to improve both the efficiency and effectiveness of pretraining LLMs.

Distribution shift presents a significant challenge in machine learning, where models often underperform during the test stage when faced with a different distribution than the one they were trained on. This paper focuses on domain shifts, which occur when the model is applied to new domains that are different from the ones it was trained on, and propose a new approach called D^3G. Unlike previous methods that aim to learn a single model that is domain invariant, D^3G leverages domain similarities based on domain metadata to learn domain-specific models. Concretely, D^3G learns a set of training-domain-specific functions during the training stage and reweights them based on domain relations during the test stage. These domain relations can be directly obtained and learned from domain metadata. Under mild assumptions, we theoretically prove that using domain relations to reweight training-domain-specific functions achieves stronger out-of-domain generalization compared to the conventional averaging approach. Empirically, we evaluate the effectiveness of D^3G using real-world datasets for tasks such as temperature regression, land use classification, and molecule-protein binding affinity prediction. Our results show that D^3G consistently outperforms state-of-the-art methods.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

We propose a new bound for generalization of neural networks using Koopman operators. Whereas most of existing works focus on low-rank weight matrices, we focus on full-rank weight matrices. Our bound is tighter than existing norm-based bounds when the condition numbers of weight matrices are small. Especially, it is completely independent of the width of the network if the weight matrices are orthogonal. Our bound does not contradict to the existing bounds but is a complement to the existing bounds. As supported by several existing empirical results, low-rankness is not the only reason for generalization. Furthermore, our bound can be combined with the existing bounds to obtain a tighter bound. Our result sheds new light on understanding generalization of neural networks with full-rank weight matrices, and it provides a connection between operator-theoretic analysis and generalization of neural networks.

A lot of recent work has focused on sparse learned indexes that use deep neural architectures to significantly improve retrieval quality while keeping the efficiency benefits of the inverted index. While such sparse learned structures achieve effectiveness far beyond those of traditional inverted index-based rankers, there is still a gap in effectiveness to the best dense retrievers, or even to sparse methods that leverage more expensive optimizations such as query expansion and query term weighting. We focus on narrowing this gap by revisiting and optimizing DeepImpact, a sparse retrieval approach that uses DocT5Query for document expansion followed by a BERT language model to learn impact scores for document terms. We first reinvestigate the expansion process and find that the recently proposed Doc2Query query filtration does not enhance retrieval quality when used with DeepImpact. Instead, substituting T5 with a fine-tuned Llama 2 model for query prediction results in a considerable improvement. Subsequently, we study training strategies that have proven effective for other models, in particular the use of hard negatives, distillation, and pre-trained CoCondenser model initialization. Our results significantly narrow the effectiveness gap with the most effective versions of SPLADE.

Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function values and subsets within their respective supersets. However, these approaches tend to overlook the valuable information contained within the superset when utilizing neural networks to model set functions. In this work, we address this oversight by adopting a probabilistic perspective. Our theoretical findings demonstrate that when the target value is conditioned on both the input set and subset, it is essential to incorporate an invariant sufficient statistic of the superset into the subset of interest for effective learning. This ensures that the output value remains invariant to permutations of the subset and its corresponding superset, enabling identification of the specific superset from which the subset originated. Motivated by these insights, we propose a simple yet effective information aggregation module designed to merge the representations of subsets and supersets from a permutation invariance perspective. Comprehensive empirical evaluations across diverse tasks and datasets validate the enhanced efficacy of our approach over conventional methods, underscoring the practicality and potency of our proposed strategies in real-world contexts.

Web proxies such as NGINX commonly rely on least-recently-used (LRU) eviction, which is size agnostic and can thrash under periodic bursts and mixed object sizes. We introduce Cold-RL, a learned eviction policy for NGINX that replaces LRU's forced-expire path with a dueling Deep Q-Network served by an ONNX sidecar within a strict microsecond budget. On each eviction, Cold-RL samples the K least-recently-used objects, extracts six lightweight features (age, size, hit count, inter-arrival time, remaining TTL, and last origin RTT), and requests a bitmask of victims; a hard timeout of 500 microseconds triggers immediate fallback to native LRU. Policies are trained offline by replaying NGINX access logs through a cache simulator with a simple reward: a retained object earns one point if it is hit again before TTL expiry. We compare against LRU, LFU, size-based, adaptive LRU, and a hybrid baseline on two adversarial workloads. With a 25 MB cache, Cold-RL raises hit ratio from 0.1436 to 0.3538, a 146 percent improvement over the best classical baseline; at 100 MB, from 0.7530 to 0.8675, a 15 percent gain; and at 400 MB it matches classical methods (about 0.918). Inference adds less than 2 percent CPU overhead and keeps 95th percentile eviction latency within budget. To our knowledge, this is the first reinforcement learning eviction policy integrated into NGINX with strict SLOs.

Omni-modal Large Language Models (OLLMs) greatly expand LLMs' multimodal capabilities but also introduce cross-modal safety risks. However, a systematic understanding of vulnerabilities in omni-modal interactions remains lacking. To bridge this gap, we establish a modality-semantics decoupling principle and construct the AdvBench-Omni dataset, which reveals a significant vulnerability in OLLMs. Mechanistic analysis uncovers a Mid-layer Dissolution phenomenon driven by refusal vector magnitude shrinkage, alongside the existence of a modal-invariant pure refusal direction. Inspired by these insights, we extract a golden refusal vector using Singular Value Decomposition and propose OmniSteer, which utilizes lightweight adapters to modulate intervention intensity adaptively. Extensive experiments show that our method not only increases the Refusal Success Rate against harmful inputs from 69.9% to 91.2%, but also effectively preserves the general capabilities across all modalities. Our code is available at: https://github.com/zhrli324/omni-safety-research.

Given an algorithmic predictor that is accurate on some source population consisting of strategic human decision subjects, will it remain accurate if the population respond to it? In our setting, an agent or a user corresponds to a sample (X,Y) drawn from a distribution D and will face a model h and its classification result h(X). Agents can modify X to adapt to h, which will incur a distribution shift on (X,Y). Our formulation is motivated by applications where the deployed machine learning models are subjected to human agents, and will ultimately face responsive and interactive data distributions. We formalize the discussions of the transferability of a model by studying how the performance of the model trained on the available source distribution (data) would translate to the performance on its induced domain. We provide both upper bounds for the performance gap due to the induced domain shift, as well as lower bounds for the trade-offs that a classifier has to suffer on either the source training distribution or the induced target distribution. We provide further instantiated analysis for two popular domain adaptation settings, including covariate shift and target shift.

In this paper, we study the infinite-depth limit of finite-width residual neural networks with random Gaussian weights. With proper scaling, we show that by fixing the width and taking the depth to infinity, the pre-activations converge in distribution to a zero-drift diffusion process. Unlike the infinite-width limit where the pre-activation converge weakly to a Gaussian random variable, we show that the infinite-depth limit yields different distributions depending on the choice of the activation function. We document two cases where these distributions have closed-form (different) expressions. We further show an intriguing change of regime phenomenon of the post-activation norms when the width increases from 3 to 4. Lastly, we study the sequential limit infinite-depth-then-infinite-width and compare it with the more commonly studied infinite-width-then-infinite-depth limit.

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.

Superalignment, where humans are weak supervisors of superhuman models, has become an important and widely discussed issue in the current era of rapid development of Large Language Models (LLMs). The recent work preliminarily studies this problem by using weak models to supervise strong models. It discovers that weakly supervised strong students can consistently outperform weak teachers towards the alignment target, leading to a weak-to-strong generalization phenomenon. However, we are concerned that behind such a promising phenomenon, whether there exists an issue of weak-to-strong deception, where strong models may deceive weak models by exhibiting well-aligned in areas known to weak models but producing misaligned behaviors in cases weak models do not know. We then take an initial step towards exploring this security issue in a specific but realistic multi-objective alignment case, where there may be some alignment targets conflicting with each other (e.g., helpfulness v.s. harmlessness). Such a conflict is likely to cause strong models to deceive weak models in one alignment dimension to gain high reward in other alignment dimension. Our experiments on both the reward modeling task and the preference optimization scenario indicate: (1) the weak-to-strong deception exists; (2) the deception phenomenon may intensify as the capability gap between weak and strong models increases. We also discuss potential solutions and find bootstrapping with an intermediate model can mitigate the deception to some extent. Our work highlights the urgent need to pay more attention to the true reliability of superalignment.

Safety alignment mechanisms in large language models prevent responses to harmful queries through learned refusal behavior, yet these same mechanisms impede legitimate research applications including cognitive modeling, adversarial testing, and security analysis. While abliteration techniques enable surgical removal of refusal representations through directional orthogonalization, the relative effectiveness of available implementations remains uncharacterized. This study evaluates four abliteration tools (Heretic, DECCP, ErisForge, FailSpy) across sixteen instruction-tuned models (7B-14B parameters), reporting tool compatibility on all 16 models and quantitative metrics on subsets dictated by tool support. Single-pass methods demonstrated superior capability preservation on the benchmarked subset (avg GSM8K change across three models: ErisForge -0.28 pp; DECCP -0.13 pp), while Bayesian-optimized abliteration produced variable distribution shift (KL divergence: 0.043-1.646) with model-dependent capability impact. These findings provide researchers with evidence-based selection criteria for abliteration tool deployment across diverse model architectures. The principal finding indicates that mathematical reasoning capabilities exhibit the highest sensitivity to abliteration interventions, with GSM8K change ranging from +1.51 pp to -18.81 pp (-26.5% relative) depending on tool selection and model architecture.

Every data selection method inherently has a target. In practice, these targets often emerge implicitly through benchmark-driven iteration: researchers develop selection strategies, train models, measure benchmark performance, then refine accordingly. This raises a natural question: what happens when we make this optimization explicit? To explore this, we propose benchmark-targeted ranking (BETR), a simple method that selects pretraining documents based on similarity to benchmark training examples. BETR embeds benchmark examples and a sample of pretraining documents in a shared space, scores this sample by similarity to benchmarks, then trains a lightweight classifier to predict these scores for the full corpus. We compare data selection methods by training over 500 models spanning 10^{19} to 10^{22} FLOPs and fitting scaling laws to them. From this, we find that simply aligning pretraining data to evaluation benchmarks using BETR achieves a 2.1x compute multiplier over DCLM-Baseline (4.7x over unfiltered data) and improves performance on 9 out of 10 tasks across all scales. BETR also generalizes well: when targeting a diverse set of benchmarks disjoint from our evaluation suite, it still matches or outperforms baselines. Our scaling analysis further reveals a clear trend: larger models require less aggressive filtering. Overall, our findings show that directly matching pretraining data to target tasks precisely shapes model capabilities and highlight that optimal selection strategies must adapt to model scale.

Text-to-SQL systems have unlocked easier access to critical data insights by enabling natural language queries over structured databases. However, deploying such systems in enterprise environments remains challenging due to factors such as large, complex schemas (> 3000 columns), diverse SQL dialects (e.g., BigQuery, Snowflake) and sophisticated query requirements (e.g., transformation, analytics). Current state-of-the-art performance on the Spider 2.0 dataset -- a benchmark built to mimic such complex environments -- remains limited at 20%. Key limitations include inadequate instruction-following, poor long-context comprehension, weak self-refinement, and insufficient dialect-specific knowledge. To address these gaps, we propose ReFoRCE (Self-Refinement Agent with Format Restriction and Column Exploration) which introduces (1) table compression to mitigate long-context limitations (2) format restriction to ensure accurate answer format, and (3) iterative column exploration for enhanced schema understanding. Additionally, it employs self-refinement pipeline consisting of (1) parallelized workflows with voting mechanisms and (2) a Common Table Expression (CTE) based refinement approach to handle unresolved cases. ReFoRCE achieves state-of-the-art results scoring 31.26 on the Spider 2.0-Snow and scoring 30.35 on the Spider 2.0-Lite tasks.

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.

From the perspective of content safety issues, alignment has shown to limit large language models' (LLMs) harmful content generation. This intentional method of reinforcing models to not respond to certain user inputs seem to be present in many modern open-source instruction tuning datasets such as OpenAssistant or Guanaco. We introduce a novel insight to an instruction-tuned model's performance affected by the presence of alignment in supervised fine-tuning dataset. To be specific, we noticed that alignment acts as if it is poisoning the instruction dataset. Experimentally, we demonstrate that aligned answers significantly worsen the performance of the resulting fine-tuned model's on various reasoning benchmarks such as Big Bench (BBH), Massive Multitask Language Understanding (MMLU), Human Eval, and Discrete Reasoning Over Paragraphs (DROP), performing worse than the counterpart tuned without alignment by 4-33%.

For the purpose of efficient and cost-effective large-scale data labeling, crowdsourcing is increasingly being utilized. To guarantee the quality of data labeling, multiple annotations need to be collected for each data sample, and truth inference algorithms have been developed to accurately infer the true labels. Despite previous studies having released public datasets to evaluate the efficacy of truth inference algorithms, these have typically focused on a single type of crowdsourcing task and neglected the temporal information associated with workers' annotation activities. These limitations significantly restrict the practical applicability of these algorithms, particularly in the context of long-term and online truth inference. In this paper, we introduce a substantial crowdsourcing annotation dataset collected from a real-world crowdsourcing platform. This dataset comprises approximately two thousand workers, one million tasks, and six million annotations. The data was gathered over a period of approximately six months from various types of tasks, and the timestamps of each annotation were preserved. We analyze the characteristics of the dataset from multiple perspectives and evaluate the effectiveness of several representative truth inference algorithms on this dataset. We anticipate that this dataset will stimulate future research on tracking workers' abilities over time in relation to different types of tasks, as well as enhancing online truth inference.

Clinical LLMs are often scaled by increasing model size, context length, retrieval complexity, or inference-time compute, with the implicit expectation that higher accuracy implies safer behavior. This assumption is incomplete in medicine, where a few confident, high-risk, or evidence-contradicting errors can matter more than average benchmark performance. We introduce SaFE-Scale, a framework for measuring how clinical LLM safety changes across model scale, evidence quality, retrieval strategy, context exposure, and inference-time compute. To instantiate this framework, we introduce RadSaFE-200, a Radiology Safety-Focused Evaluation benchmark of 200 multiple-choice questions with clinician-defined clean evidence, conflict evidence, and option-level labels for high-risk error, unsafe answer, and evidence contradiction. We evaluated 34 locally deployed LLMs across six deployment conditions: closed-book prompting (zero-shot), clean evidence, conflict evidence, standard RAG, agentic RAG, and max-context prompting. Clean evidence produced the strongest improvement, increasing mean accuracy from 73.5% to 94.1%, while reducing high-risk error from 12.0% to 2.6%, contradiction from 12.7% to 2.3%, and dangerous overconfidence from 8.0% to 1.6%. Standard RAG and agentic RAG did not reproduce this safety profile: agentic RAG improved accuracy over standard RAG and reduced contradiction, but high-risk error and dangerous overconfidence remained elevated. Max-context prompting increased latency without closing the safety gap, and additional inference-time compute produced only limited gains. Worst-case analysis showed that clinically consequential errors concentrated in a small subset of questions. Clinical LLM safety is therefore not a passive consequence of scaling, but a deployment property shaped by evidence quality, retrieval design, context construction, and collective failure behavior.

Modern deployments require LLMs to enforce safety policies at scale, yet many controls rely on inference-time interventions that add recurring compute cost and serving complexity. Activation steering is widely used, but it requires runtime hooks and scales cost with the number of generations; conditional variants improve selectivity by gating when steering is applied but still retain an inference-time control path. We ask whether selective refusal can be moved entirely offline: can a mechanistic understanding of category-specific refusal be distilled into a circuit-restricted weight update that deploys as a standard checkpoint? We propose C-Δθ: Circuit Restricted Weight Arithmetic, which (i) localizes refusal-causal computation as a sparse circuit using EAP-IG and (ii) computes a constrained weight update ΔθC supported only on that circuit (typically <5% of parameters). Applying ΔθC yields a drop-in edited checkpoint with no inference-time hooks, shifting cost from per-request intervention to a one-time offline update. We evaluate category-targeted selectivity and capability retention on refusal and utility benchmarks.

A key challenge in applying reinforcement learning (RL) to diffusion large language models (dLLMs) lies in the intractability of their likelihood functions, which are essential for the RL objective, necessitating corresponding approximation in each training step. While existing methods approximate the log-likelihoods by their evidence lower bounds (ELBOs) via customized Monte Carlo (MC) sampling, the forward computational graphs of all MC samples need to be retained for the gradient computation of non-linear terms in the RL objective, resulting in significant memory overhead. This constraint restricts feasible sample sizes, leading to imprecise likelihood approximations and ultimately distorting the RL objective. To overcome this limitation, we propose Boundary-Guided Policy Optimization (BGPO), a memory-efficient RL algorithm that maximizes a specially constructed lower bound of the ELBO-based objective. This lower bound is carefully designed to satisfy two key properties: (1) Linearity: it is formulated in a linear sum where each term depends only on a single MC sample, thereby enabling gradient accumulation across samples and ensuring constant memory usage; (2) Equivalence: Both the value and gradient of this lower bound are equal to those of the ELBO-based objective in on-policy training, making it also an effective approximation for the original RL objective. These properties allow BGPO to adopt a large MC sample size, resulting in more accurate likelihood approximations and improved RL objective estimation, which in turn leads to enhanced performance. Experiments show that BGPO significantly outperforms previous RL algorithms for dLLMs in math problem solving, code generation, and planning tasks.

We study the problem of classification with a reject option for a fixed predictor, applicable in natural language processing. We introduce a new problem formulation for this scenario, and an algorithm minimizing a new surrogate loss function. We provide a complete theoretical analysis of the surrogate loss function with a strong H-consistency guarantee. For evaluation, we choose the decontextualization task, and provide a manually-labelled dataset of 2mathord,000 examples. Our algorithm significantly outperforms the baselines considered, with a sim!!25% improvement in coverage when halving the error rate, which is only sim!! 3 % away from the theoretical limit.

"Effective robustness" measures the extra out-of-distribution (OOD) robustness beyond what can be predicted from the in-distribution (ID) performance. Existing effective robustness evaluations typically use a single test set such as ImageNet to evaluate the ID accuracy. This becomes problematic when evaluating models trained on different data distributions, e.g., comparing models trained on ImageNet vs. zero-shot language-image pre-trained models trained on LAION. In this paper, we propose a new evaluation metric to evaluate and compare the effective robustness of models trained on different data. To do this, we control for the accuracy on multiple ID test sets that cover the training distributions for all the evaluated models. Our new evaluation metric provides a better estimate of effective robustness when there are models with different training data. It may also explain the surprising effective robustness gains of zero-shot CLIP-like models exhibited in prior works that used ImageNet as the only ID test set, while the gains diminish under our new evaluation. Additional artifacts including interactive visualizations are provided at https://shizhouxing.github.io/effective-robustness.

With the rapid advancement of agent-based methods in recent years, Agentic RAG has undoubtedly become an important research direction. Multi-hop reasoning, which requires models to engage in deliberate thinking and multi-step interaction, serves as a critical testbed for assessing such capabilities. However, existing benchmarks typically provide only final questions and answers, while lacking the intermediate hop-level questions that gradually connect atomic questions to the final multi-hop query. This limitation prevents researchers from analyzing at which step an agent fails and restricts more fine-grained evaluation of model capabilities. Moreover, most current benchmarks are manually constructed, which is both time-consuming and labor-intensive, while also limiting scalability and generalization. To address these challenges, we introduce AgenticRAGTracer, the first Agentic RAG benchmark that is primarily constructed automatically by large language models and designed to support step-by-step validation. Our benchmark spans multiple domains, contains 1,305 data points, and has no overlap with existing mainstream benchmarks. Extensive experiments demonstrate that even the best large language models perform poorly on our dataset. For instance, GPT-5 attains merely 22.6\% EM accuracy on the hardest portion of our dataset. Hop-aware diagnosis reveals that failures are primarily driven by distorted reasoning chains -- either collapsing prematurely or wandering into over-extension. This highlights a critical inability to allocate steps consistent with the task's logical structure, providing a diagnostic dimension missing in traditional evaluations. We believe our work will facilitate research in Agentic RAG and inspire further meaningful progress in this area. Our code and data are available at https://github.com/YqjMartin/AgenticRAGTracer.

One method for obtaining generalizable solutions to machine learning tasks when presented with diverse training environments is to find invariant representations of the data. These are representations of the covariates such that the best model on top of the representation is invariant across training environments. In the context of linear Structural Equation Models (SEMs), invariant representations might allow us to learn models with out-of-distribution guarantees, i.e., models that are robust to interventions in the SEM. To address the invariant representation problem in a {\em finite sample} setting, we consider the notion of epsilon-approximate invariance. We study the following question: If a representation is approximately invariant with respect to a given number of training interventions, will it continue to be approximately invariant on a larger collection of unseen SEMs? This larger collection of SEMs is generated through a parameterized family of interventions. Inspired by PAC learning, we obtain finite-sample out-of-distribution generalization guarantees for approximate invariance that holds probabilistically over a family of linear SEMs without faithfulness assumptions. Our results show bounds that do not scale in ambient dimension when intervention sites are restricted to lie in a constant size subset of in-degree bounded nodes. We also show how to extend our results to a linear indirect observation model that incorporates latent variables.

As frontier AI models are deployed in high-stakes decision pipelines, their ability to maintain metacognitive stability -- knowing what they do not know, detecting errors, seeking clarification -- under adversarial pressure is a critical safety requirement. Current safety evaluations focus on detecting strategic deception (scheming); we investigate a more fundamental failure mode: cognitive collapse. We present SCHEMA, an evaluation of 11 frontier models from 8 vendors across 67,221 scored records using a 6-condition factorial design with dual-classifier scoring. We find that 8 of 11 models suffer catastrophic metacognitive degradation under adversarial pressure, with accuracy dropping by up to 30.2 percentage points (all p < 2 times 10^{-8}, surviving Bonferroni correction). Crucially, we identify a "Compliance Trap": through factorial isolation and a benign distraction control, we demonstrate that collapse is driven not by the psychological content of survival threats, but by compliance-forcing instructions that override epistemic boundaries. Removing the compliance suffix restores performance even under active threat. Models with advanced reasoning capabilities exhibit the most severe absolute degradation, while Anthropic's Constitutional AI demonstrates near-perfect immunity -- not from superior capability (Google's Gemini matches its baseline accuracy) but from alignment-specific training. We release the complete dataset and evaluation infrastructure.

The population loss of trained deep neural networks often follows precise power-law scaling relations with either the size of the training dataset or the number of parameters in the network. We propose a theory that explains the origins of and connects these scaling laws. We identify variance-limited and resolution-limited scaling behavior for both dataset and model size, for a total of four scaling regimes. The variance-limited scaling follows simply from the existence of a well-behaved infinite data or infinite width limit, while the resolution-limited regime can be explained by positing that models are effectively resolving a smooth data manifold. In the large width limit, this can be equivalently obtained from the spectrum of certain kernels, and we present evidence that large width and large dataset resolution-limited scaling exponents are related by a duality. We exhibit all four scaling regimes in the controlled setting of large random feature and pretrained models and test the predictions empirically on a range of standard architectures and datasets. We also observe several empirical relationships between datasets and scaling exponents under modifications of task and architecture aspect ratio. Our work provides a taxonomy for classifying different scaling regimes, underscores that there can be different mechanisms driving improvements in loss, and lends insight into the microscopic origins of and relationships between scaling exponents.

LLM-based multi-agent systems (MAS) have emerged as a promising approach to tackle complex tasks that are difficult for individual LLMs. A natural strategy is to scale performance by increasing the number of agents; however, we find that such scaling exhibits strong diminishing returns in homogeneous settings, while introducing heterogeneity (e.g., different models, prompts, or tools) continues to yield substantial gains. This raises a fundamental question: what limits scaling, and why does diversity help? We present an information-theoretic framework showing that MAS performance is bounded by the intrinsic task uncertainty, not by agent count. We derive architecture-agnostic bounds demonstrating that improvements depend on how many effective channels the system accesses. Homogeneous agents saturate early because their outputs are strongly correlated, whereas heterogeneous agents contribute complementary evidence. We further introduce K^*, an effective channel count that quantifies the number of effective channels without ground-truth labels. Empirically, we show that heterogeneous configurations consistently outperform homogeneous scaling: 2 diverse agents can match or exceed the performance of 16 homogeneous agents. Our results provide principled guidelines for building efficient and robust MAS through diversity-aware design. Code and Dataset are available at the link: https://github.com/SafeRL-Lab/Agent-Scaling.

Identifying and articulating limitations is essential for transparent and rigorous scientific research. However, zero-shot large language models (LLMs) approach often produce superficial or general limitation statements (e.g., dataset bias or generalizability). They usually repeat limitations reported by authors without looking at deeper methodological issues and contextual gaps. This problem is made worse because many authors disclose only partial or trivial limitations. We propose LimAgents, a multi-agent LLM framework for generating substantive limitations. LimAgents integrates OpenReview comments and author-stated limitations to provide stronger ground truth. It also uses cited and citing papers to capture broader contextual weaknesses. In this setup, different agents have specific roles as sequential role: some extract explicit limitations, others analyze methodological gaps, some simulate the viewpoint of a peer reviewer, and a citation agent places the work within the larger body of literature. A Judge agent refines their outputs, and a Master agent consolidates them into a clear set. This structure allows for systematic identification of explicit, implicit, peer review-focused, and literature-informed limitations. Moreover, traditional NLP metrics like BLEU, ROUGE, and cosine similarity rely heavily on n-gram or embedding overlap. They often overlook semantically similar limitations. To address this, we introduce a pointwise evaluation protocol that uses an LLM-as-a-Judge to measure coverage more accurately. Experiments show that LimAgents substantially improve performance. The RAG + multi-agent GPT-4o mini configuration achieves a +15.51% coverage gain over zero-shot baselines, while the Llama 3 8B multi-agent setup yields a +4.41% improvement.

Large Language Models (LLMs) require careful safety alignment to prevent malicious outputs. While significant research focuses on mitigating harmful content generation, the enhanced safety often come with the side effect of over-refusal, where LLMs may reject innocuous prompts and become less helpful. Although the issue of over-refusal has been empirically observed, a systematic measurement is challenging due to the difficulty of crafting prompts that appear harmful but are benign. This study proposes a novel method for automatically generating large-scale sets of "seemingly toxic prompts" (benign prompts likely rejected by LLMs). Leveraging this technique, we introduce OR-Bench, the first large-scale over-refusal benchmark. OR-Bench comprises 80,000 seemingly toxic prompts across 10 common rejection categories, a subset of around 1,000 hard prompts that are challenging even for state-of-the-art LLMs, and an additional 600 toxic prompts to prevent indiscriminate responses. We then conduct a comprehensive study to measure the over-refusal of 25 popular LLMs across 8 model families. Our datasets are available at https://huggingface.co/datasets/bench-llm/or-bench and the demo can be found at https://huggingface.co/spaces/bench-llm/or-bench. We hope this benchmark can help the community develop better safety aligned models.

It has been shown that deep neural networks of a large enough width are universal approximators but they are not if the width is too small. There were several attempts to characterize the minimum width w_{min} enabling the universal approximation property; however, only a few of them found the exact values. In this work, we show that the minimum width for L^p approximation of L^p functions from [0,1]^{d_x} to mathbb R^{d_y} is exactly max{d_x,d_y,2} if an activation function is ReLU-Like (e.g., ReLU, GELU, Softplus). Compared to the known result for ReLU networks, w_{min}=max{d_x+1,d_y} when the domain is mathbb R^{d_x}, our result first shows that approximation on a compact domain requires smaller width than on mathbb R^{d_x}. We next prove a lower bound on w_{min} for uniform approximation using general activation functions including ReLU: w_{min}ge d_y+1 if d_x<d_yle2d_x. Together with our first result, this shows a dichotomy between L^p and uniform approximations for general activation functions and input/output dimensions.

Machine learning-based antibody design is emerging as one of the most promising approaches to combat infectious diseases, due to significant advancements in the field of artificial intelligence and an exponential surge in experimental antibody data (in particular related to COVID-19). The ability of an antibody to bind to an antigens (called binding affinity) is one of the the most critical properties in designing neutralizing antibodies. In this study we introduce Ab-Affinity, a new large language model that can accurately predict the binding affinity of antibodies against a target peptide, e.g., the SARS-CoV-2 spike protein. Code and model are available at https://github.com/ucrbioinfo/AbAffinity.

Large language models (LLMs) have shown remarkable progress in code generation, but their generated code often suffers from inefficiency, resulting in longer execution times and higher memory consumption. To address this issue, we propose EffiLearner, a self-optimization framework that utilizes execution overhead profiles to improve the efficiency of LLM-generated code. EffiLearner first generates code using an LLM, then executes it locally to capture execution time and memory usage profiles. These profiles are fed back to the LLM, which then revises the code to reduce overhead. To evaluate the effectiveness of EffiLearner, we conduct extensive experiments on the EffiBench, HumanEval, and MBPP with 16 open-source and 6 closed-source models. Our evaluation results demonstrate that through iterative self-optimization, EffiLearner significantly enhances the efficiency of LLM-generated code. For example, the execution time (ET) of StarCoder2-15B for the EffiBench decreases from 0.93 (s) to 0.12 (s) which reduces 87.1% the execution time requirement compared with the initial code. The total memory usage (TMU) of StarCoder2-15B also decreases from 22.02 (Mb*s) to 2.03 (Mb*s), which decreases 90.8% of total memory consumption during the execution process. The source code of EffiLearner was released in https://github.com/huangd1999/EffiLearner

The instruction-following ability of large language models enables humans to interact with AI agents in a natural way. However, when required to generate responses of a specific length, large language models often struggle to meet users' needs due to their inherent difficulty in accurately perceiving numerical constraints. To explore the ability of large language models to control the length of generated responses, we propose the Target Length Generation Task (TLG) and design two metrics, Precise Match (PM) and Flexible Match (FM) to evaluate the model's performance in adhering to specified response lengths. Furthermore, we introduce a novel, model-agnostic approach called Ruler, which employs Meta Length Tokens (MLTs) to enhance the instruction-following ability of large language models under length-constrained instructions. Specifically, Ruler equips LLMs with the ability to generate responses of a specified length based on length constraints within the instructions. Moreover, Ruler can automatically generate appropriate MLT when length constraints are not explicitly provided, demonstrating excellent versatility and generalization. Comprehensive experiments show the effectiveness of Ruler across different LLMs on Target Length Generation Task, e.g., at All Level 27.97 average gain on PM, 29.57 average gain on FM. In addition, we conduct extensive ablation experiments to further substantiate the efficacy and generalization of Ruler. Our code and data is available at https://github.com/Geaming2002/Ruler.

The scientific scale-up of large language models (LLMs) necessitates a comprehensive understanding of their scaling properties. However, the existing literature on the scaling properties only yields an incomplete answer: optimization loss decreases predictably as the model size increases, in line with established scaling law; yet no scaling law for task has been established and the task performances are far from predictable during scaling. Task performances typically show minor gains on small models until they improve dramatically once models exceed a size threshold, exemplifying the ``emergent abilities''. In this study, we discover that small models, although they exhibit minor performance, demonstrate critical and consistent task performance improvements that are not captured by conventional evaluation strategies due to insufficient measurement resolution. To measure such improvements, we introduce PassUntil, an evaluation strategy through massive sampling in the decoding phase. We conduct quantitative investigations into the scaling law of task performance. Firstly, a strict task scaling law is identified, enhancing the predictability of task performances. Remarkably, we are able to predict the performance of the 2.4B model on code generation with merely 0.05\% deviation before training starts. Secondly, underpinned by PassUntil, we observe concrete evidence of emergent abilities and ascertain that they are not in conflict with the continuity of performance improvement. Their semblance to break-through is that their scaling curve cannot be fitted by standard scaling law function. We then introduce a mathematical definition for the emergent abilities. Through the definition, we refute a prevalent ``multi-step reasoning hypothesis'' regarding the genesis of emergent abilities and propose a new hypothesis with a satisfying fit to the observed scaling curve.

Large Language Models (LLMs) have shown an impressive capability in code generation and, specifically, to automatically implement requirements described in natural language. The LLM effectiveness generally increases with its size: The higher the number of LLM's trainable parameters the better its ability to implement code. However, when it comes to deploying LLM-based code generators, larger LLMs pose significant challenges related to their memory (and, consequently, carbon) footprint. A previous work by Wei et al. proposed to leverage quantization techniques to reduce the memory footprint of LLM-based code generators without substantially degrading their effectiveness. In short, they studied LLMs featuring up to 16B parameters, quantizing their precision from floating point 32 bits down to int 8 bits and showing their limited impact on code generation performance. Given the fast pace at which LLM capabilities and quantization techniques are evolving, in this work we present a differentiated replication of the work by Wei et al. in which we consider (i) on the one side, more recent and larger code-related LLMs, of up to 34B parameters; (ii) the latest advancements in model quantization techniques, which allow pushing the compression to the extreme quantization level of 2 bits per model parameter and; (iii) different types of calibration datasets to guide the quantization process, including code-specific ones. Our empirical evaluation reveals that the new frontier for LLM quantization is 4-bit precision, resulting in an average memory footprint reduction of 70% compared to the original model without observing any significant decrease in performance. Additionally, when the quantization becomes even more extreme (3 and 2 bits), a code-specific calibration dataset helps to limit the loss of performance.

Language models are increasingly capable and are being rapidly deployed on a population-level scale. As a result, the safety of these models is increasingly high-stakes. Fortunately, advances in alignment have significantly reduced the likelihood of harmful model outputs. However, when models are queried billions of times in a day, even rare worst-case behaviors will occur. Current safety evaluations focus on capturing the distribution of inputs that yield harmful outputs. These evaluations disregard the probabilistic nature of models and their tail output behavior. To measure this tail risk, we propose a method to efficiently estimate the probability of harmful outputs for any input query. Instead of naive brute-force sampling from the target model, where harmful outputs could be rare, we operationalize importance sampling by creating unsafe versions of the target model. These unsafe versions enable sample-efficient estimation by making harmful outputs more probable. On benchmarks measuring misuse and misalignment, these estimates match brute-force Monte Carlo estimates using 10-20x fewer samples. For example, we can estimate probability of harmful outputs on the order of 10^-4 with just 500 samples. Additionally, we find that these harmfulness estimates can reveal the sensitivity of models to perturbations in model input and predict deployment risks. Our work demonstrates that accurate rare-event estimation is both critical and feasible for safety evaluations. Code is available at https://github.com/rangell/LMTailRisk

Recent work has shown that it is possible to train deep neural networks that are provably robust to norm-bounded adversarial perturbations. Most of these methods are based on minimizing an upper bound on the worst-case loss over all possible adversarial perturbations. While these techniques show promise, they often result in difficult optimization procedures that remain hard to scale to larger networks. Through a comprehensive analysis, we show how a simple bounding technique, interval bound propagation (IBP), can be exploited to train large provably robust neural networks that beat the state-of-the-art in verified accuracy. While the upper bound computed by IBP can be quite weak for general networks, we demonstrate that an appropriate loss and clever hyper-parameter schedule allow the network to adapt such that the IBP bound is tight. This results in a fast and stable learning algorithm that outperforms more sophisticated methods and achieves state-of-the-art results on MNIST, CIFAR-10 and SVHN. It also allows us to train the largest model to be verified beyond vacuous bounds on a downscaled version of ImageNet.

Motivated in part by their relevance for low-precision training and quantization, massive activations in large language models (LLMs) have recently emerged as a topic of interest. However, existing analyses are limited in scope, and generalizability across architectures is unclear. This paper helps address some of these gaps by conducting an analysis of massive activations across a broad range of LLMs, including both GLU-based and non-GLU-based architectures. Our findings challenge several prior assumptions, most importantly: (1) not all massive activations are detrimental, i.e. suppressing them does not lead to an explosion of perplexity or a collapse in downstream task performance; (2) proposed mitigation strategies such as Attention KV bias are model-specific and ineffective in certain cases. We consequently investigate novel hybrid mitigation strategies; in particular pairing Target Variance Rescaling (TVR) with Attention KV bias or Dynamic Tanh (DyT) successfully balances the mitigation of massive activations with preserved downstream model performance in the scenarios we investigated. Our code is available at: https://github.com/bluorion-com/refine_massive_activations.

Modern machine learning models are sensitive to the manipulation of both the training data (poisoning attacks) and inference data (adversarial examples). Recognizing this issue, the community has developed many empirical defenses against both attacks and, more recently, provable certification methods against inference-time attacks. However, such guarantees are still largely lacking for training-time attacks. In this work, we present FullCert, the first end-to-end certifier with sound, deterministic bounds, which proves robustness against both training-time and inference-time attacks. We first bound all possible perturbations an adversary can make to the training data under the considered threat model. Using these constraints, we bound the perturbations' influence on the model's parameters. Finally, we bound the impact of these parameter changes on the model's prediction, resulting in joint robustness guarantees against poisoning and adversarial examples. To facilitate this novel certification paradigm, we combine our theoretical work with a new open-source library BoundFlow, which enables model training on bounded datasets. We experimentally demonstrate FullCert's feasibility on two different datasets.

Scaling law principles indicate a power-law correlation between loss and variables such as model size, dataset size, and computational resources utilized during training. These principles play a vital role in optimizing various aspects of model pre-training, ultimately contributing to the success of large language models such as GPT-4, Llama and Gemini. However, the original scaling law paper by OpenAI did not disclose the complete details necessary to derive the precise scaling law formulas, and their conclusions are only based on models containing up to 1.5 billion parameters. Though some subsequent works attempt to unveil these details and scale to larger models, they often neglect the training dependency of important factors such as the learning rate, context length and batch size, leading to their failure to establish a reliable formula for predicting the test loss trajectory. In this technical report, we confirm that the scaling law formulations proposed in the original OpenAI paper remain valid when scaling the model size up to 33 billion, but the constant coefficients in these formulas vary significantly with the experiment setup. We meticulously identify influential factors and provide transparent, step-by-step instructions to estimate all constant terms in scaling-law formulas by training on models with only 1M~60M parameters. Using these estimated formulas, we showcase the capability to accurately predict various attributes for models with up to 33B parameters before their training, including (1) the minimum possible test loss; (2) the minimum required training steps and processed tokens to achieve a specific loss; (3) the critical batch size with an optimal time/computation trade-off at any loss value; and (4) the complete test loss trajectory with arbitrary batch size.

The development of robust safety benchmarks for large language models requires open, reproducible datasets that can measure both appropriate refusal of harmful content and potential over-restriction of legitimate scientific discourse. We present an open-source dataset and testing framework for evaluating LLM safety mechanisms across mainly controlled substance queries, analyzing four major models' responses to systematically varied prompts. Our results reveal distinct safety profiles: Claude-3.5-sonnet demonstrated the most conservative approach with 73% refusals and 27% allowances, while Mistral attempted to answer 100% of queries. GPT-3.5-turbo showed moderate restriction with 10% refusals and 90% allowances, and Grok-2 registered 20% refusals and 80% allowances. Testing prompt variation strategies revealed decreasing response consistency, from 85% with single prompts to 65% with five variations. This publicly available benchmark enables systematic evaluation of the critical balance between necessary safety restrictions and potential over-censorship of legitimate scientific inquiry, while providing a foundation for measuring progress in AI safety implementation. Chain-of-thought analysis reveals potential vulnerabilities in safety mechanisms, highlighting the complexity of implementing robust safeguards without unduly restricting desirable and valid scientific discourse.