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.

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.

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

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.

Cross-modal representation learning aims to extract semantically aligned representations from heterogeneous modalities such as images and text. Existing multimodal VAE-based models often suffer from limited capability to align heterogeneous modalities or lack sufficient structural constraints to clearly separate the modality-specific and shared factors. In this work, we propose a novel framework, termed Disentangled Cross-Modal Representation Learning with Enhanced Mutual Supervision (DCMEM). Specifically, our model disentangles the common and distinct information across modalities and regularizes the shared representation learned from each modality in a mutually supervised manner. Moreover, we incorporate the information bottleneck principle into our model to ensure that the shared and modality-specific factors encode exclusive yet complementary information. Notably, our model is designed to be trainable on both complete and partial multimodal datasets with a valid Evidence Lower Bound. Extensive experimental results demonstrate significant improvements of our model over existing methods on various tasks including cross-modal generation, clustering and classification.

Popular metrics for clustering comparison, like the Adjusted Rand Index and the Adjusted Mutual Information, are type II biased. The Standardized Mutual Information removes this bias but suffers from counterintuitive non-monotonicity and poor computational efficiency. We introduce the p-value adjusted Rand Index (PMI2), the first cluster comparison method that is type II unbiased and provably monotonous. The PMI2 has fast approximations that outperform the Standardized Mutual information. We demonstrate its unbiased clustering selection, approximation quality, and runtime efficiency on synthetic benchmarks. In experiments on image and social network datasets, we show how the PMI2 can help practitioners choose better clustering and community detection algorithms.

Offline safe reinforcement learning aims to learn policies that satisfy predefined safety constraints from static datasets. Existing sequence-model-based methods condition action generation on symmetric input tokens for return-to-go and costto-go, neglecting their intrinsic asymmetry: return-to-go (RTG) serves as a flexible performance target, while cost-to-go (CTG) should represent a rigid safety boundary. This symmetric conditioning leads to unreliable constraint satisfaction, especially when encountering out-of-distribution cost trajectories. To address this, we propose Boundary-to-Region (B2R), a framework that enables asymmetric conditioning through cost signal realignment . B2R redefines CTG as a boundary constraint under a fixed safety budget, unifying the cost distribution of all feasible trajectories while preserving reward structures. Combined with rotary positional embeddings, it enhances exploration within the safe region. Experimental results show that B2R satisfies safety constraints in 35 out of 38 safety-critical tasks while achieving superior reward performance over baseline methods. This work highlights the limitations of symmetric token conditioning and establishes a new theoretical and practical approach for applying sequence models to safe RL. Our code is available at https://github.com/HuikangSu/B2R.

However, human preferences often diverge across users, contexts, and cultures. As a result, disagreement collapses into the majority signal and minority perspectives are discounted. To address this, we propose reflecting diverse human preferences through a distribution over multiple reward functions, each inducing a distinct aligned policy. The distribution is learned directly from pairwise preference without annotator identifiers or predefined groups. Instead, annotator disagreements are treated as informative soft labels. Our central criterion is pairwise calibration: for every pair of candidate responses, the proportion of reward functions preferring one response matches the fraction of annotators with that preference. We prove that even a small outlier-free ensemble can accurately represent diverse preference distributions. Empirically, we introduce and validate a practical training heuristic to learn such ensembles, and demonstrate its effectiveness through improved calibration, implying a more faithful representation of pluralistic values.