Spatial Transcriptomics (ST) is a technology that measures gene expression profiles within tissue sections while retaining spatial context. It reveals localized gene expression patterns and tissue heterogeneity, both of which are essential for understanding disease etiology. However, its high cost has driven efforts to predict spatial gene expression from whole slide images. Despite recent advancements, current methods still face significant limitations, such as under-exploitation of high-level biological context, over-reliance on exemplar retrievals, and inadequate alignment of heterogeneous modalities. To address these challenges, we propose DKAN, a novel Dual-path Knowledge-Augmented contrastive alignment Network that predicts spatially resolved gene expression by integrating histopathological images and gene expression profiles through a biologically informed approach. Specifically, we introduce an effective gene semantic representation module that leverages the external gene database to provide additional biological insights, thereby enhancing gene expression prediction. Further, we adopt a unified, one-stage contrastive learning paradigm, seamlessly combining contrastive learning and supervised learning to eliminate reliance on exemplars, complemented with an adaptive weighting mechanism. Additionally, we propose a dual-path contrastive alignment module that employs gene semantic features as dynamic cross-modal coordinators to enable effective heterogeneous feature integration. Through extensive experiments across three public ST datasets, DKAN demonstrates superior performance over state-of-the-art models, establishing a new benchmark for spatial gene expression prediction and offering a powerful tool for advancing biological and clinical research.

Mechanistic interpretability aspires to reverse-engineer neural networks into explicit algorithms, while model editing seeks to modify specific behaviours without retraining. Both areas are typically evaluated with informal evidence and ad-hoc experiments, with few explicit guarantees about how far an extracted or edited model can drift from the original on relevant inputs. We introduce BlockCert, a framework for certified blockwise extraction of transformer mechanisms, and outline how a lightweight extension can support certified local edits. Given a pre-trained transformer and a prompt distribution, BlockCert extracts structured surrogate implementations for residual blocks together with machine-checkable certificates that bound approximation error, record coverage metrics, and hash the underlying artifacts. We formalize a simple Lipschitz-based composition theorem in Lean 4 that lifts these local guarantees to a global deviation bound. Empirically, we apply the framework to GPT-2 small, TinyLlama-1.1B-Chat, and Llama-3.2-3B. Across these models we obtain high per-block coverage and small residual errors on the evaluated prompts, and in the TinyLlama setting we show that a fully stitched model matches the baseline perplexity within approximately 6e-5 on stress prompts. Our results suggest that blockwise extraction with explicit certificates is feasible for real transformer language models and offers a practical bridge between mechanistic interpretability and formal reasoning about model behaviour.

Transformers have defined the state-of-the-art for clinical prediction tasks involving electronic health records (EHRs). The recently introduced Mamba architecture outperformed an advanced Transformer (Transformer++) based on Llama in handling long context lengths, while using fewer model parameters. Despite the impressive performance of these architectures, a systematic approach to empirically analyze model performance and efficiency under various settings is not well established in the medical domain. The performances of six sequence models were investigated across three architecture classes (Transformers, Transformers++, Mambas) in a large Swedish heart failure (HF) cohort (N = 42820), providing a clinically relevant case study. Patient data included diagnoses, vital signs, laboratories, medications and procedures extracted from in-hospital EHRs. The models were evaluated on three one-year prediction tasks: clinical instability (a readmission phenotype) after initial HF hospitalization, mortality after initial HF hospitalization and mortality after latest hospitalization. Ablations account for modifications of the EHR-based input patient sequence, architectural model configurations, and temporal preprocessing techniques for data collection. Llama achieves the highest predictive discrimination, best calibration, and showed robustness across all tasks, followed by Mambas. Both architectures demonstrate efficient representation learning, with tiny configurations surpassing other large-scaled Transformers. At equal model size, Llama and Mambas achieve superior performance using 25% less training data. This paper presents a first ablation study with systematic design choices for input tokenization, model configuration and temporal data preprocessing. Future model development in clinical prediction tasks using EHRs could build upon this study's recommendation as a starting point.

Test-time thinking (that is, generating explicit intermediate reasoning chains) is known to boost performance in large language models and has recently shown strong gains for large vision language models (LVLMs). However, despite these promising results, there is still no systematic analysis of how thinking actually affects visual reasoning. We provide the first such analysis with a large scale, controlled comparison of thinking for LVLMs, evaluating ten variants from the InternVL3.5 and Qwen3-VL families on MMMU-val under generous token budgets and multi pass decoding. We show that more thinking is not always better; long chains often yield long wrong trajectories that ignore the image and underperform the same models run in standard instruct mode. A deeper analysis reveals that certain short lookback phrases, which explicitly refer back to the image, are strongly enriched in successful trajectories and correlate with better visual grounding. Building on this insight, we propose uncertainty guided lookback, a training free decoding strategy that combines an uncertainty signal with adaptive lookback prompts and breadth search. Our method improves overall MMMU performance, delivers the largest gains in categories where standard thinking is weak, and outperforms several strong decoding baselines, setting a new state of the art under fixed model families and token budgets. We further show that this decoding strategy generalizes, yielding consistent improvements on five additional benchmarks, including two broad multimodal suites and math focused visual reasoning datasets.

Modern AI workloads, especially Mixture-of-Experts (MoE) architectures, increasingly demand low-latency, fine-grained GPU-to-GPU communication with device-side control. Traditional GPU communication follows a host-initiated model, where the CPU orchestrates all communication operations - a characteristic of the CUDA runtime. Although robust for collective operations, applications requiring tight integration of computation and communication can benefit from device-initiated communication that eliminates CPU coordination overhead. NCCL 2.28 introduces the Device API with three operation modes: Load/Store Accessible (LSA) for NVLink/PCIe, Multimem for NVLink SHARP, and GPU-Initiated Networking (GIN) for network RDMA. This paper presents the GIN architecture, design, semantics, and highlights its impact on MoE communication. GIN builds on a three-layer architecture: i) NCCL Core host-side APIs for device communicator setup and collective memory window registration; ii) Device-side APIs for remote memory operations callable from CUDA kernels; and iii) A network plugin architecture with dual semantics (GPUDirect Async Kernel-Initiated and Proxy) for broad hardware support. The GPUDirect Async Kernel-Initiated backend leverages DOCA GPUNetIO for direct GPU-to-NIC communication, while the Proxy backend provides equivalent functionality via lock-free GPU-to-CPU queues over standard RDMA networks. We demonstrate GIN's practicality through integration with DeepEP, an MoE communication library. Comprehensive benchmarking shows that GIN provides device-initiated communication within NCCL's unified runtime, combining low-latency operations with NCCL's collective algorithms and production infrastructure.

As more autonomous vehicles operate on public roads, understanding real-world behavior of autonomous vehicles is critical to analyzing traffic safety, making policies, and public acceptance. This paper proposes SVBRD-LLM, a framework that automatically discovers, verifies, and applies interpretable behavioral rules from real traffic videos through zero-shot prompt engineering. The framework extracts vehicle trajectories using YOLOv8 and ByteTrack, computes kinematic features, and employs GPT-5 zero-shot prompting to compare autonomous and human-driven vehicles, generating 35 structured behavioral rule hypotheses. These rules are tested on a validation set, iteratively refined based on failure cases to filter spurious correlations, and compiled into a high-confidence rule library. The framework is evaluated on an independent test set for speed change prediction, lane change prediction, and autonomous vehicle identification tasks. Experiments on over 1500 hours of real traffic videos show that the framework achieves 90.0% accuracy and 93.3% F1-score in autonomous vehicle identification. The discovered rules clearly reveal distinctive characteristics of autonomous vehicles in speed control smoothness, lane change conservativeness, and acceleration stability, with each rule accompanied by semantic description, applicable context, and validation confidence.

Although CS programs are booming, introductory courses like CS1 still adopt a one-size-fits-all formats that can exacerbate cognitive load and discourage learners with autism, ADHD, dyslexia and other neurological conditions. These call for compassionate pedagogies and Universal Design For Learning (UDL) to create learning environments and materials where cognitive diversity is welcomed. To address this, we introduce DiverseClaire a pilot study, which simulates students including neurodiverse profiles using LLMs and diverse personas. By leveraging Bloom's Taxonomy and UDL, DiverseClaire compared UDL-transformed lecture slides with traditional formats. To evaluate DiverseClaire controlled experiments, we used the evaluation metric the average score. The findings revealed that the simulated neurodiverse students struggled with learning due to lecture slides that were in inaccessible formats. These results highlight the need to provide course materials in multiple formats for diverse learner preferences. Data from our pilot study will be made available to assist future CS1 instructors.

All-in-One Image Restoration (AIO-IR) aims to develop a unified model that can handle multiple degradations under complex conditions. However, existing methods often rely on task-specific designs or latent routing strategies, making it hard to adapt to real-world scenarios with various degradations. W e propose F APE-IR, a Frequency-Aware Planning and Execution framework for image restoration. It uses a frozen Multimodal Large Language Model (MLLM) as a planner to analyze degraded images and generate concise, frequency-aware restoration plans. These plans guide a LoRA-based Mixture-of-Experts (LoRA-MoE) module within a diffusion-based executor, which dynamically selects high-or low-frequency experts, complemented by frequency features of the input image. T o further improve restoration quality and reduce artifacts, we introduce adversarial training and a frequency regularization loss. By coupling semantic planning with frequency-based restoration, F APE-IR offers a unified and interpretable solution for all-in-one image restoration. Extensive experiments show that F APE-IR achieves state-of-the-art performance across seven restoration tasks and exhibits strong zero-shot generalization under mixed degradations.

Existing tool-augmented large language models (LLMs) encounter significant challenges when processing complex queries. Current frameworks such as ReAct are prone to local optimization traps due to their reliance on incremental decision-making processes. To address these limitations, we propose a novel Planner-centric Plan-Execute paradigm that fundamentally resolves local optimization bottlenecks through architectural innovation. Central to our approach is a novel Planner model that performs global Directed Acyclic Graph (DAG) planning for complex queries, enabling optimized execution beyond conventional tool coordination. We also introduce ComplexTool-Plan, a large-scale benchmark dataset featuring complex queries that demand sophisticated multi-tool composition and coordination capabilities. Additionally, we develop a two-stage training methodology that integrates Supervised Fine-Tuning (SFT) with Group Relative Policy Optimization (GRPO), systematically enhancing the Planner's tool selection accuracy and global planning awareness through structured DAG-based planning. When integrated with a capable executor, our framework achieves state-of-the-art performance on the StableToolBench benchmark for complex user queries, demonstrating superior end-to-end execution capabilities and robust handling of intricate multi-tool workflows.

Large language models (LLMs) are increasingly used both to make decisions in domains such as health, education and law, and to simulate human behavior. Yet how closely LLMs mirror actual human decision-making remains poorly understood. This gap is critical: misalignment could produce harmful outcomes in practical applications, while failure to replicate human behavior renders LLMs ineffective for social simulations. Here, we address this gap by developing a digital twin of game-theoretic experiments and introducing a systematic prompting and probing framework for machine-behavioral evaluation. Testing three open-source models (Llama, Mistral and Qwen), we find that Llama reproduces human cooperation patterns with high fidelity, capturing human deviations from rational choice theory, while Qwen aligns closely with Nash equilibrium predictions. Notably, we achieved population-level behavioral replication without persona-based prompting, simplifying the simulation process. Extending beyond the original human-tested games, we generate and preregister testable hypotheses for novel game configurations outside the original parameter grid. Our findings demonstrate that appropriately calibrated LLMs can replicate aggregate human behavioral patterns and enable systematic exploration of unexplored experimental spaces, offering a complementary approach to traditional research in the social and behavioral sciences that generates new empirical predictions about human social decision-making.