LogicVista: Multimodal LLM Logical Reasoning Benchmark in Visual Contexts

We propose LogicVista, an evaluation benchmark that assesses the integrated logical reasoning capabilities of multimodal large language models (MLLMs) in Visual contexts. Recent advancements in MLLMs have demonstrated various fascinating abilities, from crafting poetry based on an image to performing mathematical reasoning. However, there is still a lack of systematic evaluation of MLLMs' proficiency in logical reasoning tasks, which are essential for activities like navigation and puzzle-solving. Thus we evaluate general logical cognition abilities across 5 logical reasoning tasks encompassing 9 different capabilities, using a sample of 448 multiple-choice questions. Each question is annotated with the correct answer and the human-written reasoning behind the selection, enabling both open-ended and multiple-choice evaluation. A total of 8 MLLMs are comprehensively evaluated using LogicVista. Code and Data Available at https://github.com/Yijia-Xiao/LogicVista.

Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible.

AgentReview: Exploring Peer Review Dynamics with LLM Agents

Peer review is fundamental to the integrity and advancement of scientific publication. Traditional methods of peer review analyses often rely on exploration and statistics of existing peer review data, which do not adequately address the multivariate nature of the process, account for the latent variables, and are further constrained by privacy concerns due to the sensitive nature of the data. We introduce AgentReview, the first large language model (LLM) based peer review simulation framework, which effectively disentangles the impacts of multiple latent factors and addresses the privacy issue. Our study reveals significant insights, including a notable 37.1% variation in paper decisions due to reviewers' biases, supported by sociological theories such as the social influence theory, altruism fatigue, and authority bias. We believe that this study could offer valuable insights to improve the design of peer review mechanisms.

Deconstructing The Ethics of Large Language Models from Long-standing Issues to New-emerging Dilemmas

Large Language Models (LLMs) have achieved unparalleled success across diverse language modeling tasks in recent years. However, this progress has also intensified ethical concerns, impacting the deployment of LLMs in everyday contexts. This paper provides a comprehensive survey of ethical challenges associated with LLMs, from longstanding issues such as copyright infringement, systematic bias, and data privacy, to emerging problems like truthfulness and social norms. We critically analyze existing research aimed at understanding, examining, and mitigating these ethical risks. Our survey underscores integrating ethical standards and societal values into the development of LLMs, thereby guiding the development of responsible and ethically aligned language models.

PGraphDTA: Improving Drug Target Interaction Prediction using Protein Language Models and Contact Maps

Developing and discovering new drugs is a complex and resource-intensive endeavor that often involves substantial costs, time investment, and safety concerns. A key aspect of drug discovery involves identifying novel drug-target (DT) interactions. Existing computational methods for predicting DT interactions have primarily focused on binary classification tasks, aiming to determine whether a DT pair interacts or not. However, protein-ligand interactions exhibit a continuum of binding strengths, known as binding affinity, presenting a persistent challenge for accurate prediction. In this study, we investigate various techniques employed in Drug Target Interaction (DTI) prediction and propose novel enhancements to enhance their performance. Our approaches include the integration of Protein Language Models (PLMs) and the incorporation of Contact Map information as an inductive bias within current models. Through extensive experimentation, we demonstrate that our proposed approaches outperform the baseline models considered in this study, presenting a compelling case for further development in this direction. We anticipate that the insights gained from this work will significantly narrow the search space for potential drugs targeting specific proteins, thereby accelerating drug discovery. Code and data for PGraphDTA are available at https://anonymous.4open.science/r/PGraphDTA.

Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

Knowledge graphs (KGs) have emerged as a powerful framework for representing and integrating complex biomedical information. However, assembling KGs from diverse sources remains a significant challenge in several aspects, including entity alignment, scalability, and the need for continuous updates to keep pace with scientific advancements. Moreover, the representative power of KGs is often limited by the scarcity of multi-modal data integration. To overcome these challenges, we propose Know2BIO, a general-purpose heterogeneous KG benchmark for the biomedical domain. Know2BIO integrates data from 30 diverse sources, capturing intricate relationships across 11 biomedical categories. It currently consists of ~219,000 nodes and ~6,200,000 edges. Know2BIO is capable of user-directed automated updating to reflect the latest knowledge in biomedical science. Furthermore, Know2BIO is accompanied by multi-modal data: node features including text descriptions, protein and compound sequences and structures, enabling the utilization of emerging natural language processing methods and multi-modal data integration strategies. We evaluate KG representation models on Know2BIO, demonstrating its effectiveness as a benchmark for KG representation learning in the biomedical field. Data and source code of Know2BIO are available at https://github.com/Yijia-Xiao/Know2BIO/.

Large Language Models Can Be Good Privacy Protection Learners

The proliferation of Large Language Models (LLMs) has driven considerable interest in fine-tuning them with domain-specific data to create specialized language models. Nevertheless, such domain-specific fine-tuning data often contains sensitive personally identifiable information (PII). Direct fine-tuning LLMs on this data without privacy protection poses a risk of leakage. To address this challenge, we introduce Privacy Protection Language Models (PPLM), a novel paradigm for fine-tuning LLMs that effectively injects domain-specific knowledge while safeguarding data privacy. Our work offers a theoretical analysis for model design and delves into various techniques such as corpus curation, penalty-based unlikelihood in training loss, and instruction-based tuning, etc. Extensive experiments across diverse datasets and scenarios demonstrate the effectiveness of our approaches. In particular, instruction tuning with both positive and negative examples, stands out as a promising method, effectively protecting private data while enhancing the model's knowledge. Our work underscores the potential for Large Language Models as robust privacy protection learners.

Benchmarking Foundation Models with Language-Model-as-an-Examiner

Numerous benchmarks have been established to assess the performance of foundation models on open-ended question answering, which serves as a comprehensive test of a model's ability to understand and generate language in a manner similar to humans. Most of these works focus on proposing new datasets, however, we see two main issues within previous benchmarking pipelines, namely testing leakage and evaluation automation. In this paper, we propose a novel benchmarking framework, Language-Model-as-an-Examiner, where the LM serves as a knowledgeable examiner that formulates questions based on its knowledge and evaluates responses in a reference-free manner. Our framework allows for effortless extensibility as various LMs can be adopted as the examiner, and the questions can be constantly updated given more diverse trigger topics. For a more comprehensive and equitable evaluation, we devise three strategies: (1) We instruct the LM examiner to generate questions across a multitude of domains to probe for a broad acquisition, and raise follow-up questions to engage in a more in-depth assessment. (2) Upon evaluation, the examiner combines both scoring and ranking measurements, providing a reliable result as it aligns closely with human annotations. (3) We additionally propose a decentralized Peer-examination method to address the biases in a single examiner. Our data and benchmarking results are available at: https://lmexam.com.

SPLDExtraTrees: Robust machine learning approach for predicting kinase inhibitor resistance

Drug resistance is a major threat to the global health and a significant concern throughout the clinical treatment of diseases and drug development. The mutation in proteins that is related to drug binding is a common cause for adaptive drug resistance. Therefore, quantitative estimations of how mutations would affect the interaction between a drug and the target protein would be of vital significance for the drug development and the clinical practice. Computational methods that rely on molecular dynamics simulations, Rosetta protocols, as well as machine learning methods have been proven to be capable of predicting ligand affinity changes upon protein mutation. However, the severely limited sample size and heavy noise induced overfitting and generalization issues have impeded wide adoption of machine learning for studying drug resistance. In this paper, we propose a robust machine learning method, termed SPLDExtraTrees, which can accurately predict ligand binding affinity changes upon protein mutation and identify resistance-causing mutations. Especially, the proposed method ranks training data following a specific scheme that starts with easy-to-learn samples and gradually incorporates harder and diverse samples into the training, and then iterates between sample weight recalculations and model updates. In addition, we calculate additional physics-based structural features to provide the machine learning model with the valuable domain knowledge on proteins for this data-limited predictive tasks. The experiments substantiate the capability of the proposed method for predicting kinase inhibitor resistance under three scenarios, and achieves predictive accuracy comparable to that of molecular dynamics and Rosetta methods with much less computational costs.

A Deep Learning Inference Scheme Based on Pipelined Matrix Multiplication Acceleration Design and Non-uniform Quantization

Matrix multiplication is the bedrock in Deep Learning inference application. When it comes to hardware acceleration on edge computing devices, matrix multiplication often takes up a great majority of the time. To achieve better performance in edge computing, we introduce a low-power Multi-layer Perceptron (MLP) accelerator based on a pipelined matrix multiplication scheme and a nonuniform quantization methodology. The implementation is running on Field-programmable Gate Array (FPGA) devices and tested its performance on handwritten digit classification and Q-learning tasks. Results show that our method can achieve better performance with fewer power consumption.