In real clinical practice, clinicians must sift through noisy and often conflicting information, progressively gathering and sequencing evidence before reaching conclusions. However, existing tuning methods for medical AI models are typically monologue-based — that is, models are fine-tuned on static question answering (QA) tasks or medical articles, which fail to reflect the interactive and iterative nature of clinical reasoning. To bridge this gap, we introduce MuddyMaze, a benchmark designed to expose the limitations of current monologue-based tuning, and construct a large dialogue dataset of 22.2k doctor–patient interactions that capture stepwise diagnostic reasoning validated by medical experts. Building on those, we propose dialogue-tuning, a new fine-tuning paradigm that captures the internal reasoning dynamics unfolding across interactions.

To assess the effectiveness of our approach, we evaluated dialogue-tuned models on MuddyMaze, where they outperform monologue-tuned baselines (e.g., MedQA) by +16.1% in one-round and +4.1% in multi-round evidence ranking, while maintaining or even improving accuracy on standard medical QA benchmarks (e.g., PubMedQA). These results indicate that dialogue-tuning not only enhances reasoning robustness and evidence integration but also preserves the factual precision of traditional QA performance.

Multimodal Large Language Models (MLLMs) show strong potential for cross-modal understanding by integrating powerful language models with multimodal encoders. However, extending MLLMs to handle a diverse range of modalities introduces two critical and intertwined challenges: (1) the reliance on fully paired multimodal data, often scarce or costly to acquire across all modalities, and (2) the computational inefficiency from processing numerous modality tokens and requiring substantial model updates for each new modality. To address these challenges, we enable MLLMs to handle missing modalities by generating representations for absent inputs. Furthermore, recognizing that an increasing number of modalities leads to linearly scaling token counts and that lengthy generated sequences can hinder performance, we employ a dual-stage compression mechanism. It first reduces the number of tokens per modality and then condenses information from multiple modalities into a single, compact token sequence. This culminates in Flex-M³, a novel MLLM framework designed for flexible and efficient learning across arbitrary combinations of modalities. Experiments across diverse multimodal benchmarks and backbones demonstrate that Flex-M³ robustly handles varied modality inputs and scales efficiently. Notably, Flex-M outperforms its counterpart trained on only full-modality data, with consistent improvements of 2.29%, 3.15%, 11.01% on multimodal reasoning tasks NExT-QA, MUSIC-AVQA, SQA3D. Moreover, Flex-M³ demonstrates superior robustness during inference, even when a high proportion of modalities are missing from the input samples, showcasing its capacity for complex, data-scarce multimodal applications.

As large language models (LLMs) are increasingly deployed in diverse applications, including chatbot assistants and code generation, aligning their behavior with safety and ethical standards has become paramount. However, jailbreak attacks, which exploit vulnerabilities to elicit unintended or harmful outputs, threaten LLMs safety significantly. In this paper, we introduce Layer-AdvPatcher, a novel methodology designed to defend against jailbreak attacks by utilizing an unlearning strategy to patch specific layers within LLMs through self-augmented datasets. Our insight is that certain layer(s), tend to produce affirmative tokens when faced with harmful prompts. By identifying these layers and adversarially exposing them to generate more harmful data, one can understand their inherent and diverse vulnerabilities to attacks. With these exposures, we then “unlearn” these issues, reducing the impact of affirmative tokens and hence minimizing jailbreak risks while keeping the model’s responses to safe queries intact.We conduct extensive experiments on two models, four benchmark datasets, and multiple state-of-the-art jailbreak attacks to demonstrate the efficacy of our approach. Results indicate that our framework reduces the harmfulness and attack success rate of jailbreak attacks without compromising utility for benign queries compared to recent defense methods. Our code is publicly available at: https://github.com/oyy2000/LayerAdvPatcher

Multimodal Large Language Models (MLLMs) have gained increasing popularity as a promising framework for leveraging the strong language reasoning capabilities in the vision-language domain. Given a wide range of MLLMs, model merging potentially offers a cheap way to aggregate their diverse knowledge into a single MLLM. However, directly plug-in existing model merging approaches often leads to suboptimal performance due to (1) inclusion of harmful models that have over-confident predictions in the target task; (2) the lack of specialized designs for vision-language inputs. To tackle these pain points, we conduct pioneering investigations to dissect the merging procedures and propose an uncertainty-guided MLLM merging algorithm, i.e., UQ-Merge, which i) identifies beneficial candidates for merging, ii) determines the merging order and the number of helpful candidates, and iii) performs appropriate merging. Within our framework, we consider uncertainty quantification on both text and vision inputs to examine the MLLM prediction confidence, and then decide whether and when a MLLM needs to be included. It is worth mentioning that our vision-language uncertainty quantification does not require access to sample labels, making it more practical in various scenarios. Extensive experiments consistently demonstrate the superior MLLM merging performance of UQ-Merge in both held-in and held-out vision-language benchmarks. For example, compared to existing state-of-the-art merging methods, UQ-Merge brings substantial performance improvements of up to 44.3% on average accuracy in 12 datasets. Codes are available at https://anonymous.4open.science/r/UQ-Merge-7CD7.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6\\% increase in drug response prediction correlation, 9.6\\% improvement in single-cell drug classification AUC, and 1.1\\% average gain in gene perturbation prediction accuracy.

The development of performant pre-trained models has driven the advancement of routing-based expert models tailored to specific tasks. However, these methods often favor generalization over performance on held-in tasks. This limitation adversely impacts practical applicability, as real-world deployments require robust performance across both known and novel tasks. We observe that current token-level routing mechanisms neglect the global semantic context of the input task. To address this, we propose a novel method, Global and Local Instruction Driven Expert Router (GLIDER) that proposes a multi-scale routing mechanism, encompassing a semantic global router and a learned local router. The global router leverages recent LLMs’ semantic reasoning capabilities to generate task-specific instructions from the input query, guiding expert selection across all layers. This global guidance is complemented by a local router that facilitates token-level routing decisions within each module, enabling finer control and enhanced performance on unseen and challenging tasks. Our experiments using T5-based expert models for T0 and FLAN tasks demonstrate that Glider achieves substantially improved held-in performance while maintaining strong generalization on held-out tasks. Additionally, we perform ablations experiments to dive deeper into the components of Glider and plot routing distributions to show that Glider can effectively retrieve the correct expert for held-in tasks while also demonstrating compositional capabilities for held-out tasks. Our experiments highlight the importance of our multi-scale routing that leverages LLM-driven semantic reasoning for MoErging methods.