Neural scaling laws are observed in a range of domains, to date with no universal understanding of why they occur. Recent theories suggest that loss power laws arise from Zipf's law, a power law observed in domains like natural language. One theory suggests that language scaling laws emerge when Zipf-distributed task quanta are learned in descending order of frequency. In this paper we examine power-law scaling in AlphaZero, a reinforcement learning algorithm, using a model of language-model scaling. We find that game states in training and inference data scale with Zipf's law, which is known to arise from the tree structure of the environment, and examine the correlation between scaling-law and Zipf'slaw exponents. In agreement with the quanta scaling model, we find that agents optimize state loss in descending order of frequency, even though this order scales inversely with modelling complexity. We also find that inverse scaling, the failure of models to improve with size, is correlated with unusual Zipf curves where end-game states are among the most frequent states. We show evidence that larger models shift their focus to these less-important states, sacrificing their understanding of important early-game states.

Biomedical research data portals are essential resources for scientific inquiry, and interactive exploratory visualizations are an integral component for querying such data repositories. Increasingly, machine learning is being integrated into visualization systems to create natural language interfaces where questions about data can be answered with visualizations, and follow-up questions can build on the previous state. This paper introduces a framework that takes abstract low-level questions about data and a visualization grammar specification that can answer such a question, reifies them with data entities and fields that meet certain constraints, and paraphrases the question language to produce the final collection of realized data-question-visualization triplets. Furthermore, we can link these foundational elements together to construct chains of queries, visualizations, and follow-up queries. We developed an open-source review interface for evaluating the results of these datasets. We applied this framework to five biomedical research data repositories, resulting in DQVis, a dataset of 1.08 million dataquestion-visualization triplets and 11.4 thousand two-step question samples. Five visualization experts provided feedback on the generated dataset through our review interface. We present a summary of their input and publish the full reviews as an additional resource alongside the dataset.

What does it truly mean for a language model to "reason" strategically, and can scaling up alone guarantee intelligent, context-aware decisions? Strategic decisionmaking requires adaptive reasoning, where agents anticipate and respond to others' actions under uncertainty. Yet, most evaluations of large language models (LLMs) for strategic decision-making often rely heavily on Nash Equilibrium (NE) benchmarks, overlook reasoning depth, and fail to reveal the mechanisms behind model behavior. To address this gap, we introduce a behavioral game-theoretic evaluation framework that disentangles intrinsic reasoning from contextual influence. Using this framework, we evaluate 22 state-of-the-art LLMs across diverse strategic scenarios. We find models like GPT-o3-mini, GPT-o1, and DeepSeek-R1 lead in reasoning depth. Through thinking chain analysis, we identify distinct reasoning styles--such as maximin or belief-based strategies--and show that longer reasoning chains do not consistently yield better decisions. Furthermore, embedding demographic personas reveals context-sensitive shifts: some models (e.g., GPT4o, Claude-3-Opus) improve when assigned female identities, while others (e.g., Gemini 2.0) show diminished reasoning under minority sexuality personas. These findings underscore that technical sophistication alone is insufficient; alignment with ethical standards, human expectations, and situational nuance is essential for the responsible deployment of LLMs in interactive settings.

The AlphaFold Protein Structure Database (AFDB) offers unparalleled structural coverage at near-experimental accuracy, positioning it as a valuable resource for data-driven protein design. However, its direct use in training deep models that are sensitive to fine-grained atomic geometry--such as inverse folding--exposes a critical limitation. Comparative analysis of structural feature distributions reveals that AFDB structures exhibit distinct statistical regularities, reflecting a systematic geometric bias that deviates from the conformational diversity found in experimentally determined structures from the Protein Data Bank (PDB). While AFDB structures are cleaner and more idealized, PDB structures capture the intrinsic variability and physical realism essential for generalization in downstream tasks. To address this discrepancy, we introduce a Debiasing Structure AutoEncoder (DeSAE) that learns to reconstruct native-like conformations from intentionally corrupted backbone geometries. By training the model to recover plausible structural states, DeSAE implicitly captures a more robust and natural structural manifold. At inference, applying DeSAE to AFDB structures produces debiased representations that significantly improve inverse folding performance across multiple benchmarks, and also enhance other structure-conditioned modeling tasks. This work highlights the critical impact of subtle systematic biases in predicted structures and presents a principled framework for debiasing, significantly boosting the performance of structure-based learning tasks like inverse folding.

Prompt tuning has emerged as a key technique for adapting large pre-trained Decision Transformers (DTs) in offline Reinforcement Learning (RL), particularly in multi-task and few-shot settings. The Prompting Decision Transformer (PDT) enables task generalization via trajectory prompts sampled uniformly from expert demonstrations - without accounting for prompt informativeness. In this work, we propose a bandit-based prompt-tuning method that learns to construct optimal trajectory prompts from demonstration data at inference time. We devise a structured bandit architecture operating in the trajectory prompt space, achieving linear rather than combinatorial scaling with prompt size. Additionally, we show that the pretrained PDT itself can serve as a powerful feature extractor for the bandit, enabling efficient reward modeling across various environments. We theoretically establish regret bounds and demonstrate empirically that our method consistently enhances performance across a wide range of tasks, high-dimensional environments, and out-of-distribution scenarios, outperforming existing baselines in prompt tuning.

Predicting the binding affinity of protein-ligand complexes plays a vital role in drug discovery. Unfortunately, progress has been hindered by the lack of large-scale and high-quality binding affinity labels. The widely used PDBbind dataset has fewer than 20K labeled complexes. Self-supervised learning, especially graph contrastive learning (GCL), provides a unique opportunity to break the barrier by pretraining graph neural network models based on vast unlabeled complexes and fine-tuning the models on much fewer labeled complexes. However, the problem faces unique challenges, including a lack of a comprehensive unlabeled dataset with well-defined positive/negative complex pairs and the need to design GCL algorithms that incorporate the unique characteristics of such data.

Foundation Models (FMs) have demonstrated remarkable success in fields like computer vision and natural language processing, yet their application to combinatorial optimization remains underexplored. Optimization problems, often modeled as graphs, pose unique challenges due to their diverse structures, varying distributions, and NP-hard complexity. To address these challenges, we propose OPTFM, the first graph foundation model for general combinatorial optimization. OPTFM introduces a scalable multi-view graph transformer with hybrid self-attention and cross-attention to model large-scale heterogeneous graphs in O(N)time complexity while maintaining semantic consistency throughout the attention computation.

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the original and reconstructed graphs and leverages a differentiable node matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.1

Although COLMAP has long remained the predominant method for camera parameter optimization in static scenes, it is constrained by its lengthy runtime and reliance on ground truth (GT) motion masks for application to dynamic scenes. Many efforts attempted to improve it by incorporating more priors as supervision such as GT focal length, motion masks, 3D point clouds, camera poses, and metric depth, which, however, are typically unavailable in casually captured RGB videos. In this paper, we propose a novel method for more accurate and efficient camera parameter optimization in dynamic scenes solely supervised by a single RGB video, dubbed ROS-Cam. Our method consists of three key components: (1) Patch-wise Tracking Filters, to establish robust and maximally sparse hinge-like relations across the RGB video.

Reinforcement learning (RL) has shown great effectiveness for fine-tuning large language models (LLMs) using tasks that are challenging yet easily verifiable, such as math reasoning or code generation. However, extending this success to visual perception in vision-language models (VLMs) has been impeded by the scarcity of vision-centric tasks that are simultaneously challenging and unambiguously verifiable. To this end, we introduce ViCrit (Visual Caption Hallucination Critic), an RL proxy task that trains VLMs to localize a subtle, synthetic visual hallucination injected into paragraphs of human-written image captions. Starting from a 200-word captions, we inject a single, subtle visual description error--altering a few words on objects, attributes, counts, or spatial relations--and task the model to pinpoint the corrupted span given the image and the modified caption. This formulation preserves the full perceptual difficulty while providing a binary, exactmatch reward that is easy to compute and unambiguous. Models trained with the ViCrit Task exhibit substantial gains across a variety of VL benchmarks. Crucially, the improvements transfer beyond natural-image training data to abstract image reasoning and visual math, showing promises of learning to perceive rather than barely memorizing seen objects. To facilitate evaluation, we further introduce ViCrit-Bench, a category-balanced diagnostic benchmark that systematically probes perception errors across diverse image domains and error types. Together, our results demonstrate that fine-grained hallucination criticism is an effective and generalizable objective for enhancing visual perception in VLMs.