AD-GPT: Large Language Models in Alzheimer's Disease

Large language models (LLMs) have emerged as powerful tools for medical information retrieval, yet their accuracy and depth remain limited in specialized domains such as Alzheimer's disease (AD), a growing global health challenge. To address this gap, we introduce AD-GPT, a domain-specific generative pre-trained transformer designed to enhance the retrieval and analysis of AD-related genetic and neurobiological information. AD-GPT integrates diverse biomedical data sources, including potential AD-associated genes, molecular genetic information, and key gene variants linked to brain regions. We develop a stacked LLM architecture combining Llama3 and BERT, optimized for four critical tasks in AD research: (1) genetic information retrieval, (2) gene-brain region relationship assessment, (3) gene-AD relationship analysis, and (4) brain region-AD relationship mapping. Comparative evaluations against state-of-the-art LLMs demonstrate AD-GPT's superior precision and reliability across these tasks, underscoring its potential as a robust and specialized AI tool for advancing AD research and biomarker discovery.

Advances and Challenges in Foundation Agents: From Brain-Inspired Intelligence to Evolutionary, Collaborative, and Safe Systems

The advent of large language models (LLMs) has catalyzed a transformative shift in artificial intelligence, paving the way for advanced intelligent agents capable of sophisticated reasoning, robust perception, and versatile action across diverse domains. As these agents increasingly drive AI research and practical applications, their design, evaluation, and continuous improvement present intricate, multifaceted challenges. This survey provides a comprehensive overview, framing intelligent agents within a modular, brain-inspired architecture that integrates principles from cognitive science, neuroscience, and computational research. We structure our exploration into four interconnected parts. First, we delve into the modular foundation of intelligent agents, systematically mapping their cognitive, perceptual, and operational modules onto analogous human brain functionalities, and elucidating core components such as memory, world modeling, reward processing, and emotion-like systems. Second, we discuss self-enhancement and adaptive evolution mechanisms, exploring how agents autonomously refine their capabilities, adapt to dynamic environments, and achieve continual learning through automated optimization paradigms, including emerging AutoML and LLM-driven optimization strategies. Third, we examine collaborative and evolutionary multi-agent systems, investigating the collective intelligence emerging from agent interactions, cooperation, and societal structures, highlighting parallels to human social dynamics. Finally, we address the critical imperative of building safe, secure, and beneficial AI systems, emphasizing intrinsic and extrinsic security threats, ethical alignment, robustness, and practical mitigation strategies necessary for trustworthy real-world deployment.

GyralNet Subnetwork Partitioning via Differentiable Spectral Modularity Optimization

Understanding the structural and functional organization of the human brain requires a detailed examination of cortical folding patterns, among which the three-hinge gyrus (3HG) has been identified as a key structural landmark. GyralNet, a network representation of cortical folding, models 3HGs as nodes and gyral crests as edges, highlighting their role as critical hubs in cortico-cortical connectivity. However, existing methods for analyzing 3HGs face significant challenges, including the sub-voxel scale of 3HGs at typical neuroimaging resolutions, the computational complexity of establishing cross-subject correspondences, and the oversimplification of treating 3HGs as independent nodes without considering their community-level relationships. To address these limitations, we propose a fully differentiable subnetwork partitioning framework that employs a spectral modularity maximization optimization strategy to modularize the organization of 3HGs within GyralNet. By incorporating topological structural similarity and DTI-derived connectivity patterns as attribute features, our approach provides a biologically meaningful representation of cortical organization. Extensive experiments on the Human Connectome Project (HCP) dataset demonstrate that our method effectively partitions GyralNet at the individual level while preserving the community-level consistency of 3HGs across subjects, offering a robust foundation for understanding brain connectivity.

Bridging Technology and Humanities: Evaluating the Impact of Large Language Models on Social Sciences Research with DeepSeek-R1

In recent years, the development of Large Language Models (LLMs) has made significant breakthroughs in the field of natural language processing and has gradually been applied to the field of humanities and social sciences research. LLMs have a wide range of application value in the field of humanities and social sciences because of its strong text understanding, generation and reasoning capabilities. In humanities and social sciences research, LLMs can analyze large-scale text data and make inferences. This article analyzes the large language model DeepSeek-R1 from seven aspects: low-resource language translation, educational question-answering, student writing improvement in higher education, logical reasoning, educational measurement and psychometrics, public health policy analysis, and art education.Then we compare the answers given by DeepSeek-R1 in the seven aspects with the answers given by o1-preview. DeepSeek-R1 performs well in the humanities and social sciences, answering most questions correctly and logically, and can give reasonable analysis processes and explanations. Compared with o1-preview, it can automatically generate reasoning processes and provide more detailed explanations, which is suitable for beginners or people who need to have a detailed understanding of this knowledge, while o1-preview is more suitable for quick reading. Through analysis, it is found that LLM has broad application potential in the field of humanities and social sciences, and shows great advantages in improving text analysis efficiency, language communication and other fields. LLM's powerful language understanding and generation capabilities enable it to deeply explore complex problems in the field of humanities and social sciences, and provide innovative tools for academic research and practical applications.

Core-Periphery Principle Guided State Space Model for Functional Connectome Classification

Understanding the organization of human brain networks has become a central focus in neuroscience, particularly in the study of functional connectivity, which plays a crucial role in diagnosing neurological disorders. Advances in functional magnetic resonance imaging and machine learning techniques have significantly improved brain network analysis. However, traditional machine learning approaches struggle to capture the complex relationships between brain regions, while deep learning methods, particularly Transformer-based models, face computational challenges due to their quadratic complexity in long-sequence modeling. To address these limitations, we propose a Core-Periphery State-Space Model (CP-SSM), an innovative framework for functional connectome classification. Specifically, we introduce Mamba, a selective state-space model with linear complexity, to effectively capture long-range dependencies in functional brain networks. Furthermore, inspired by the core-periphery (CP) organization, a fundamental characteristic of brain networks that enhances efficient information transmission, we design CP-MoE, a CP-guided Mixture-of-Experts that improves the representation learning of brain connectivity patterns. We evaluate CP-SSM on two benchmark fMRI datasets: ABIDE and ADNI. Experimental results demonstrate that CP-SSM surpasses Transformer-based models in classification performance while significantly reducing computational complexity. These findings highlight the effectiveness and efficiency of CP-SSM in modeling brain functional connectivity, offering a promising direction for neuroimaging-based neurological disease diagnosis.

Unveiling the Mathematical Reasoning in DeepSeek Models: A Comparative Study of Large Language Models

With the rapid evolution of Artificial Intelligence (AI), Large Language Models (LLMs) have reshaped the frontiers of various fields, spanning healthcare, public health, engineering, science, agriculture, education, arts, humanities, and mathematical reasoning. Among these advancements, DeepSeek models have emerged as noteworthy contenders, demonstrating promising capabilities that set them apart from their peers. While previous studies have conducted comparative analyses of LLMs, few have delivered a comprehensive evaluation of mathematical reasoning across a broad spectrum of LLMs. In this work, we aim to bridge this gap by conducting an in-depth comparative study, focusing on the strengths and limitations of DeepSeek models in relation to their leading counterparts. In particular, our study systematically evaluates the mathematical reasoning performance of two DeepSeek models alongside five prominent LLMs across three independent benchmark datasets. The findings reveal several key insights: 1). DeepSeek-R1 consistently achieved the highest accuracy on two of the three datasets, demonstrating strong mathematical reasoning capabilities. 2). The distilled variant of LLMs significantly underperformed compared to its peers, highlighting potential drawbacks in using distillation techniques. 3). In terms of response time, Gemini 2.0 Flash demonstrated the fastest processing speed, outperforming other models in efficiency, which is a crucial factor for real-time applications. Beyond these quantitative assessments, we delve into how architecture, training, and optimization impact LLMs' mathematical reasoning. Moreover, our study goes beyond mere performance comparison by identifying key areas for future advancements in LLM-driven mathematical reasoning. This research enhances our understanding of LLMs' mathematical reasoning and lays the groundwork for future advancements

From Task-Specific Models to Unified Systems: A Review of Model Merging Approaches

Model merging has achieved significant success, with numerous innovative methods proposed to enhance capabilities by combining multiple models. However, challenges persist due to the lack of a unified framework for classification and systematic comparative analysis, leading to inconsistencies in terminologies and categorizations. Meanwhile, as an increasing number of fine-tuned models are publicly available, their original training data often remain inaccessible due to privacy concerns or intellectual property restrictions. This makes traditional multi-task learning based on shared training data impractical. In scenarios where direct access to training data is infeasible, merging model parameters to create a unified model with broad generalization across multiple domains becomes crucial, further underscoring the importance of model merging techniques. Despite the rapid progress in this field, a comprehensive taxonomy and survey summarizing recent advances and predicting future directions are still lacking. This paper addresses these gaps by establishing a new taxonomy of model merging methods, systematically comparing different approaches, and providing an overview of key developments. By offering a structured perspective on this evolving area, we aim to help newcomers quickly grasp the field's landscape and inspire further innovations.

A Survey on Post-training of Large Language Models

The emergence of Large Language Models (LLMs) has fundamentally transformed natural language processing, making them indispensable across domains ranging from conversational systems to scientific exploration. However, their pre-trained architectures often reveal limitations in specialized contexts, including restricted reasoning capacities, ethical uncertainties, and suboptimal domain-specific performance. These challenges necessitate advanced post-training language models (PoLMs) to address these shortcomings, such as OpenAI-o1/o3 and DeepSeek-R1 (collectively known as Large Reasoning Models, or LRMs). This paper presents the first comprehensive survey of PoLMs, systematically tracing their evolution across five core paradigms: Fine-tuning, which enhances task-specific accuracy; Alignment, which ensures alignment with human preferences; Reasoning, which advances multi-step inference despite challenges in reward design; Efficiency, which optimizes resource utilization amidst increasing complexity; and Integration and Adaptation, which extend capabilities across diverse modalities while addressing coherence issues. Charting progress from ChatGPT's foundational alignment strategies to DeepSeek-R1's innovative reasoning advancements, we illustrate how PoLMs leverage datasets to mitigate biases, deepen reasoning capabilities, and enhance domain adaptability. Our contributions include a pioneering synthesis of PoLM evolution, a structured taxonomy categorizing techniques and datasets, and a strategic agenda emphasizing the role of LRMs in improving reasoning proficiency and domain flexibility. As the first survey of its scope, this work consolidates recent PoLM advancements and establishes a rigorous intellectual framework for future research, fostering the development of LLMs that excel in precision, ethical robustness, and versatility across scientific and societal applications.

A Practical Memory Injection Attack against LLM Agents

Agents based on large language models (LLMs) have demonstrated strong capabilities in a wide range of complex, real-world applications. However, LLM agents with a compromised memory bank may easily produce harmful outputs when the past records retrieved for demonstration are malicious. In this paper, we propose a novel Memory INJection Attack, MINJA, that enables the injection of malicious records into the memory bank by only interacting with the agent via queries and output observations. These malicious records are designed to elicit a sequence of malicious reasoning steps leading to undesirable agent actions when executing the victim user's query. Specifically, we introduce a sequence of bridging steps to link the victim query to the malicious reasoning steps. During the injection of the malicious record, we propose an indication prompt to guide the agent to autonomously generate our designed bridging steps. We also propose a progressive shortening strategy that gradually removes the indication prompt, such that the malicious record will be easily retrieved when processing the victim query comes after. Our extensive experiments across diverse agents demonstrate the effectiveness of MINJA in compromising agent memory. With minimal requirements for execution, MINJA enables any user to influence agent memory, highlighting practical risks of LLM agents.

SearchRAG: Can Search Engines Be Helpful for LLM-based Medical Question Answering?

Large Language Models (LLMs) have shown remarkable capabilities in general domains but often struggle with tasks requiring specialized knowledge. Conventional Retrieval-Augmented Generation (RAG) techniques typically retrieve external information from static knowledge bases, which can be outdated or incomplete, missing fine-grained clinical details essential for accurate medical question answering. In this work, we propose SearchRAG, a novel framework that overcomes these limitations by leveraging real-time search engines. Our method employs synthetic query generation to convert complex medical questions into search-engine-friendly queries and utilizes uncertainty-based knowledge selection to filter and incorporate the most relevant and informative medical knowledge into the LLM's input. Experimental results demonstrate that our method significantly improves response accuracy in medical question answering tasks, particularly for complex questions requiring detailed and up-to-date knowledge.