From Intention To Implementation: Automating Biomedical Research via LLMs

Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to revolutionize this process by automating various steps. Still, significant challenges remain, including the need for multidisciplinary expertise, logicality of experimental design, and performance measurements. This paper introduces BioResearcher, the first end-to-end automated system designed to streamline the entire biomedical research process involving dry lab experiments. BioResearcher employs a modular multi-agent architecture, integrating specialized agents for search, literature processing, experimental design, and programming. By decomposing complex tasks into logically related sub-tasks and utilizing a hierarchical learning approach, BioResearcher effectively addresses the challenges of multidisciplinary requirements and logical complexity. Furthermore, BioResearcher incorporates an LLM-based reviewer for in-process quality control and introduces novel evaluation metrics to assess the quality and automation of experimental protocols. BioResearcher successfully achieves an average execution success rate of 63.07% across eight previously unmet research objectives. The generated protocols averagely outperform typical agent systems by 22.0% on five quality metrics. The system demonstrates significant potential to reduce researchers' workloads and accelerate biomedical discoveries, paving the way for future innovations in automated research systems.

Infant Agent: A Tool-Integrated, Logic-Driven Agent with Cost-Effective API Usage

Despite the impressive capabilities of large language models (LLMs), they currently exhibit two primary limitations, \textbf{\uppercase\expandafter{\romannumeral 1}}: They struggle to \textbf{autonomously solve the real world engineering problem}. \textbf{\uppercase\expandafter{\romannumeral 2}}: They remain \textbf{challenged in reasoning through complex logic problems}. To address these challenges, we developed the \textsc{Infant Agent}, integrating task-aware functions, operators, a hierarchical management system, and a memory retrieval mechanism. Together, these components enable large language models to sustain extended reasoning processes and handle complex, multi-step tasks efficiently, all while significantly reducing API costs. Using the \textsc{Infant Agent}, GPT-4o's accuracy on the SWE-bench-lite dataset rises from $\mathbf{0.33\%}$ to $\mathbf{30\%}$, and in the AIME-2024 mathematics competition, it increases GPT-4o's accuracy from $\mathbf{13.3\%}$ to $\mathbf{37\%}$.

Systematically Analyzing Prompt Injection Vulnerabilities in Diverse LLM Architectures

This study systematically analyzes the vulnerability of 36 large language models (LLMs) to various prompt injection attacks, a technique that leverages carefully crafted prompts to elicit malicious LLM behavior. Across 144 prompt injection tests, we observed a strong correlation between model parameters and vulnerability, with statistical analyses, such as logistic regression and random forest feature analysis, indicating that parameter size and architecture significantly influence susceptibility. Results revealed that 56 percent of tests led to successful prompt injections, emphasizing widespread vulnerability across various parameter sizes, with clustering analysis identifying distinct vulnerability profiles associated with specific model configurations. Additionally, our analysis uncovered correlations between certain prompt injection techniques, suggesting potential overlaps in vulnerabilities. These findings underscore the urgent need for robust, multi-layered defenses in LLMs deployed across critical infrastructure and sensitive industries. Successful prompt injection attacks could result in severe consequences, including data breaches, unauthorized access, or misinformation. Future research should explore multilingual and multi-step defenses alongside adaptive mitigation strategies to strengthen LLM security in diverse, real-world environments.

Apollo: Band-sequence Modeling for High-Quality Audio Restoration

Audio restoration has become increasingly significant in modern society, not only due to the demand for high-quality auditory experiences enabled by advanced playback devices, but also because the growing capabilities of generative audio models necessitate high-fidelity audio. Typically, audio restoration is defined as a task of predicting undistorted audio from damaged input, often trained using a GAN framework to balance perception and distortion. Since audio degradation is primarily concentrated in mid- and high-frequency ranges, especially due to codecs, a key challenge lies in designing a generator capable of preserving low-frequency information while accurately reconstructing high-quality mid- and high-frequency content. Inspired by recent advancements in high-sample-rate music separation, speech enhancement, and audio codec models, we propose Apollo, a generative model designed for high-sample-rate audio restoration. Apollo employs an explicit frequency band split module to model the relationships between different frequency bands, allowing for more coherent and higher-quality restored audio. Evaluated on the MUSDB18-HQ and MoisesDB datasets, Apollo consistently outperforms existing SR-GAN models across various bit rates and music genres, particularly excelling in complex scenarios involving mixtures of multiple instruments and vocals. Apollo significantly improves music restoration quality while maintaining computational efficiency. The source code for Apollo is publicly available at https://github.com/JusperLee/Apollo.

Revolutionizing Database Q&A with Large Language Models: Comprehensive Benchmark and Evaluation

The development of Large Language Models (LLMs) has revolutionized Q&A across various industries, including the database domain. However, there is still a lack of a comprehensive benchmark to evaluate the capabilities of different LLMs and their modular components in database Q&A. To this end, we introduce DQA, the first comprehensive database Q&A benchmark. DQA features an innovative LLM-based method for automating the generation, cleaning, and rewriting of database Q&A, resulting in over 240,000 Q&A pairs in English and Chinese. These Q&A pairs cover nearly all aspects of database knowledge, including database manuals, database blogs, and database tools. This inclusion allows for additional assessment of LLMs' Retrieval-Augmented Generation (RAG) and Tool Invocation Generation (TIG) capabilities in the database Q&A task. Furthermore, we propose a comprehensive LLM-based database Q&A testbed on DQA. This testbed is highly modular and scalable, with both basic and advanced components like Question Classification Routing (QCR), RAG, TIG, and Prompt Template Engineering (PTE). Besides, DQA provides a complete evaluation pipeline, featuring diverse metrics and a standardized evaluation process to ensure comprehensiveness, accuracy, and fairness. We use DQA to evaluate the database Q&A capabilities under the proposed testbed comprehensively. The evaluation reveals findings like (i) the strengths and limitations of nine different LLM-based Q&A bots and (ii) the performance impact and potential improvements of various service components (e.g., QCR, RAG, TIG). We hope our benchmark and findings will better guide the future development of LLM-based database Q&A research.

Xinyu: An Efficient LLM-based System for Commentary Generation

Commentary provides readers with a deep understanding of events by presenting diverse arguments and evidence. However, creating commentary is a time-consuming task, even for skilled commentators. Large language models (LLMs) have simplified the process of natural language generation, but their direct application in commentary creation still faces challenges due to unique task requirements. These requirements can be categorized into two levels: 1) fundamental requirements, which include creating well-structured and logically consistent narratives, and 2) advanced requirements, which involve generating quality arguments and providing convincing evidence. In this paper, we introduce Xinyu, an efficient LLM-based system designed to assist commentators in generating Chinese commentaries. To meet the fundamental requirements, we deconstruct the generation process into sequential steps, proposing targeted strategies and supervised fine-tuning (SFT) for each step. To address the advanced requirements, we present an argument ranking model for arguments and establish a comprehensive evidence database that includes up-to-date events and classic books, thereby strengthening the substantiation of the evidence with retrieval augmented generation (RAG) technology. To evaluate the generated commentaries more fairly, corresponding to the two-level requirements, we introduce a comprehensive evaluation metric that considers five distinct perspectives in commentary generation. Our experiments confirm the effectiveness of our proposed system. We also observe a significant increase in the efficiency of commentators in real-world scenarios, with the average time spent on creating a commentary dropping from 4 hours to 20 minutes. Importantly, such an increase in efficiency does not compromise the quality of the commentaries.

RepNeXt: A Fast Multi-Scale CNN using Structural Reparameterization

In the realm of resource-constrained mobile vision tasks, the pursuit of efficiency and performance consistently drives innovation in lightweight Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs). While ViTs excel at capturing global context through self-attention mechanisms, their deployment in resource-limited environments is hindered by computational complexity and latency. Conversely, lightweight CNNs are favored for their parameter efficiency and low latency. This study investigates the complementary advantages of CNNs and ViTs to develop a versatile vision backbone tailored for resource-constrained applications. We introduce RepNeXt, a novel model series integrates multi-scale feature representations and incorporates both serial and parallel structural reparameterization (SRP) to enhance network depth and width without compromising inference speed. Extensive experiments demonstrate RepNeXt's superiority over current leading lightweight CNNs and ViTs, providing advantageous latency across various vision benchmarks. RepNeXt-M4 matches RepViT-M1.5's 82.3\% accuracy on ImageNet within 1.5ms on an iPhone 12, outperforms its AP$^{box}$ by 1.1 on MS-COCO, and reduces parameters by 0.7M. Codes and models are available at https://github.com/suous/RepNeXt.

Semantic-Rearrangement-Based Multi-Level Alignment for Domain Generalized Segmentation

Domain generalized semantic segmentation is an essential computer vision task, for which models only leverage source data to learn the capability of generalized semantic segmentation towards the unseen target domains. Previous works typically address this challenge by global style randomization or feature regularization. In this paper, we argue that given the observation that different local semantic regions perform different visual characteristics from the source domain to the target domain, methods focusing on global operations are hard to capture such regional discrepancies, thus failing to construct domain-invariant representations with the consistency from local to global level. Therefore, we propose the Semantic-Rearrangement-based Multi-Level Alignment (SRMA) to overcome this problem. SRMA first incorporates a Semantic Rearrangement Module (SRM), which conducts semantic region randomization to enhance the diversity of the source domain sufficiently. A Multi-Level Alignment module (MLA) is subsequently proposed with the help of such diversity to establish the global-regional-local consistent domain-invariant representations. By aligning features across randomized samples with domain-neutral knowledge at multiple levels, SRMA provides a more robust way to handle the source-target domain gap. Extensive experiments demonstrate the superiority of SRMA over the current state-of-the-art works on various benchmarks.

Reasoning on Efficient Knowledge Paths:Knowledge Graph Guides Large Language Model for Domain Question Answering

Large language models (LLMs), such as GPT3.5, GPT4 and LLAMA2 perform surprisingly well and outperform human experts on many tasks. However, in many domain-specific evaluations, these LLMs often suffer from hallucination problems due to insufficient training of relevant corpus. Furthermore, fine-tuning large models may face problems such as the LLMs are not open source or the construction of high-quality domain instruction is difficult. Therefore, structured knowledge databases such as knowledge graph can better provide domain background knowledge for LLMs and make full use of the reasoning and analysis capabilities of LLMs. In some previous works, LLM was called multiple times to determine whether the current triplet was suitable for inclusion in the subgraph when retrieving subgraphs through a question. Especially for the question that require a multi-hop reasoning path, frequent calls to LLM will consume a lot of computing power. Moreover, when choosing the reasoning path, LLM will be called once for each step, and if one of the steps is selected incorrectly, it will lead to the accumulation of errors in the following steps. In this paper, we integrated and optimized a pipeline for selecting reasoning paths from KG based on LLM, which can reduce the dependency on LLM. In addition, we propose a simple and effective subgraph retrieval method based on chain of thought (CoT) and page rank which can returns the paths most likely to contain the answer. We conduct experiments on three datasets: GenMedGPT-5k [14], WebQuestions [2], and CMCQA [21]. Finally, RoK can demonstrate that using fewer LLM calls can achieve the same results as previous SOTAs models.

Gull: A Generative Multifunctional Audio Codec

We introduce Gull, a generative multifunctional audio codec. Gull is a general purpose neural audio compression and decompression model which can be applied to a wide range of tasks and applications such as real-time communication, audio super-resolution, and codec language models. The key components of Gull include (1) universal-sample-rate modeling via subband modeling schemes motivated by recent progress in audio source separation, (2) gain-shape representations motivated by traditional audio codecs, (3) improved residual vector quantization modules for simpler training, (4) elastic decoder network that enables user-defined model size and complexity during inference time, (5) built-in ability for audio super-resolution without the increase of bitrate. We compare Gull with existing traditional and neural audio codecs and show that Gull is able to achieve on par or better performance across various sample rates, bitrates and model complexities in both subjective and objective evaluation metrics.