Large Language Models as Biomedical Hypothesis Generators: A Comprehensive Evaluation

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

Intuitive Fine-Tuning: Towards Unifying SFT and RLHF into a Single Process

Supervised Fine-Tuning (SFT) and Reinforcement Learning from Human Feedback (RLHF) are two fundamental processes for enhancing the capabilities of Language Models (LMs) post pre-training, aligning them better with human preferences. Although SFT advances in training efficiency, RLHF delivers better alignment, thus they are often combined. However, common practices simply apply them sequentially without unifying their optimization targets, resulting in a trade-off between fitting different objectives, and ignoring the opportunities to bridge the paradigm gap and take the strength from both. To obtain a unified understanding, we interpret SFT and RLHF using two sub-processes -- Preference Estimation and Transition Optimization -- defined at token level within the Markov Decision Process (MDP) framework. This modeling shows that SFT is only a specialized case of RLHF with inferior estimation and optimization. RLHF evaluates the quality of model's entire generated answer, whereas SFT only scores predicted tokens based on preceding tokens from target answers. Therefore, SFT overestimates the ability of model, leading to inferior optimization. Building on this view, we introduce Intuitive Fine-tuning (IFT) to integrate SFT and RLHF into a single process. IFT captures LMs' intuitive sense of the entire answers through a temporal residual connection, while using a single policy and the same volume of non-preference-labeled data as SFT. Our experiments show that IFT performs comparably or even superiorly to sequential recipes of SFT and some typical alignment methods across several tasks, particularly those requires generation, reasoning, and fact-following abilities. An explainable Frozen Lake game further validates the effectiveness of IFT.

Large Language Models are Zero Shot Hypothesis Proposers

Significant scientific discoveries have driven the progress of human civilisation. The explosion of scientific literature and data has created information barriers across disciplines that have slowed the pace of scientific discovery. Large Language Models (LLMs) hold a wealth of global and interdisciplinary knowledge that promises to break down these information barriers and foster a new wave of scientific discovery. However, the potential of LLMs for scientific discovery has not been formally explored. In this paper, we start from investigating whether LLMs can propose scientific hypotheses. To this end, we construct a dataset consist of background knowledge and hypothesis pairs from biomedical literature. The dataset is divided into training, seen, and unseen test sets based on the publication date to control visibility. We subsequently evaluate the hypothesis generation capabilities of various top-tier instructed models in zero-shot, few-shot, and fine-tuning settings, including both closed and open-source LLMs. Additionally, we introduce an LLM-based multi-agent cooperative framework with different role designs and external tools to enhance the capabilities related to generating hypotheses. We also design four metrics through a comprehensive review to evaluate the generated hypotheses for both ChatGPT-based and human evaluations. Through experiments and analyses, we arrive at the following findings: 1) LLMs surprisingly generate untrained yet validated hypotheses from testing literature. 2) Increasing uncertainty facilitates candidate generation, potentially enhancing zero-shot hypothesis generation capabilities. These findings strongly support the potential of LLMs as catalysts for new scientific discoveries and guide further exploration.

Social Interaction-Aware Dynamical Models and Decision Making for Autonomous Vehicles

Interaction-aware Autonomous Driving (IAAD) is a rapidly growing field of research that focuses on the development of autonomous vehicles (AVs) that are capable of interacting safely and efficiently with human road users. This is a challenging task, as it requires the autonomous vehicle to be able to understand and predict the behaviour of human road users. In this literature review, the current state of IAAD research is surveyed in this work. Commencing with an examination of terminology, attention is drawn to challenges and existing models employed for modelling the behaviour of drivers and pedestrians. Next, a comprehensive review is conducted on various techniques proposed for interaction modelling, encompassing cognitive methods, machine learning approaches, and game-theoretic methods. The conclusion is reached through a discussion of potential advantages and risks associated with IAAD, along with the illumination of pivotal research inquiries necessitating future exploration.

Non-Local ConvLSTM for Video Compression Artifact Reduction

Video compression artifact reduction aims to recover high-quality videos from low-quality compressed videos. Most existing approaches use a single neighboring frame or a pair of neighboring frames (preceding and/or following the target frame) for this task. Furthermore, as frames of high quality overall may contain low-quality patches, and high-quality patches may exist in frames of low quality overall, current methods focusing on nearby peak-quality frames (PQFs) may miss high-quality details in low-quality frames. To remedy these shortcomings, in this paper we propose a novel end-to-end deep neural network called non-local ConvLSTM (NL-ConvLSTM in short) that exploits multiple consecutive frames. An approximate non-local strategy is introduced in NL-ConvLSTM to capture global motion patterns and trace the spatiotemporal dependency in a video sequence. This approximate strategy makes the non-local module work in a fast and low space-cost way. Our method uses the preceding and following frames of the target frame to generate a residual, from which a higher quality frame is reconstructed. Experiments on two datasets show that NL-ConvLSTM outperforms the existing methods.

Learning Competitive and Discriminative Reconstructions for Anomaly Detection

Most of the existing methods for anomaly detection use only positive data to learn the data distribution, thus they usually need a pre-defined threshold at the detection stage to determine whether a test instance is an outlier. Unfortunately, a good threshold is vital for the performance and it is really hard to find an optimal one. In this paper, we take the discriminative information implied in unlabeled data into consideration and propose a new method for anomaly detection that can learn the labels of unlabelled data directly. Our proposed method has an end-to-end architecture with one encoder and two decoders that are trained to model inliers and outliers' data distributions in a competitive way. This architecture works in a discriminative manner without suffering from overfitting, and the training algorithm of our model is adopted from SGD, thus it is efficient and scalable even for large-scale datasets. Empirical studies on 7 datasets including KDD99, MNIST, Caltech-256, and ImageNet etc. show that our model outperforms the state-of-the-art methods.

Global Semantic Consistency for Zero-Shot Learning

In image recognition, there are many cases where training samples cannot cover all target classes. Zero-shot learning (ZSL) utilizes the class semantic information to classify samples of the unseen categories that have no corresponding samples contained in the training set. In this paper, we propose an end-to-end framework, called Global Semantic Consistency Network (GSC-Net for short), which makes complete use of the semantic information of both seen and unseen classes, to support effective zero-shot learning. We also adopt a soft label embedding loss to further exploit the semantic relationships among classes. To adapt GSC-Net to a more practical setting, Generalized Zero-shot Learning (GZSL), we introduce a parametric novelty detection mechanism. Our approach achieves the state-of-the-art performance on both ZSL and GZSL tasks over three visual attribute datasets, which validates the effectiveness and advantage of the proposed framework.