Soochow University
Abstract:Whether Large Language Models (LLMs) develop coherent internal world models remains a core debate. While conventional Next-Token Prediction (NTP) focuses on one-step-ahead supervision, Multi-Token Prediction (MTP) has shown promise in learning more structured representations. In this work, we provide a theoretical perspective analyzing the gradient inductive bias of MTP, supported by empirical evidence, showing that MTP promotes the convergence toward internal belief states by inducing representational contractivity via gradient coupling. However, we reveal that standard MTP often suffers from structural hallucinations, where discrete token supervision encourages illegal shortcuts in latent space that violate environmental constraints. To address this, we propose a novel method Latent Semantic Enhancement MTP (LSE-MTP), which anchors predictions to ground-truth hidden state trajectories. Experiments on synthetic graphs and real-world Manhattan Taxi Ride show that LSE-MTP effectively bridges the gap between discrete tokens and continuous state representations, enhancing representation alignment, reducing structural hallucinations, and improving robustness to perturbations.
Abstract:Recent studies show that neural retrievers often display source bias, favoring passages generated by LLMs over human-written ones, even when both are semantically similar. This bias has been considered an inherent flaw of retrievers, raising concerns about the fairness and reliability of modern information access systems. Our work challenges this view by showing that source bias stems from supervision in retrieval datasets rather than the models themselves. We found that non-semantic differences, like fluency and term specificity, exist between positive and negative documents, mirroring differences between LLM and human texts. In the embedding space, the bias direction from negatives to positives aligns with the direction from human-written to LLM-generated texts. We theoretically show that retrievers inevitably absorb the artifact imbalances in the training data during contrastive learning, which leads to their preferences over LLM texts. To mitigate the effect, we propose two approaches: 1) reducing artifact differences in training data and 2) adjusting LLM text vectors by removing their projection on the bias vector. Both methods substantially reduce source bias. We hope our study alleviates some concerns regarding LLM-generated texts in information access systems.
Abstract:Background: Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Accurate survival prediction is essential for treatment stratification, yet existing pathology foundation models often overlook organ-specific features critical for CRC prognostication. Methods: We propose MorphDistill, a two-stage framework that distills complementary knowledge from multiple pathology foundation models into a compact CRC-specific encoder. In Stage I, a student encoder is trained using dimension-agnostic multi-teacher relational distillation with supervised contrastive regularization on large-scale colorectal datasets. This preserves inter-sample relationships from ten foundation models without explicit feature alignment. In Stage II, the encoder extracts patch-level features from whole-slide images, which are aggregated via attention-based multiple instance learning to predict five-year survival. Results: On the Alliance/CALGB 89803 cohort (n=424, stage III CRC), MorphDistill achieves an AUC of 0.68 (SD 0.08), an approximately 8% relative improvement over the strongest baseline (AUC 0.63). It also attains a C-index of 0.661 and a hazard ratio of 2.52 (95% CI: 1.73-3.65), outperforming all baselines. On an external TCGA cohort (n=562), it achieves a C-index of 0.628, demonstrating strong generalization across datasets and robustness across clinical subgroups. Conclusion: MorphDistill enables task-specific representation learning by integrating knowledge from multiple foundation models into a unified encoder. This approach provides an efficient strategy for prognostic modeling in computational pathology, with potential for broader oncology applications. Further validation across additional cohorts and disease stages is warranted.
Abstract:Interactive documents help readers engage with complex ideas through dynamic visualization, interactive animations, and exploratory interfaces. However, creating such documents remains costly, as it requires both domain expertise and web development skills. Recent Large Language Model (LLM)-based agents can automate content creation, but directly applying them to interactive document generation often produces outputs that are difficult to control. To address this, we present ViviDoc, to the best of our knowledge the first work to systematically address interactive document generation. ViviDoc introduces a multi-agent pipeline (Planner, Styler, Executor, Evaluator). To make the generation process controllable, we provide three levels of human control: (1) the Document Specification (DocSpec) with SRTC Interaction Specifications (State, Render, Transition, Constraint) for structured planning, (2) a content-aware Style Palette for customizing writing and interaction styles, and (3) chat-based editing for iterative refinement. We also construct ViviBench, a benchmark of 101 topics derived from real-world interactive documents across 11 domains, along with a taxonomy of 8 interaction types and a 4-dimensional automated evaluation framework validated against human ratings (Pearson r > 0.84). Experiments show that ViviDoc achieves the highest content richness and interaction quality in both automated and human evaluation. A 12-person user study confirms that the system is easy to use, provides effective control over the generation process, and produces documents that satisfy users.
Abstract:Model visualization (ModelVis) has emerged as a major research direction, yet existing taxonomies are largely organized by data or tasks, making it difficult to treat models as first-class analysis objects. We present a model-centric two-stage framework that employs abstract listeners to capture spatial and temporal model behaviors, and then connects the translated model behavior data to the classical InfoVis pipeline. To apply the framework at scale, we build a retrieval-augmented human--large language model (LLM) extraction workflow and curate a corpus of 128 VIS/VAST ModelVis papers with 331 coded figures. Our analysis shows a dominant result-centric priority on visualizing model outcomes, quantitative/nominal data type, statistical charts, and performance evaluation. Citation-weighted trends further indicate that less frequent model-mechanism-oriented studies have disproportionately high impact while are less investigated recently. Overall, the framework is a general approach for comparing existing ModelVis systems and guiding possible future designs.
Abstract:As agentic AI systems become increasingly capable of generating and optimizing GPU kernels, progress is constrained by benchmarks that reward speedup over software baselines rather than proximity to hardware-efficient execution. We present SOL-ExecBench, a benchmark of 235 CUDA kernel optimization problems extracted from 124 production and emerging AI models spanning language, diffusion, vision, audio, video, and hybrid architectures, targeting NVIDIA Blackwell GPUs. The benchmark covers forward and backward workloads across BF16, FP8, and NVFP4, including kernels whose best performance is expected to rely on Blackwell-specific capabilities. Unlike prior benchmarks that evaluate kernels primarily relative to software implementations, SOL-ExecBench measures performance against analytically derived Speed-of-Light (SOL) bounds computed by SOLAR, our pipeline for deriving hardware-grounded SOL bounds, yielding a fixed target for hardware-efficient optimization. We report a SOL Score that quantifies how much of the gap between a release-defined scoring baseline and the hardware SOL bound a candidate kernel closes. To support robust evaluation of agentic optimizers, we additionally provide a sandboxed harness with GPU clock locking, L2 cache clearing, isolated subprocess execution, and static analysis based checks against common reward-hacking strategies. SOL-ExecBench reframes GPU kernel benchmarking from beating a mutable software baseline to closing the remaining gap to hardware Speed-of-Light.
Abstract:This paper investigates physical-layer security (PLS) enabled by graph neural networks (GNNs). We propose a two-stage heterogeneous GNN (HGNN) to maximize the secrecy energy efficiency (SEE) of a reconfigurable intelligent surface (RIS)-assisted multi-input-single-output (MISO) system that serves multiple legitimate users (LUs) and eavesdroppers (Eves). The first stage formulates the system as a bipartite graph involving three types of nodes-RIS reflecting elements, LUs, and Eves-with the goal of generating the RIS phase shift matrix. The second stage models the system as a fully connected graph with two types of nodes (LUs and Eves), aiming to produce beamforming and artificial noise (AN) vectors. Both stages adopt an HGNN integrated with a multi-head attention mechanism, and the second stage incorporates two output methods: beam-direct and model-based approaches. The two-stage HGNN is trained in an unsupervised manner and designed to scale with the number of RIS reflecting elements, LUs, and Eves. Numerical results demonstrate that the proposed two-stage HGNN outperforms state-of-the-art GNNs in RIS-aided PLS scenarios. Compared with convex optimization algorithms, it reduces the average running time by three orders of magnitude with a performance loss of less than $4\%$. Additionally, the scalability of the two-stage HGNN is validated through extensive simulations.
Abstract:Deep research systems powered by LLM agents have transformed complex information seeking by automating the iterative retrieval, filtering, and synthesis of insights from massive-scale web sources. However, existing systems predominantly follow an autonomous "query-to-report" paradigm, limiting users to a passive role and failing to integrate their personal insights, contextual knowledge, and evolving research intents. This paper addresses the lack of human-in-the-loop collaboration in the agentic research process. Through a formative study, we identify that current systems hinder effective human-agent collaboration in terms of process observability, real-time steerability, and context navigation efficiency. Informed by these findings, we propose InterDeepResearch, an interactive deep research system backed by a dedicated research context management framework. The framework organizes research context into a hierarchical architecture with three levels (information, actions, and sessions), enabling dynamic context reduction to prevent LLM context exhaustion and cross-action backtracing for evidence provenance. Built upon this framework, the system interface integrates three coordinated views for visual sensemaking, and dedicated interaction mechanisms for interactive research context navigation. Evaluation on the Xbench-DeepSearch-v1 and Seal-0 benchmarks shows that InterDeepResearch achieves competitive performance compared to state-of-the-art deep research systems, while a formal user study demonstrates its effectiveness in supporting human-agent collaborative information seeking. Project page with system demo: https://github.com/bopan3/InterDeepResearch.
Abstract:Background and objectives: Colorectal cancer histopathological grading depends on accurate segmentation of glandular structures. Current deep learning approaches rely on large scale pixel level annotations that are labor intensive and difficult to obtain in routine clinical practice. Weakly supervised semantic segmentation offers a promising alternative. However, class activation map based methods often produce incomplete pseudo masks that emphasize highly discriminative regions and fail to supervise unannotated glandular structures. We propose a weakly supervised teacher student framework that leverages sparse pathologist annotations and an Exponential Moving Average stabilized teacher network to generate refined pseudo masks. Methods: The framework integrates confidence based filtering, adaptive fusion of teacher predictions with limited ground truth, and curriculum guided refinement to progressively segment unannotated glandular regions. The method was evaluated on an institutional colorectal cancer cohort from The Ohio State University Wexner Medical Center consisting of 60 hematoxylin and eosin stained whole slide images and on public datasets including the Gland Segmentation dataset, TCGA COAD, TCGA READ, and SPIDER. Results: On the Gland Segmentation dataset the framework achieved a mean Intersection over Union of 80.10 and a mean Dice coefficient of 89.10. Cross cohort evaluation demonstrated robust generalization on TCGA COAD and TCGA READ without additional annotations, while reduced performance on SPIDER reflected domain shift. Conclusions: The proposed framework provides an annotation efficient and generalizable approach for gland segmentation in colorectal histopathology.
Abstract:Pathology underpins modern diagnosis and cancer care, yet its most valuable asset, the accumulated experience encoded in millions of narrative reports, remains largely inaccessible. Although institutions are rapidly digitizing pathology workflows, storing data without effective mechanisms for retrieval and reasoning risks transforming archives into a passive data repository, where institutional knowledge exists but cannot meaningfully inform patient care. True progress requires not only digitization, but the ability for pathologists to interrogate prior similar cases in real time while evaluating a new diagnostic dilemma. We present PathoScribe, a unified retrieval-augmented large language model (LLM) framework designed to transform static pathology archives into a searchable, reasoning-enabled living library. PathoScribe enables natural language case exploration, automated cohort construction, clinical question answering, immunohistochemistry (IHC) panel recommendation, and prompt-controlled report transformation within a single architecture. Evaluated on 70,000 multi-institutional surgical pathology reports, PathoScribe achieved perfect Recall@10 for natural language case retrieval and demonstrated high-quality retrieval-grounded reasoning (mean reviewer score 4.56/5). Critically, the system operationalized automated cohort construction from free-text eligibility criteria, assembling research-ready cohorts in minutes (mean 9.2 minutes) with 91.3% agreement to human reviewers and no eligible cases incorrectly excluded, representing orders-of-magnitude reductions in time and cost compared to traditional manual chart review. This work establishes a scalable foundation for converting digital pathology archives from passive storage systems into active clinical intelligence platforms.