Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

Jailbreaking? One Step Is Enough!

Large language models (LLMs) excel in various tasks but remain vulnerable to jailbreak attacks, where adversaries manipulate prompts to generate harmful outputs. Examining jailbreak prompts helps uncover the shortcomings of LLMs. However, current jailbreak methods and the target model's defenses are engaged in an independent and adversarial process, resulting in the need for frequent attack iterations and redesigning attacks for different models. To address these gaps, we propose a Reverse Embedded Defense Attack (REDA) mechanism that disguises the attack intention as the "defense". intention against harmful content. Specifically, REDA starts from the target response, guiding the model to embed harmful content within its defensive measures, thereby relegating harmful content to a secondary role and making the model believe it is performing a defensive task. The attacking model considers that it is guiding the target model to deal with harmful content, while the target model thinks it is performing a defensive task, creating an illusion of cooperation between the two. Additionally, to enhance the model's confidence and guidance in "defensive" intentions, we adopt in-context learning (ICL) with a small number of attack examples and construct a corresponding dataset of attack examples. Extensive evaluations demonstrate that the REDA method enables cross-model attacks without the need to redesign attack strategies for different models, enables successful jailbreak in one iteration, and outperforms existing methods on both open-source and closed-source models.

Opportunities and Challenges of Large Language Models for Low-Resource Languages in Humanities Research

Low-resource languages serve as invaluable repositories of human history, embodying cultural evolution and intellectual diversity. Despite their significance, these languages face critical challenges, including data scarcity and technological limitations, which hinder their comprehensive study and preservation. Recent advancements in large language models (LLMs) offer transformative opportunities for addressing these challenges, enabling innovative methodologies in linguistic, historical, and cultural research. This study systematically evaluates the applications of LLMs in low-resource language research, encompassing linguistic variation, historical documentation, cultural expressions, and literary analysis. By analyzing technical frameworks, current methodologies, and ethical considerations, this paper identifies key challenges such as data accessibility, model adaptability, and cultural sensitivity. Given the cultural, historical, and linguistic richness inherent in low-resource languages, this work emphasizes interdisciplinary collaboration and the development of customized models as promising avenues for advancing research in this domain. By underscoring the potential of integrating artificial intelligence with the humanities to preserve and study humanity's linguistic and cultural heritage, this study fosters global efforts towards safeguarding intellectual diversity.

QueEn: A Large Language Model for Quechua-English Translation

Recent studies show that large language models (LLMs) are powerful tools for working with natural language, bringing advances in many areas of computational linguistics. However, these models face challenges when applied to low-resource languages due to limited training data and difficulty in understanding cultural nuances. In this paper, we propose QueEn, a novel approach for Quechua-English translation that combines Retrieval-Augmented Generation (RAG) with parameter-efficient fine-tuning techniques. Our method leverages external linguistic resources through RAG and uses Low-Rank Adaptation (LoRA) for efficient model adaptation. Experimental results show that our approach substantially exceeds baseline models, with a BLEU score of 17.6 compared to 1.5 for standard GPT models. The integration of RAG with fine-tuning allows our system to address the challenges of low-resource language translation while maintaining computational efficiency. This work contributes to the broader goal of preserving endangered languages through advanced language technologies.

DRiVE: Diffusion-based Rigging Empowers Generation of Versatile and Expressive Characters

Recent advances in generative models have enabled high-quality 3D character reconstruction from multi-modal. However, animating these generated characters remains a challenging task, especially for complex elements like garments and hair, due to the lack of large-scale datasets and effective rigging methods. To address this gap, we curate AnimeRig, a large-scale dataset with detailed skeleton and skinning annotations. Building upon this, we propose DRiVE, a novel framework for generating and rigging 3D human characters with intricate structures. Unlike existing methods, DRiVE utilizes a 3D Gaussian representation, facilitating efficient animation and high-quality rendering. We further introduce GSDiff, a 3D Gaussian-based diffusion module that predicts joint positions as spatial distributions, overcoming the limitations of regression-based approaches. Extensive experiments demonstrate that DRiVE achieves precise rigging results, enabling realistic dynamics for clothing and hair, and surpassing previous methods in both quality and versatility. The code and dataset will be made public for academic use upon acceptance.

OracleSage: Towards Unified Visual-Linguistic Understanding of Oracle Bone Scripts through Cross-Modal Knowledge Fusion

Oracle bone script (OBS), as China's earliest mature writing system, present significant challenges in automatic recognition due to their complex pictographic structures and divergence from modern Chinese characters. We introduce OracleSage, a novel cross-modal framework that integrates hierarchical visual understanding with graph-based semantic reasoning. Specifically, we propose (1) a Hierarchical Visual-Semantic Understanding module that enables multi-granularity feature extraction through progressive fine-tuning of LLaVA's visual backbone, (2) a Graph-based Semantic Reasoning Framework that captures relationships between visual components and semantic concepts through dynamic message passing, and (3) OracleSem, a semantically enriched OBS dataset with comprehensive pictographic and semantic annotations. Experimental results demonstrate that OracleSage significantly outperforms state-of-the-art vision-language models. This research establishes a new paradigm for ancient text interpretation while providing valuable technical support for archaeological studies.

Transcending Language Boundaries: Harnessing LLMs for Low-Resource Language Translation

Large Language Models (LLMs) have demonstrated remarkable success across a wide range of tasks and domains. However, their performance in low-resource language translation, particularly when translating into these languages, remains underexplored. This gap poses significant challenges, as linguistic barriers hinder the cultural preservation and development of minority communities. To address this issue, this paper introduces a novel retrieval-based method that enhances translation quality for low-resource languages by focusing on key terms, which involves translating keywords and retrieving corresponding examples from existing data. To evaluate the effectiveness of this method, we conducted experiments translating from English into three low-resource languages: Cherokee, a critically endangered indigenous language of North America; Tibetan, a historically and culturally significant language in Asia; and Manchu, a language with few remaining speakers. Our comparison with the zero-shot performance of GPT-4o and LLaMA 3.1 405B, highlights the significant challenges these models face when translating into low-resource languages. In contrast, our retrieval-based method shows promise in improving both word-level accuracy and overall semantic understanding by leveraging existing resources more effectively.

Towards Next-Generation Medical Agent: How o1 is Reshaping Decision-Making in Medical Scenarios

Artificial Intelligence (AI) has become essential in modern healthcare, with large language models (LLMs) offering promising advances in clinical decision-making. Traditional model-based approaches, including those leveraging in-context demonstrations and those with specialized medical fine-tuning, have demonstrated strong performance in medical language processing but struggle with real-time adaptability, multi-step reasoning, and handling complex medical tasks. Agent-based AI systems address these limitations by incorporating reasoning traces, tool selection based on context, knowledge retrieval, and both short- and long-term memory. These additional features enable the medical AI agent to handle complex medical scenarios where decision-making should be built on real-time interaction with the environment. Therefore, unlike conventional model-based approaches that treat medical queries as isolated questions, medical AI agents approach them as complex tasks and behave more like human doctors. In this paper, we study the choice of the backbone LLM for medical AI agents, which is the foundation for the agent's overall reasoning and action generation. In particular, we consider the emergent o1 model and examine its impact on agents' reasoning, tool-use adaptability, and real-time information retrieval across diverse clinical scenarios, including high-stakes settings such as intensive care units (ICUs). Our findings demonstrate o1's ability to enhance diagnostic accuracy and consistency, paving the way for smarter, more responsive AI tools that support better patient outcomes and decision-making efficacy in clinical practice.

Legal Evalutions and Challenges of Large Language Models

In this paper, we review legal testing methods based on Large Language Models (LLMs), using the OPENAI o1 model as a case study to evaluate the performance of large models in applying legal provisions. We compare current state-of-the-art LLMs, including open-source, closed-source, and legal-specific models trained specifically for the legal domain. Systematic tests are conducted on English and Chinese legal cases, and the results are analyzed in depth. Through systematic testing of legal cases from common law systems and China, this paper explores the strengths and weaknesses of LLMs in understanding and applying legal texts, reasoning through legal issues, and predicting judgments. The experimental results highlight both the potential and limitations of LLMs in legal applications, particularly in terms of challenges related to the interpretation of legal language and the accuracy of legal reasoning. Finally, the paper provides a comprehensive analysis of the advantages and disadvantages of various types of models, offering valuable insights and references for the future application of AI in the legal field.

ReLayout: Towards Real-World Document Understanding via Layout-enhanced Pre-training

Recent approaches for visually-rich document understanding (VrDU) uses manually annotated semantic groups, where a semantic group encompasses all semantically relevant but not obviously grouped words. As OCR tools are unable to automatically identify such grouping, we argue that current VrDU approaches are unrealistic. We thus introduce a new variant of the VrDU task, real-world visually-rich document understanding (ReVrDU), that does not allow for using manually annotated semantic groups. We also propose a new method, ReLayout, compliant with the ReVrDU scenario, which learns to capture semantic grouping through arranging words and bringing the representations of words that belong to the potential same semantic group closer together. Our experimental results demonstrate the performance of existing methods is deteriorated with the ReVrDU task, while ReLayout shows superiour performance.