arXiv subjects

Jiashu He

Publications and source records attributed to Jiashu He.

11 recordsLinked to original sources

arXiv2026

Learning Interpretable Tumor Microenvironment Representations by Fitting Pan-Cancer Cell State-Niche Correlation

In the tumor microenvironment, cell's state is influenced by cell-cell interactions (CCIs) with neighboring cells in its niches. Identifying dysregulated CCIs that are associated with pathogenic process pinpoints targets for drug discovery. Imaging-based spatial transcriptomics and single-cell RNA sequencing provide, respectively, single-cell spatial information and transcriptome-wide measurements needed to study CCIs, but neither modality provides both. Existing spatial transcriptomics foundation models also cannot effectively learn from spatially resolved single-cell data with full-transcriptome coverage, explicitly infer the CCI mechanisms driving cell state-niche associations, or interpretable enough to support direct biological interpretations. Here, we present GITIII-scale, a hierarchical, interpretable pan-cancer spatial transcriptomics foundation model for TME representation learning that investigates cell state-niche associations and their underlying ligand-receptor (LR) signaling pathways. GITIII-scale uses transformers to model interactions between pairs of cells at defined spatial distances, an interpretable single-layer graph transformer without a feed-forward network to decompose how each gene in a receiver cell is influenced by each neighboring sender cell, and a graph transformer to generate cellular-neighborhood embeddings. Trained on our assembled pan-cancer database of specimen-matched scRNA-seq and imaging-based spatial transcriptomics datasets, GITIII-scale generated TME embeddings that recovered niche-associated state changes more accurately than existing spatial transcriptomics foundation models in cancer types unseen during training. A case study of an unseen breast cancer dataset further demonstrated the model's interpretability by identifying potentially drug-targetable LR pathways associated with endothelial overgrowth and tumorigenesis.

q-bio.GN↗

arXiv2026

Think Twice Before You Write -- an Entropy-based Decoding Strategy to Enhance LLM Reasoning

Decoding strategies play a central role in shaping the reasoning ability of large language models (LLMs). Traditional methods such as greedy decoding and beam search often suffer from error propagation, while sampling-based approaches introduce randomness without adequate robustness. Self-consistency improves reliability by aggregating multiple rollouts, but incurs significant computational overhead. We propose an entropy-guided decoding framework that introduces token-level adaptivity into generation. At each step, the model computes the entropy of the token distribution, identifies high-uncertainty positions, and selectively branches on these vulnerable points. A dynamic pool of partial rollouts is maintained and expanded until solutions are completed, concentrating computation where uncertainty is greatest and avoiding unnecessary exploration in confident regions. To enable efficient termination, we apply a rollout-level Entropy After (EAT) stopping criterion by performing entropy evaluation after the full reasoning trace, rather than incrementally at every step. Experiments on GSM8K, AMC2023, and their perturbed variants demonstrate that our method achieves consistently strong accuracy. Notably, on smaller LLMs, performance is comparable to GPT-5 while operating at a fraction of the cost.

cs.CL↗

arXiv2026

TransportAgents: a multi-agents LLM framework for traffic accident severity prediction

Accurate prediction of traffic crash severity is critical for improving emergency response and public safety planning. Although recent large language models (LLMs) exhibit strong reasoning capabilities, their single-agent architectures often struggle with heterogeneous, domain-specific crash data and tend to generate biased or unstable predictions. To address these limitations, this paper proposes TransportAgents, a hybrid multi-agent framework that integrates category-specific LLM reasoning with a multilayer perceptron (MLP) integration module. Each specialized agent focuses on a particular subset of traffic information, such as demographics, environmental context, or incident details, to produce intermediate severity assessments that are subsequently fused into a unified prediction. Extensive experiments on two complementary U.S. datasets, the Consumer Product Safety Risk Management System (CPSRMS) and the National Electronic Injury Surveillance System (NEISS), demonstrate that TransportAgents consistently outperforms both traditional machine learning and advanced LLM-based baselines. Across three representative backbones, including closed-source models such as GPT-3.5 and GPT-4o, as well as open-source models such as LLaMA-3.3, the framework exhibits strong robustness, scalability, and cross-dataset generalizability. A supplementary distributional analysis further shows that TransportAgents produces more balanced and well-calibrated severity predictions than standard single-agent LLM approaches, highlighting its interpretability and reliability for safety-critical decision support applications.

cs.AI↗

arXiv2025

PersonaMem-v2: Towards Personalized Intelligence via Learning Implicit User Personas and Agentic Memory

Personalization is one of the next milestones in advancing AI capability and alignment. We introduce PersonaMem-v2, the state-of-the-art dataset for LLM personalization that simulates 1,000 realistic user-chatbot interactions on 300+ scenarios, 20,000+ user preferences, and 128k-token context windows, where most user preferences are implicitly revealed to reflect real-world interactions. Using this data, we investigate how reinforcement fine-tuning enables a model to improve its long-context reasoning capabilities for user understanding and personalization. We also develop a framework for training an agentic memory system, which maintains a single, human-readable memory that grows with each user over time. In our experiments, frontier LLMs still struggle with implicit personalization, achieving only 37-48% accuracy. While they support long context windows, reasoning remains the bottleneck for implicit personalization tasks. Using reinforcement fine-tuning, we successfully train Qwen3-4B to outperforms GPT-5, reaching 53% accuracy in implicit personalization. Moreover, our agentic memory framework achieves state-of-the-art 55% accuracy while using 16x fewer input tokens, relying on a 2k-token memory instead of full 32k conversation histories. These results underscore the impact of our dataset and demonstrate agentic memory as a scalable path toward real-world personalized intelligence.

cs.CL↗

arXiv2025

StgcDiff: Spatial-Temporal Graph Condition Diffusion for Sign Language Transition Generation

Sign language transition generation seeks to convert discrete sign language segments into continuous sign videos by synthesizing smooth transitions. However,most existing methods merely concatenate isolated signs, resulting in poor visual coherence and semantic accuracy in the generated videos. Unlike textual languages,sign language is inherently rich in spatial-temporal cues, making it more complex to model. To address this,we propose StgcDiff, a graph-based conditional diffusion framework that generates smooth transitions between discrete signs by capturing the unique spatial-temporal dependencies of sign language. Specifically, we first train an encoder-decoder architecture to learn a structure-aware representation of spatial-temporal skeleton sequences. Next, we optimize a diffusion denoiser conditioned on the representations learned by the pre-trained encoder, which is tasked with predicting transition frames from noise. Additionally, we design the Sign-GCN module as the key component in our framework, which effectively models the spatial-temporal features. Extensive experiments conducted on the PHOENIX14T, USTC-CSL100,and USTC-SLR500 datasets demonstrate the superior performance of our method.

cs.CV↗

arXiv2025

E-bike agents: Large Language Model-Driven E-Bike Accident Analysis and Severity Prediction

E-bikes have rapidly gained popularity as a sustainable form of urban mobility, yet their safety implications remain underexplored. This paper analyzes injury incidents involving e-bikes and traditional bicycles using two sources of data, the CPSRMS (Consumer Product Safety Risk Management System Information Security Review Report) and NEISS (National Electronic Injury Surveillance System) datasets. We propose a standardized classification framework to identify and quantify injury causes and severity. By integrating incident narratives with demographic attributes, we reveal key differences in mechanical failure modes, injury severity patterns, and affected user groups. While both modes share common causes, such as loss of control and pedal malfunctions, e-bikes present distinct risks, including battery-related fires and brake failures. These findings highlight the need for tailored safety interventions and infrastructure design to support the safe integration of micromobility devices into urban transportation networks.

cs.AI↗

arXiv2025

SAKE: Structured Agentic Knowledge Extrapolation for Complex LLM Reasoning via Reinforcement Learning

Knowledge extrapolation is the process of inferring novel information by combining and extending existing knowledge that is explicitly available. It is essential for solving complex questions in specialized domains where retrieving comprehensive external knowledge is impractical. We propose SAKE (Structured Agentic Knowledge Extrapolation), a RL powered agentic framework that trains LLMs to autonomously retrieve and extrapolate structured knowledge through tool-augmented reinforcement learning. SAKE defines two external KG tools: entity group construction and cross-group triplet retrieval. The model learns to interleave these 2 retrieval tools during a three-turn rollout: extracting key entities, filtering relevant concept groups, and associative reasoning by constructing new triplets through analogy. The entire pipeline is optimized end-to-end with GRPO using a reward that combines output format and answer correctness, teaching the model what to retrieve and how to reason over it. Our experiments proved that SAKE fine-tuned Qwen2.5-7B model surpasses GPT-3.5-Turbo with state-of-the-art agentic KG reasoning on both biomedical (75.4% vs. 70.1%) and commonsense (81.3% vs. 74.7%) benchmarks, while reducing token usage by over 90%. These results demonstrate that associative reasoning over incomplete structured knowledge does not require large models with complex, multi-step prompting, thus can be learned end-to-end by small, open-weight models through reinforcement learning with the right tools and training signal. Our code is available at https://github.com/jxfan99/SAKE.

cs.CL↗

arXiv2025

GeoGrid-Bench: Can Foundation Models Understand Multimodal Gridded Geo-Spatial Data?

We present GeoGrid-Bench, a benchmark designed to evaluate the ability of foundation models to understand geo-spatial data in the grid structure. Geo-spatial datasets pose distinct challenges due to their dense numerical values, strong spatial and temporal dependencies, and unique multimodal representations including tabular data, heatmaps, and geographic visualizations. To assess how foundation models can support scientific research in this domain, GeoGrid-Bench features large-scale, real-world data covering 16 climate variables across 150 locations and extended time frames. The benchmark includes approximately 3,200 question-answer pairs, systematically generated from 8 domain expert-curated templates to reflect practical tasks encountered by human scientists. These range from basic queries at a single location and time to complex spatiotemporal comparisons across regions and periods. Our evaluation reveals that vision-language models perform best overall, and we provide a fine-grained analysis of the strengths and limitations of different foundation models in different geo-spatial tasks. This benchmark offers clearer insights into how foundation models can be effectively applied to geo-spatial data analysis and used to support scientific research.

cs.CL↗

arXiv2024

GIVE: Structured Reasoning of Large Language Models with Knowledge Graph Inspired Veracity Extrapolation

Existing approaches based on context prompting or reinforcement learning (RL) to improve the reasoning capacities of large language models (LLMs) depend on the LLMs' internal knowledge to produce reliable Chain-Of-Thought (CoT). However, no matter the size of LLMs, certain problems cannot be resolved in a single forward pass. Meanwhile, agent-based reasoning systems require access to a comprehensive nonparametric knowledge base, which is often costly or not feasible for use in scientific and niche domains. We present Graph Inspired Veracity Extrapolation (GIVE), a novel reasoning method that merges parametric and non-parametric memories to improve accurate reasoning with minimal external input. GIVE guides the LLM agent to select the most pertinent expert data (observe), engage in query-specific divergent thinking (reflect), and then synthesize this information to produce the final output (speak). Extensive experiments demonstrated the following benefits of our framework: (1) GIVE boosts the performance of LLMs across various sizes. (2) In some scenarios, GIVE allows smaller LLMs to surpass larger, more sophisticated ones in scientific tasks (GPT3.5T + GIVE > GPT4). (3) GIVE is effective on scientific and open-domain assessments. (4) GIVE is a training-free method that enables LLMs to tackle new problems that extend beyond their training data (up to 43.5% -> 88.2%} accuracy improvement). (5) GIVE allows LLM agents to reason using both restricted (very small) and noisy (very large) knowledge sources, accommodating knowledge graphs (KG) ranging from 135 to more than 840k nodes. (6) The reasoning process involved in GIVE is fully interpretable.

cs.AI↗

arXiv2023

T-GAE: Transferable Graph Autoencoder for Network Alignment

Network alignment is the task of establishing one-to-one correspondences between the nodes of different graphs. Although finding a plethora of applications in high-impact domains, this task is known to be NP-hard in its general form. Existing optimization algorithms do not scale up as the size of the graphs increases. While being able to reduce the matching complexity, current GNN approaches fit a deep neural network on each graph and requires re-train on unseen samples, which is time and memory inefficient. To tackle both challenges we propose T-GAE, a transferable graph autoencoder framework that leverages transferability and stability of GNNs to achieve efficient network alignment on out-of-distribution graphs without retraining. We prove that GNN-generated embeddings can achieve more accurate alignment compared to classical spectral methods. Our experiments on real-world benchmarks demonstrate that T-GAE outperforms the state-of-the-art optimization method and the best GNN approach by up to 38.7% and 50.8%, respectively, while being able to reduce 90% of the training time when matching out-of-distribution large scale networks. We conduct ablation studies to highlight the effectiveness of the proposed encoder architecture and training objective in enhancing the expressiveness of GNNs to match perturbed graphs. T-GAE is also proved to be flexible to utilize matching algorithms of different complexities. Our code is available at https://github.com/Jason-Tree/T-GAE.

cs.LG↗

arXiv2021

Performance analysis of facial recognition: A critical review through glass factor

COVID-19 pandemic and social distancing urge a reliable human face recognition system in different abnormal situations. However, there is no research which studies the influence of glass factor in facial recognition system. This paper provides a comprehensive review of glass factor. The study contains two steps: data collection and accuracy test. Data collection includes collecting human face images through different situations, such as clear glasses, glass with water and glass with mist. Based on the collected data, an existing state-of-the-art face detection and recognition system built upon MTCNN and Inception V1 deep nets is tested for further analysis. Experimental data supports that 1) the system is robust for classification when comparing real-time images and 2) it fails at determining if two images are of same person by comparing real-time disturbed image with the frontal ones.

cs.CV↗