$D^{2}R^{2}$: Discrete Diffusion with Regulation Reinforcement for Single-Cell Perturbation Prediction

Predicting single-cell transcriptomic responses to genetic perturbations is central to functional genomics and virtual-cell modeling. Existing approaches, however, typically predict an entire expression profile as a whole, leaving the order in which individual gene responses are generated unmodeled. To address this problem, we introduce \textbf{$D^{2}R^{2}$} (\textbf{D}iscrete \textbf{D}iffusion with \textbf{R}egulation \textbf{R}einforcement), which reformulates perturbation prediction as regulation-guided gene-wise progressive generation. A Masked Discrete Diffusion Model represents expression as ordinal tokens and reconstructs a fully masked profile step by step, allowing generated gene responses to condition those that remain masked. A Regulatory Policy Module initializes the generation policy from a gene regulatory network inferred from control cells and adapts it to the perturbation and current partially generated state. Then, group-relative policy optimization refines only the ordering policy using final perturbation-effect agreement as reward. Across Norman19 and VCC-H1, $D^{2}R^{2}$ achieves the best performance on all five metrics on Norman19 and remains competitive on H1. Controlled ablations holding the generator and generation budget fixed show that biological-prior ordering improves over random ordering and is more reliable than uncertainty-based heuristics, whereas reversing the biological-prior ordering degrades every metric. Biological analyses further show that the refined policy prioritizes regulatory genes early while promoting perturbation-specific transcription factors and responsive genes. These results establish gene generation order as an effective, controllable, and biologically interpretable dimension of single-cell perturbation prediction.

CARE: Confidence-Aware Reasoning for Reliable Medical VQA

Reinforcement Fine-Tuning (RFT) has enabled medical Multimodal Large Language Models (MLLMs) to produce Chain-of-Thought (CoT) reasoning for visual question answering, yet these models suffer from $\textit{confidence miscalibration}$---a systematic gap between expressed certainty and actual diagnostic accuracy that undermines clinical trust. We propose $\textbf{CARE}$, a $\textbf{C}$onfidence-$\textbf{A}$ware medical $\textbf{RE}$asoning framework that jointly optimizes accuracy and calibration through a dual-stage pipeline. First, a scalable Medical-CoT synthesis provides structured cold-start data for Supervised Fine-Tuning. Second, Group Relative Policy Optimization (GRPO) with a novel $\textbf{Confidence-Aware Reward (CAR)}$ mechanism ties the model's confidence to diagnostic correctness within the reward signal. Across three Medical VQA benchmarks, $\textbf{CARE}$ achieves the highest diagnostic accuracy while obtaining the lowest Expected Calibration Error and Hallucination Rate, establishing a foundation for trustworthy clinical decision support. Our code is available at https://github.com/anotherbricki/CARE.

Living-Harness Is an Interactive-Agent Evolver

Large language model (LLM) agents may recover from a failure within an episode or after a retry, yet the same execution failure can recur in later tasks because post-episode feedback rarely revises the persistent harness that guides future interactions. Static harnesses improve reliability through fixed tools, context, memory, and workflow structures, but remain unchanged after deployment. We propose $\textbf{Living-Harness}$, a self-evolving agent harness that converts each completed trajectory and its evaluator signals into posterior evidence for bounded harness updates. Guided by a domain-level $\textbf{Evolution-SOP}$ ($\textbf{S}$tandard $\textbf{O}$perating $\textbf{P}$rocedure), Living-Harness extracts an episode abstraction and structured update evidence, and writes two complementary forms of procedural knowledge: episodic memory that records trigger conditions, failure patterns, and recovery actions, and a state graph that records state nodes, repair edges, and transition rules. The updated harness state is retrieved to guide future interactions, while tools and base context remain frozen, allowing procedural repairs to accumulate across evolution cycles. On eight interactive environments derived from $τ^2$-Bench and MultiWOZ-2.4, Living-Harness improves average Pass@1 over the strongest interactive baseline by 10.07 and 9.91 percentage points, respectively, and supports retrieval-only reuse of the evolved harness state across model backbones.

Confidence Calibration for Multimodal LLMs: An Empirical Study through Medical VQA

Multimodal Large Language Models (MLLMs) show great potential in medical tasks, but their elicited confidence often misaligns with actual accuracy, potentially leading to misdiagnosis or overlooking correct advice. This study presents the first comprehensive analysis of the relationship between accuracy and confidence in medical MLLMs. It proposes a novel method that combines Multi-Strategy Fusion-Based Interrogation (MS-FBI) with auxiliary expert LLM assessment, aiming to improve confidence calibration in Medical Visual Question Answering (VQA). Experiments demonstrate that our method reduces the Expected Calibration Error (ECE) by an average of 40\% across three Medical VQA datasets, significantly enhancing MLLMs' reliability. The findings highlight the importance of domain-specific calibration for MLLMs in healthcare, offering a more trustworthy solution for AI-assisted diagnosis.

Linking Perception, Confidence and Accuracy in MLLMs

Recent advances in Multi-modal Large Language Models (MLLMs) have predominantly focused on enhancing visual perception to improve accuracy. However, a critical question remains unexplored: Do models know when they do not know? Through a probing experiment, we reveal a severe confidence miscalibration problem in MLLMs. To address this, we propose Confidence-Driven Reinforcement Learning (CDRL), which uses original-noise image pairs and a novel confidence-based reward to enhance perceptual sensitivity and robustly calibrate the model's confidence. Beyond training benefits, calibrated confidence enables more effective test-time scaling as a free lunch. We further propose Confidence-Aware Test-Time Scaling (CA-TTS), which dynamically coordinates Self-Consistency, Self-Reflection, and Visual Self-Check modules guided by confidence signals. An Expert Model acts in multiple roles (e.g., Planner, Critic, Voter) to schedule these modules and provide external verification. Our integrated framework establishes new state-of-the-art results with consistent 8.8% gains across four benchmarks. More ablation studies demonstrate the effectiveness of each module and scaling superiority.

Unmasking Reasoning Processes: A Process-aware Benchmark for Evaluating Structural Mathematical Reasoning in LLMs

Recent large language models (LLMs) achieve near-saturation accuracy on many established mathematical reasoning benchmarks, raising concerns about their ability to diagnose genuine reasoning competence. This saturation largely stems from the dominance of template-based computation and shallow arithmetic decomposition in existing datasets, which underrepresent reasoning skills such as multi-constraint coordination, constructive logical synthesis, and spatial inference. To address this gap, we introduce ReasoningMath-Plus, a benchmark of 150 carefully curated problems explicitly designed to evaluate structural reasoning. Each problem emphasizes reasoning under interacting constraints, constructive solution formation, or non-trivial structural insight, and is annotated with a minimal reasoning skeleton to support fine-grained process-level evaluation. Alongside the dataset, we introduce HCRS (Hazard-aware Chain-based Rule Score), a deterministic step-level scoring function, and train a Process Reward Model (PRM) on the annotated reasoning traces. Empirically, while leading models attain relatively high final-answer accuracy (up to 5.8/10), HCRS-based holistic evaluation yields substantially lower scores (average 4.36/10, best 5.14/10), showing that answer-only metrics can overestimate reasoning robustness.