Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical challenges in bioinformatics such as the scarcity of annotated data and the presence of data noise. FMs are particularly adept at handling large-scale, unlabeled data, a common scenario in biological contexts due to the time-consuming and costly nature of experimentally determining labeled data. This characteristic has allowed FMs to excel and achieve notable results in various downstream validation tasks, demonstrating their ability to represent diverse biological entities effectively. Undoubtedly, FMs have ushered in a new era in computational biology, especially in the realm of deep learning. The primary goal of this survey is to conduct a systematic investigation and summary of FMs in bioinformatics, tracing their evolution, current research status, and the methodologies employed. Central to our focus is the application of FMs to specific biological problems, aiming to guide the research community in choosing appropriate FMs for their research needs. We delve into the specifics of the problem at hand including sequence analysis, structure prediction, function annotation, and multimodal integration, comparing the structures and advancements against traditional methods. Furthermore, the review analyses challenges and limitations faced by FMs in biology, such as data noise, model explainability, and potential biases. Finally, we outline potential development paths and strategies for FMs in future biological research, setting the stage for continued innovation and application in this rapidly evolving field. This comprehensive review serves not only as an academic resource but also as a roadmap for future explorations and applications of FMs in biology.

Despite the impressive capabilities of large language models (LLMs) across diverse applications, they still suffer from trustworthiness issues, such as hallucinations and misalignments. Retrieval-augmented language models (RAG) have been proposed to enhance the credibility of generations by grounding external knowledge, but the theoretical understandings of their generation risks remains unexplored. In this paper, we answer: 1) whether RAG can indeed lead to low generation risks, 2) how to provide provable guarantees on the generation risks of RAG and vanilla LLMs, and 3) what sufficient conditions enable RAG models to reduce generation risks. We propose C-RAG, the first framework to certify generation risks for RAG models. Specifically, we provide conformal risk analysis for RAG models and certify an upper confidence bound of generation risks, which we refer to as conformal generation risk. We also provide theoretical guarantees on conformal generation risks for general bounded risk functions under test distribution shifts. We prove that RAG achieves a lower conformal generation risk than that of a single LLM when the quality of the retrieval model and transformer is non-trivial. Our intensive empirical results demonstrate the soundness and tightness of our conformal generation risk guarantees across four widely-used NLP datasets on four state-of-the-art retrieval models.

In recent times, significant advancements have been made in the field of large language models (LLMs), represented by GPT series models. To optimize task execution, users often engage in multi-round conversations with GPT models hosted in cloud environments. These multi-round conversations, potentially replete with private information, require transmission and storage within the cloud. However, this operational paradigm introduces additional attack surfaces. In this paper, we first introduce a specific Conversation Reconstruction Attack targeting GPT models. Our introduced Conversation Reconstruction Attack is composed of two steps: hijacking a session and reconstructing the conversations. Subsequently, we offer an exhaustive evaluation of the privacy risks inherent in conversations when GPT models are subjected to the proposed attack. However, GPT-4 demonstrates certain robustness to the proposed attacks. We then introduce two advanced attacks aimed at better reconstructing previous conversations, specifically the UNR attack and the PBU attack. Our experimental findings indicate that the PBU attack yields substantial performance across all models, achieving semantic similarity scores exceeding 0.60, while the UNR attack is effective solely on GPT-3.5. Our results reveal the concern about privacy risks associated with conversations involving GPT models and aim to draw the community's attention to prevent the potential misuse of these models' remarkable capabilities. We will responsibly disclose our findings to the suppliers of related large language models.

Despite their powerful semantic understanding and code generation capabilities, Large Language Models (LLMs) still face challenges when dealing with complex tasks. Multi agent strategy generation and motion control are highly complex domains that inherently require experts from multiple fields to collaborate. To enhance multi agent strategy generation and motion control, we propose an innovative architecture that employs the concept of a cloud edge end hierarchical structure. By leveraging multiple large language models with distinct areas of expertise, we can efficiently generate strategies and perform task decomposition. Introducing the cosine similarity approach,aligning task decomposition instructions with robot task sequences at the vector level, we can identify subtasks with incomplete task decomposition and iterate on them multiple times to ultimately generate executable machine task sequences.The robot is guided through these task sequences to complete tasks of higher complexity. With this architecture, we implement the process of natural language control of robots to perform complex tasks, and successfully address the challenge of multi agent execution of open tasks in open scenarios and the problem of task decomposition.

Despite the remarkable code generation abilities of large language models LLMs, they still face challenges in complex task handling. Robot development, a highly intricate field, inherently demands human involvement in task allocation and collaborative teamwork . To enhance robot development, we propose an innovative automated collaboration framework inspired by real-world robot developers. This framework employs multiple LLMs in distinct roles analysts, programmers, and testers. Analysts delve deep into user requirements, enabling programmers to produce precise code, while testers fine-tune the parameters based on user feedback for practical robot application. Each LLM tackles diverse, critical tasks within the development process. Clear collaboration rules emulate real world teamwork among LLMs. Analysts, programmers, and testers form a cohesive team overseeing strategy, code, and parameter adjustments . Through this framework, we achieve complex robot development without requiring specialized knowledge, relying solely on non experts participation.

Humans make numerous inferences in text comprehension to understand discourse. This paper aims to understand the commonalities and disparities in the inference judgments between humans and state-of-the-art Large Language Models (LLMs). Leveraging a comprehensively curated entailment verification benchmark, we evaluate both human and LLM performance across various reasoning categories. Our benchmark includes datasets from three categories (NLI, contextual QA, and rationales) that include multi-sentence premises and different knowledge types, thereby evaluating the inference capabilities in complex reasoning instances. Notably, our findings reveal LLMs' superiority in multi-hop reasoning across extended contexts, while humans excel in tasks necessitating simple deductive reasoning. Leveraging these insights, we introduce a fine-tuned Flan-T5 model that outperforms GPT-3.5 and rivals with GPT-4, offering a robust open-source solution for entailment verification. As a practical application, we showcase the efficacy of our finetuned model in enhancing self-consistency in model-generated explanations, resulting in a 6% performance boost on average across three multiple-choice question-answering datasets.

The Stanceosaurus corpus (Zheng et al., 2022) was designed to provide high-quality, annotated, 5-way stance data extracted from Twitter, suitable for analyzing cross-cultural and cross-lingual misinformation. In the Stanceosaurus 2.0 iteration, we extend this framework to encompass Russian and Spanish. The former is of current significance due to prevalent misinformation amid escalating tensions with the West and the violent incursion into Ukraine. The latter, meanwhile, represents an enormous community that has been largely overlooked on major social media platforms. By incorporating an additional 3,874 Spanish and Russian tweets over 41 misinformation claims, our objective is to support research focused on these issues. To demonstrate the value of this data, we employed zero-shot cross-lingual transfer on multilingual BERT, yielding results on par with the initial Stanceosaurus study with a macro F1 score of 43 for both languages. This underlines the viability of stance classification as an effective tool for identifying multicultural misinformation.

Large Language Models (LLMs) have achieved remarkable success in code completion, as evidenced by their essential roles in developing code assistant services such as Copilot. Being trained on in-file contexts, current LLMs are quite effective in completing code for single source files. However, it is challenging for them to conduct repository-level code completion for large software projects that require cross-file information. Existing research on LLM-based repository-level code completion identifies and integrates cross-file contexts, but it suffers from low accuracy and limited context length of LLMs. In this paper, we argue that Integrated Development Environments (IDEs) can provide direct, accurate and real-time cross-file information for repository-level code completion. We propose IDECoder, a practical framework that leverages IDE native static contexts for cross-context construction and diagnosis results for self-refinement. IDECoder utilizes the rich cross-context information available in IDEs to enhance the capabilities of LLMs of repository-level code completion. We conducted preliminary experiments to validate the performance of IDECoder and observed that this synergy represents a promising trend for future exploration.

The advent of large language models (LLMs) such as ChatGPT, PaLM, and GPT-4 has catalyzed remarkable advances in natural language processing, demonstrating human-like language fluency and reasoning capacities. This position paper introduces the concept of Professional Agents (PAgents), an application framework harnessing LLM capabilities to create autonomous agents with controllable, specialized, interactive, and professional-level competencies. We posit that PAgents can reshape professional services through continuously developed expertise. Our proposed PAgents framework entails a tri-layered architecture for genesis, evolution, and synergy: a base tool layer, a middle agent layer, and a top synergy layer. This paper aims to spur discourse on promising real-world applications of LLMs. We argue the increasing sophistication and integration of PAgents could lead to AI systems exhibiting professional mastery over complex domains, serving critical needs, and potentially achieving artificial general intelligence.

As Large Language Models make a breakthrough in natural language processing tasks (NLP), multimodal technique becomes extremely popular. However, it has been shown that multimodal NLP are vulnerable to adversarial attacks, where the outputs of a model can be dramatically changed by a perturbation to the input. While several defense techniques have been proposed both in computer vision and NLP models, the multimodal robustness of models have not been fully explored. In this paper, we study the adversarial robustness provided by modifying loss function of pre-trained multimodal models, by restricting top K softmax outputs. Based on the evaluation and scoring, our experiments show that after a fine-tuning, adversarial robustness of pre-trained models can be significantly improved, against popular attacks. Further research should be studying, such as output diversity, generalization and the robustness-performance trade-off of this kind of loss functions. Our code will be available after this paper is accepted