HiST: A Hierarchical Sparse Transformer for Cross-Modal Spatial Transcriptomics Modeling

Spatial transcriptomics (ST) links gene expression with tissue morphology but remains expensive and low-throughput, motivating surrogates that infer expression from routine histology. Whole-slide H&E-to-ST inference pairs a gigapixel image with gene measurements at a sparse, irregular set of locations, making multiscale modeling challenging without incurring dense-grid overhead or quadratic token mixing. We propose HiST, a hierarchical sparse transformer that treats measured locations as a lattice-indexed sparse field and builds a dyadic encoder--decoder directly on the active tissue footprint. HiST combines sparse window attention for local geometric correspondence with resolution-changing operators for rapid multiscale context integration. For a fixed window size, the dominant runtime and memory scale with the number of observed locations rather than the dense slide area. To mitigate slide-specific acquisition variation, HiST adds a bottlenecked global conditioning pathway via a \emph{slide calibration token} that summarizes slide-level context and conditions local representations. On a multi-organ benchmark spanning diverse tissues and acquisition sources, HiST improves predictive performance over recent baselines while reducing runtime and peak memory.

MIRA: A Bilingual Benchmark for Medical Information Response Audit

Large language models (LLMs) are increasingly used to provide public-facing health information, yet existing safety evaluations overlook whether responses preserve comparable medical information across different user phrasings of the same question. To address this, we introduce the Medical Information Response Audit (MIRA), a bilingual, controlled benchmark that assesses whether LLMs provide comparable medical information across user-side language, register, and health literacy signals. MIRA contains 4,320 prompts built from 60 medically reviewed, low-risk health questions. Across five mainstream LLMs, models answered all medical questions, but responses to low health-literacy signals consistently omitted more key information, provided fewer concrete next steps, and offered less support for independent judgment. We term this pattern Differential Information Dilution (DID). Language effects are model-specific rather than uniformly worse for non-English prompts. A comparison with 300 real-world health queries provides preliminary evidence of rank-order validity. A knowledge-guided mitigation prompt reduces information dilution for most models, with the largest reductions in underinformative simplification observed for Claude (~8%) and Qwen (~6%).

Exploiting Label-Independent Regularization from Spatial Dependencies for Whole Slide Image Analysis

Whole slide images, with their gigapixel-scale panoramas of tissue samples, are pivotal for precise disease diagnosis. However, their analysis is hindered by immense data size and scarce annotations. Existing MIL methods face challenges due to the fundamental imbalance where a single bag-level label must guide the learning of numerous patch-level features. This sparse supervision makes it difficult to reliably identify discriminative patches during training, leading to unstable optimization and suboptimal solutions. We propose a spatially regularized MIL framework that leverages inherent spatial relationships among patch features as label-independent regularization signals. Our approach learns a shared representation space by jointly optimizing feature-induced spatial reconstruction and label-guided classification objectives, enforcing consistency between intrinsic structural patterns and supervisory signals. Experimental results on multiple public datasets demonstrate significant improvements over state-of-the-art methods, offering a promising direction.

Addressing Overthinking in Large Vision-Language Models via Gated Perception-Reasoning Optimization

Large Vision-Language Models (LVLMs) have exhibited strong reasoning capabilities through chain-of-thought mechanisms that generate step-by-step rationales. However, such slow-thinking approaches often lead to overthinking, where models produce excessively verbose responses even for simple queries, resulting in test-time inefficiency and even degraded accuracy. Prior work has attempted to mitigate this issue via adaptive reasoning strategies, but these methods largely overlook a fundamental bottleneck: visual perception failures. We argue that stable reasoning critically depends on low-level visual grounding, and that reasoning errors often originate from imperfect perception rather than insufficient deliberation. To address this limitation, we propose Gated Perception-Reasoning Optimization (GPRO), a meta-reasoning controller that dynamically routes computation among three decision paths at each generation step: a lightweight fast path, a slow perception path for re-examining visual inputs, and a slow reasoning path for internal self-reflection. To learn this distinction, we derive large-scale failure attribution supervision from approximately 790k samples, using teacher models to distinguish perceptual hallucinations from reasoning errors. We then train the controller with multi-objective reinforcement learning to optimize the trade-off between task accuracy and computational cost under uncertainty. Experiments on five benchmarks demonstrate that GPRO substantially improves both accuracy and efficiency, outperforming recent slow-thinking methods while generating significantly shorter responses.

Synthetic Clinical Notes for Rare ICD Codes: A Data-Centric Framework for Long-Tail Medical Coding

Automatic ICD coding from clinical text is a critical task in medical NLP but remains hindered by the extreme long-tail distribution of diagnostic codes. Thousands of rare and zero-shot ICD codes are severely underrepresented in datasets like MIMIC-III, leading to low macro-F1 scores. In this work, we propose a data-centric framework that generates high-quality synthetic discharge summaries to mitigate this imbalance. Our method constructs realistic multi-label code sets anchored on rare codes by leveraging real-world co-occurrence patterns, ICD descriptions, synonyms, taxonomy, and similar clinical notes. Using these structured prompts, we generate 90,000 synthetic notes covering 7,902 ICD codes, significantly expanding the training distribution. We fine-tune two state-of-the-art transformer-based models, PLM-ICD and GKI-ICD, on both the original and extended datasets. Experiments show that our approach modestly improves macro-F1 while maintaining strong micro-F1, outperforming prior SOTA. While the gain may seem marginal relative to the computational cost, our results demonstrate that carefully crafted synthetic data can enhance equity in long-tail ICD code prediction.

SoundMind: RL-Incentivized Logic Reasoning for Audio-Language Models

While large language models have shown reasoning capabilities, their application to the audio modality, particularly in large audio-language models (ALMs), remains significantly underdeveloped. Addressing this gap requires a systematic approach, involving a capable base model, high-quality reasoning-oriented audio data, and effective training algorithms. In this study, we present a comprehensive solution: we introduce the Audio Logical Reasoning (ALR) dataset, consisting of 6,446 text-audio annotated samples specifically designed for complex reasoning tasks. Building on this resource, we propose SoundMind, a rule-based reinforcement learning (RL) algorithm tailored to endow ALMs with deep bimodal reasoning abilities. By training Qwen2.5-Omni-7B on the ALR dataset using SoundMind, our approach achieves state-of-the-art performance in audio logical reasoning. This work highlights the impact of combining high-quality, reasoning-focused datasets with specialized RL techniques, advancing the frontier of auditory intelligence in language models. Our code and the proposed dataset are available at https://github.com/xid32/SoundMind.

Music's Multimodal Complexity in AVQA: Why We Need More than General Multimodal LLMs

While recent Multimodal Large Language Models exhibit impressive capabilities for general multimodal tasks, specialized domains like music necessitate tailored approaches. Music Audio-Visual Question Answering (Music AVQA) particularly underscores this, presenting unique challenges with its continuous, densely layered audio-visual content, intricate temporal dynamics, and the critical need for domain-specific knowledge. Through a systematic analysis of Music AVQA datasets and methods, this position paper identifies that specialized input processing, architectures incorporating dedicated spatial-temporal designs, and music-specific modeling strategies are critical for success in this domain. Our study provides valuable insights for researchers by highlighting effective design patterns empirically linked to strong performance, proposing concrete future directions for incorporating musical priors, and aiming to establish a robust foundation for advancing multimodal musical understanding. This work is intended to inspire broader attention and further research, supported by a continuously updated anonymous GitHub repository of relevant papers: https://github.com/xid32/Survey4MusicAVQA.

Assessing and Mitigating Medical Knowledge Drift and Conflicts in Large Language Models

Large Language Models (LLMs) have great potential in the field of health care, yet they face great challenges in adapting to rapidly evolving medical knowledge. This can lead to outdated or contradictory treatment suggestions. This study investigated how LLMs respond to evolving clinical guidelines, focusing on concept drift and internal inconsistencies. We developed the DriftMedQA benchmark to simulate guideline evolution and assessed the temporal reliability of various LLMs. Our evaluation of seven state-of-the-art models across 4,290 scenarios demonstrated difficulties in rejecting outdated recommendations and frequently endorsing conflicting guidance. Additionally, we explored two mitigation strategies: Retrieval-Augmented Generation and preference fine-tuning via Direct Preference Optimization. While each method improved model performance, their combination led to the most consistent and reliable results. These findings underscore the need to improve LLM robustness to temporal shifts to ensure more dependable applications in clinical practice.

Learning Musical Representations for Music Performance Question Answering

Music performances are representative scenarios for audio-visual modeling. Unlike common scenarios with sparse audio, music performances continuously involve dense audio signals throughout. While existing multimodal learning methods on the audio-video QA demonstrate impressive capabilities in general scenarios, they are incapable of dealing with fundamental problems within the music performances: they underexplore the interaction between the multimodal signals in performance and fail to consider the distinctive characteristics of instruments and music. Therefore, existing methods tend to answer questions regarding musical performances inaccurately. To bridge the above research gaps, (i) given the intricate multimodal interconnectivity inherent to music data, our primary backbone is designed to incorporate multimodal interactions within the context of music; (ii) to enable the model to learn music characteristics, we annotate and release rhythmic and music sources in the current music datasets; (iii) for time-aware audio-visual modeling, we align the model's music predictions with the temporal dimension. Our experiments show state-of-the-art effects on the Music AVQA datasets. Our code is available at https://github.com/xid32/Amuse.

Temporal Working Memory: Query-Guided Segment Refinement for Enhanced Multimodal Understanding

Multimodal foundation models (MFMs) have demonstrated significant success in tasks such as visual captioning, question answering, and image-text retrieval. However, these models face inherent limitations due to their finite internal capacity, which restricts their ability to process extended temporal sequences, a crucial requirement for comprehensive video and audio analysis. To overcome these challenges, we introduce a specialized cognitive module, temporal working memory (TWM), which aims to enhance the temporal modeling capabilities of MFMs. It selectively retains task-relevant information across temporal dimensions, ensuring that critical details are preserved throughout the processing of video and audio content. The TWM uses a query-guided attention approach to focus on the most informative multimodal segments within temporal sequences. By retaining only the most relevant content, TWM optimizes the use of the model's limited capacity, enhancing its temporal modeling ability. This plug-and-play module can be easily integrated into existing MFMs. With our TWM, nine state-of-the-art models exhibit significant performance improvements across tasks such as video captioning, question answering, and video-text retrieval. By enhancing temporal modeling, TWM extends the capability of MFMs to handle complex, time-sensitive data effectively. Our code is available at https://github.com/xid32/NAACL_2025_TWM.