OpenRaiser/Intern-Atlas huggingface dataset:
MRI Embeddings Complement Clinical Predictors for Cognitive Decline Modeling in Alzheimer's Disease Cohorts
Venue: arXiv cs.CV 2025
Year: 2025

Accurate modeling of cognitive decline in Alzheimer's disease is essential for early stratification and personalized management. While tabular predictors provide robust markers of global risk, their ability to capture subtle brain changes remains limited. In this study, we evaluate the predictive contributions of tabular and imaging-based representations, with a focus on transformer-derived Magnetic Resonance Imaging (MRI) embeddings. We introduce a trajectory-aware labeling strategy based on Dynamic Time Warping clustering to capture heterogeneous patterns of cognitive change, and train a 3D Vision Transformer (ViT) via unsupervised reconstruction on harmonized and augmented MRI data to obtain anatomy-preserving embeddings without progression labels. The pretrained encoder embeddings are subsequently assessed using both traditional machine learning classifiers and deep learning heads, and compared against tabular representations and convolutional network baselines. Results highlight complementary strengths across modalities. Clinical and volumetric features achieved the highest AUCs of around 0.70 for predicting mild and severe progression, underscoring their utility in capturing global decline trajectories. In contrast, MRI embeddings from the ViT model were most effective in distinguishing cognitively stable individuals with an AUC of 0.71. However, all approaches struggled in the heterogeneous moderate group. These findings indicate that clinical features excel in identifying high-risk extremes, whereas transformer-based MRI embeddings are more sensitive to subtle markers of stability, motivating multimodal fusion strategies for AD progression modeling.
3D-Guided Scalable Flow Matching for Generating Volumetric Tissue Spatial Transcriptomics from Serial Histology
Venue: arXiv cs.CV 2025
Year: 2025

A scalable and robust 3D tissue transcriptomics profile can enable a holistic understanding of tissue organization and provide deeper insights into human biology and disease. Most predictive algorithms that infer ST directly from histology treat each section independently and ignore 3D structure, while existing 3D-aware approaches are not generative and do not scale well. We present Holographic Tissue Expression Inpainting and Analysis (HoloTea), a 3D-aware flow-matching framework that imputes spot-level gene expression from H&E while explicitly using information from adjacent sections. Our key idea is to retrieve morphologically corresponding spots on neighboring slides in a shared feature space and fuse this cross section context into a lightweight ControlNet, allowing conditioning to follow anatomical continuity. To better capture the count nature of the data, we introduce a 3D-consistent prior for flow matching that combines a learned zero-inflated negative binomial (ZINB) prior with a spatial-empirical prior constructed from neighboring sections. A global attention block introduces 3D H&E scaling linearly with the number of spots in the slide, enabling training and inference on large 3D ST datasets. Across three spatial transcriptomics datasets spanning different tissue types and resolutions, HoloTea consistently improves 3D expression accuracy and generalization compared to 2D and 3D baselines. We envision HoloTea advancing the creation of accurate 3D virtual tissues, ultimately accelerating biomarker discovery and deepening our understanding of disease.
Gallant: Voxel Grid-based Humanoid Locomotion and Local-navigation across 3D Constrained Terrains
Venue: arXiv cs.RO 2025
Year: 2025

Robust humanoid locomotion requires accurate and globally consistent perception of the surrounding 3D environment. However, existing perception modules, mainly based on depth images or elevation maps, offer only partial and locally flattened views of the environment, failing to capture the full 3D structure. This paper presents Gallant, a voxel-grid-based framework for humanoid locomotion and local navigation in 3D constrained terrains. It leverages voxelized LiDAR data as a lightweight and structured perceptual representation, and employs a z-grouped 2D CNN to map this representation to the control policy, enabling fully end-to-end optimization. A high-fidelity LiDAR simulation that dynamically generates realistic observations is developed to support scalable, LiDAR-based training and ensure sim-to-real consistency. Experimental results show that Gallant's broader perceptual coverage facilitates the use of a single policy that goes beyond the limitations of previous methods confined to ground-level obstacles, extending to lateral clutter, overhead constraints, multi-level structures, and narrow passages. Gallant also firstly achieves near 100% success rates in challenging scenarios such as stair climbing and stepping onto elevated platforms through improved end-to-end optimization.
M-CALLM: Multi-level Context Aware LLM Framework for Group Interaction Prediction
Venue: arXiv cs.HC 2025
Year: 2025

This paper explores how large language models can leverage multi-level contextual information to predict group coordination patterns in collaborative mixed reality environments. We demonstrate that encoding individual behavioral profiles, group structural properties, and temporal dynamics as natural language enables LLMs to break through the performance ceiling of statistical models. We build M-CALLM, a framework that transforms multimodal sensor streams into hierarchical context for LLM-based prediction, and evaluate three paradigms (zero-shot prompting, few-shot learning, and supervised fine-tuning) against statistical baselines across intervention mode (real-time prediction) and simulation mode (autoregressive forecasting) Head-to-head comparison on 16 groups (64 participants, ~25 hours) demonstrates that context-aware LLMs achieve 96% accuracy for conversation prediction, a 3.2x improvement over LSTM baselines, while maintaining sub-35ms latency. However, simulation mode reveals brittleness with 83% degradation due to cascading errors. Deep-dive into modality-specific performance shows conversation depends on temporal patterns, proximity benefits from group structure (+6%), while shared attention fails completely (0% recall), exposing architectural limitations. We hope this work spawns new ideas for building intelligent collaborative sensing systems that balance semantic reasoning capabilities with fundamental constraints.
Machine Learning Models for Predicting Smoking-Related Health Decline and Disease Risk
Venue: arXiv cs.LG 2025
Year: 2025

Smoking continues to be a major preventable cause of death worldwide, affecting millions through damage to the heart, metabolism, liver, and kidneys. However, current medical screening methods often miss the early warning signs of smoking-related health problems, leading to late-stage diagnoses when treatment options become limited. This study presents a systematic comparative evaluation of machine learning approaches for smoking-related health risk assessment, emphasizing clinical interpretability and practical deployment over algorithmic innovation. We analyzed health screening data from 55,691 individuals, examining various health indicators, including body measurements, blood tests, and demographic information. We tested three advanced prediction algorithms - Random Forest, XGBoost, and LightGBM - to determine which could most accurately identify people at high risk. This study employed a cross-sectional design to classify current smoking status based on health screening biomarkers, not to predict future disease development. Our Random Forest model performed best, achieving an Area Under the Curve (AUC) of 0.926, meaning it could reliably distinguish between high-risk and lower-risk individuals. Using SHAP (SHapley Additive exPlanations) analysis to understand what the model was detecting, we found that key health markers played crucial roles in prediction: blood pressure levels, triglyceride concentrations, liver enzyme readings, and kidney function indicators (serum creatinine) were the strongest signals of declining health in smokers.
Quadratic Term Correction on Heaps' Law
Venue: arXiv cs.CL 2025
Year: 2025

Heaps' or Herdan's law characterizes the word-type vs. word-token relation by a power-law function, which is concave in linear-linear scale but a straight line in log-log scale. However, it has been observed that even in log-log scale, the type-token curve is still slightly concave, invalidating the power-law relation. At the next-order approximation, we have shown, by twenty English novels or writings (some are translated from another language to English), that quadratic functions in log-log scale fit the type-token data perfectly. Regression analyses of log(type)-log(token) data with both a linear and quadratic term consistently lead to a linear coefficient of slightly larger than 1, and a quadratic coefficient around -0.02. Using the ``random drawing colored ball from the bag with replacement" model, we have shown that the curvature of the log-log scale is identical to a ``pseudo-variance" which is negative. Although a pseudo-variance calculation may encounter numeric instability when the number of tokens is large, due to the large values of pseudo-weights, this formalism provides a rough estimation of the curvature when the number of tokens is small.
SMRC: Aligning Large Language Models with Student Reasoning for Mathematical Error Correction
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) often make reasoning errors when solving mathematical problems, and how to automatically detect and correct these errors has become an important research direction. However, existing approaches \textit{mainly focus on self-correction within the model}, which falls short of the ``teacher-style`` correction required in educational settings, \textit{i.e.}, systematically guiding and revising a student's problem-solving process. To address this gap, we propose \texttt{SMRC} (\textit{\underline{S}tudent \underline{M}athematical \underline{R}easoning \underline{C}orrection}), a novel method that aligns LLMs with student reasoning. Specifically, \texttt{SMRC} formulates student reasoning as a multi-step sequential decision problem and introduces Monte Carlo Tree Search (MCTS) to explore optimal correction paths. To reduce the cost of the annotating process-level rewards, we leverage breadth-first search (BFS) guided by LLMs and final-answer evaluation to generate reward signals, which are then distributed across intermediate reasoning steps via a back-propagation mechanism, enabling fine-grained process supervision. Additionally, we construct a benchmark for high school mathematics, MSEB (Multi-Solution Error Benchmark), consisting of 158 instances that include problem statements, student solutions, and correct reasoning steps. We further propose a dual evaluation protocol centered on \textbf{solution accuracy} and \textbf{correct-step retention}, offering a comprehensive measure of educational applicability. Experiments demonstrate that \texttt{SMRC} significantly outperforms existing methods on two public datasets (ProcessBench and MR-GSM8K) and our MSEB in terms of effectiveness and overall performance. The code and data are available at https://github.com/Mind-Lab-ECNU/SMRC.
Encoding and Understanding Astrophysical Information in Large Language Model-Generated Summaries
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models have demonstrated the ability to generalize well at many levels across domains, modalities, and even shown in-context learning capabilities. This enables research questions regarding how they can be used to encode physical information that is usually only available from scientific measurements, and loosely encoded in textual descriptions. Using astrophysics as a test bed, we investigate if LLM embeddings can codify physical summary statistics that are obtained from scientific measurements through two main questions: 1) Does prompting play a role on how those quantities are codified by the LLM? and 2) What aspects of language are most important in encoding the physics represented by the measurement? We investigate this using sparse autoencoders that extract interpretable features from the text.
Ground Truth Generation for Multilingual Historical NLP using LLMs
Venue: arXiv cs.CL 2025
Year: 2025

Historical and low-resource NLP remains challenging due to limited annotated data and domain mismatches with modern, web-sourced corpora. This paper outlines our work in using large language models (LLMs) to create ground-truth annotations for historical French (16th-20th centuries) and Chinese (1900-1950) texts. By leveraging LLM-generated ground truth on a subset of our corpus, we were able to fine-tune spaCy to achieve significant gains on period-specific tests for part-of-speech (POS) annotations, lemmatization, and named entity recognition (NER). Our results underscore the importance of domain-specific models and demonstrate that even relatively limited amounts of synthetic data can improve NLP tools for under-resourced corpora in computational humanities research.
Attention via Synaptic Plasticity is All You Need: A Biologically Inspired Spiking Neuromorphic Transformer
Venue: arXiv cs.NE 2025
Year: 2025

Attention is the brain's ability to selectively focus on a few specific aspects while ignoring irrelevant ones. This biological principle inspired the attention mechanism in modern Transformers. Transformers now underpin large language models (LLMs) such as GPT, but at the cost of massive training and inference energy, leading to a large carbon footprint. While brain attention emerges from neural circuits, Transformer attention relies on dot-product similarity to weight elements in the input sequence. Neuromorphic computing, especially spiking neural networks (SNNs), offers a brain-inspired path to energy-efficient intelligence. Despite recent work on attention-based spiking Transformers, the core attention layer remains non-neuromorphic. Current spiking attention (i) relies on dot-product or element-wise similarity suited to floating-point operations, not event-driven spikes; (ii) keeps attention matrices that suffer from the von Neumann bottleneck, limiting in-memory computing; and (iii) still diverges from brain-like computation. To address these issues, we propose the Spiking STDP Transformer (S$^{2}$TDPT), a neuromorphic Transformer that implements self-attention through spike-timing-dependent plasticity (STDP), embedding query--key correlations in synaptic weights. STDP, a core mechanism of memory and learning in the brain and widely studied in neuromorphic devices, naturally enables in-memory computing and supports non-von Neumann hardware. On CIFAR-10 and CIFAR-100, our model achieves 94.35\% and 78.08\% accuracy with only four timesteps and 0.49 mJ on CIFAR-100, an 88.47\% energy reduction compared to a standard ANN Transformer. Grad-CAM shows that the model attends to semantically relevant regions, enhancing interpretability. Overall, S$^{2}$TDPT illustrates how biologically inspired attention can yield energy-efficient, hardware-friendly, and explainable neuromorphic models.
HyMAD: A Hybrid Multi-Activity Detection Approach for Border Surveillance and Monitoring
Venue: arXiv cs.CV 2025
Year: 2025

Seismic sensing has emerged as a promising solution for border surveillance and monitoring; the seismic sensors that are often buried underground are small and cannot be noticed easily, making them difficult for intruders to detect, avoid, or vandalize. This significantly enhances their effectiveness compared to highly visible cameras or fences. However, accurately detecting and distinguishing between overlapping activities that are happening simultaneously, such as human intrusions, animal movements, and vehicle rumbling, remains a major challenge due to the complex and noisy nature of seismic signals. Correctly identifying simultaneous activities is critical because failing to separate them can lead to misclassification, missed detections, and an incomplete understanding of the situation, thereby reducing the reliability of surveillance systems. To tackle this problem, we propose HyMAD (Hybrid Multi-Activity Detection), a deep neural architecture based on spatio-temporal feature fusion. The framework integrates spectral features extracted with SincNet and temporal dependencies modeled by a recurrent neural network (RNN). In addition, HyMAD employs self-attention layers to strengthen intra-modal representations and a cross-modal fusion module to achieve robust multi-label classification of seismic events. e evaluate our approach on a dataset constructed from real-world field recordings collected in the context of border surveillance and monitoring, demonstrating its ability to generalize to complex, simultaneous activity scenarios involving humans, animals, and vehicles. Our method achieves competitive performance and offers a modular framework for extending seismic-based activity recognition in real-world security applications.
Why Do We Code? A Theory on Motivations and Challenges in Software Engineering from Education to Practice
Venue: arXiv cs.SE 2025
Year: 2025

Motivations and challenges jointly shape how individuals enter, persist, and evolve within software engineering (SE), yet their interplay remains underexplored across the transition from education to professional practice. We conducted 15 semi-structured interviews and employed the Gioia Methodology, an adapted grounded theory methodology from organizational behavior, to inductively derive taxonomies of motivations and challenges, and build the Exposure-Pursuit-Evaluation (EPE) Process Model. Our findings reveal that impactful early exposure triggers intrinsic motivations, while non-impactful exposure requires an extrinsic push (e.g., career/ personal goals, external validation). We identify curiosity and avoiding alternatives as a distinct educational drivers, and barriers to belonging as the only challenge persisting across education and career. Our findings show that career progression challenges (e.g., navigating the corporate world) constrain extrinsic fulfillment while technical training challenges, barriers to belonging and threats to motivation constrain intrinsic fulfillment. The theory shows how unmet motivations and recurring challenges influence persistence, career shifts, or departure from the field. Our results provide a grounded model for designing interventions that strengthen intrinsic fulfillment and reduce systemic barriers in SE education and practice.
LAUD: Integrating Large Language Models with Active Learning for Unlabeled Data
Venue: arXiv cs.LG 2025
Year: 2025

Large language models (LLMs) have shown a remarkable ability to generalize beyond their pre-training data, and fine-tuning LLMs can elevate performance to human-level and beyond. However, in real-world scenarios, lacking labeled data often prevents practitioners from obtaining well-performing models, thereby forcing practitioners to highly rely on prompt-based approaches that are often tedious, inefficient, and driven by trial and error. To alleviate this issue of lacking labeled data, we present a learning framework integrating LLMs with active learning for unlabeled dataset (LAUD). LAUD mitigates the cold-start problem by constructing an initial label set with zero-shot learning. Experimental results show that LLMs derived from LAUD outperform LLMs with zero-shot or few-shot learning on commodity name classification tasks, demonstrating the effectiveness of LAUD.
Optimizing Agricultural Research: A RAG-Based Approach to Mycorrhizal Fungi Information
Venue: arXiv cs.IR 2025
Year: 2025

Retrieval-Augmented Generation (RAG) represents a transformative approach within natural language processing (NLP), combining neural information retrieval with generative language modeling to enhance both contextual accuracy and factual reliability of responses. Unlike conventional Large Language Models (LLMs), which are constrained by static training corpora, RAG-powered systems dynamically integrate domain-specific external knowledge sources, thereby overcoming temporal and disciplinary limitations. In this study, we present the design and evaluation of a RAG-enabled system tailored for Mycophyto, with a focus on advancing agricultural applications related to arbuscular mycorrhizal fungi (AMF). These fungi play a critical role in sustainable agriculture by enhancing nutrient acquisition, improving plant resilience under abiotic and biotic stresses, and contributing to soil health. Our system operationalizes a dual-layered strategy: (i) semantic retrieval and augmentation of domain-specific content from agronomy and biotechnology corpora using vector embeddings, and (ii) structured data extraction to capture predefined experimental metadata such as inoculation methods, spore densities, soil parameters, and yield outcomes. This hybrid approach ensures that generated responses are not only semantically aligned but also supported by structured experimental evidence. To support scalability, embeddings are stored in a high-performance vector database, allowing near real-time retrieval from an evolving literature base. Empirical evaluation demonstrates that the proposed pipeline retrieves and synthesizes highly relevant information regarding AMF interactions with crop systems, such as tomato (Solanum lycopersicum). The framework underscores the potential of AI-driven knowledge discovery to accelerate agroecological innovation and enhance decision-making in sustainable farming systems.
COMPASS: Context-Modulated PID Attention Steering System for Hallucination Mitigation
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) often generate fluent but factually incorrect statements despite having access to relevant evidence, a failure mode rooted in how they allocate attention between contextual and parametric knowledge. Understanding and steering this internal behavior is key both for trustworthy deployment and for scientific interpretability of model mechanisms. We introduce COMPASS (Context-Modulated PID Attention Steering System), a lightweight, interpretable control framework that embeds a model-based feedback loop directly within decoding. COMPASS quantifies context reliance via a transparent metric, the Context Reliance Score (CRS), which serves as an online probe of how attention heads ground generation in evidence. Using this interpretable signal, a PID controller dynamically modulates attention heads to maintain factual consistency without retraining or multi-pass decoding. Across benchmarks (HotpotQA, XSum, HaluEval, RAGTruth), COMPASS consistently reduces contextual hallucination rates (2.8 to 5.8 percent absolute) while revealing how distinct attention heads contribute to evidence alignment. These results highlight feedback-driven interpretability as a pathway toward scientific understanding of LLM behavior.