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.

Enhance the Image: Super Resolution using Artificial Intelligence in MRI

This chapter provides an overview of deep learning techniques for improving the spatial resolution of MRI, ranging from convolutional neural networks, generative adversarial networks, to more advanced models including transformers, diffusion models, and implicit neural representations. Our exploration extends beyond the methodologies to scrutinize the impact of super-resolved images on clinical and neuroscientific assessments. We also cover various practical topics such as network architectures, image evaluation metrics, network loss functions, and training data specifics, including downsampling methods for simulating low-resolution images and dataset selection. Finally, we discuss existing challenges and potential future directions regarding the feasibility and reliability of deep learning-based MRI super-resolution, with the aim to facilitate its wider adoption to benefit various clinical and neuroscientific applications.

Artificial Intelligence for Neuro MRI Acquisition: A Review

Magnetic resonance imaging (MRI) has significantly benefited from the resurgence of artificial intelligence (AI). By leveraging AI's capabilities in large-scale optimization and pattern recognition, innovative methods are transforming the MRI acquisition workflow, including planning, sequence design, and correction of acquisition artifacts. These emerging algorithms demonstrate substantial potential in enhancing the efficiency and throughput of acquisition steps. This review discusses several pivotal AI-based methods in neuro MRI acquisition, focusing on their technological advances, impact on clinical practice, and potential risks.

Deployment Prior Injection for Run-time Calibratable Object Detection

With a strong alignment between the training and test distributions, object relation as a context prior facilitates object detection. Yet, it turns into a harmful but inevitable training set bias upon test distributions that shift differently across space and time. Nevertheless, the existing detectors cannot incorporate deployment context prior during the test phase without parameter update. Such kind of capability requires the model to explicitly learn disentangled representations with respect to context prior. To achieve this, we introduce an additional graph input to the detector, where the graph represents the deployment context prior, and its edge values represent object relations. Then, the detector behavior is trained to bound to the graph with a modified training objective. As a result, during the test phase, any suitable deployment context prior can be injected into the detector via graph edits, hence calibrating, or "re-biasing" the detector towards the given prior at run-time without parameter update. Even if the deployment prior is unknown, the detector can self-calibrate using deployment prior approximated using its own predictions. Comprehensive experimental results on the COCO dataset, as well as cross-dataset testing on the Objects365 dataset, demonstrate the effectiveness of the run-time calibratable detector.

Spiking-PhysFormer: Camera-Based Remote Photoplethysmography with Parallel Spike-driven Transformer

Artificial neural networks (ANNs) can help camera-based remote photoplethysmography (rPPG) in measuring cardiac activity and physiological signals from facial videos, such as pulse wave, heart rate and respiration rate with better accuracy. However, most existing ANN-based methods require substantial computing resources, which poses challenges for effective deployment on mobile devices. Spiking neural networks (SNNs), on the other hand, hold immense potential for energy-efficient deep learning owing to their binary and event-driven architecture. To the best of our knowledge, we are the first to introduce SNNs into the realm of rPPG, proposing a hybrid neural network (HNN) model, the Spiking-PhysFormer, aimed at reducing power consumption. Specifically, the proposed Spiking-PhyFormer consists of an ANN-based patch embedding block, SNN-based transformer blocks, and an ANN-based predictor head. First, to simplify the transformer block while preserving its capacity to aggregate local and global spatio-temporal features, we design a parallel spike transformer block to replace sequential sub-blocks. Additionally, we propose a simplified spiking self-attention mechanism that omits the value parameter without compromising the model's performance. Experiments conducted on four datasets-PURE, UBFC-rPPG, UBFC-Phys, and MMPD demonstrate that the proposed model achieves a 12.4\% reduction in power consumption compared to PhysFormer. Additionally, the power consumption of the transformer block is reduced by a factor of 12.2, while maintaining decent performance as PhysFormer and other ANN-based models.

UGG: Unified Generative Grasping

Dexterous grasping aims to produce diverse grasping postures with a high grasping success rate. Regression-based methods that directly predict grasping parameters given the object may achieve a high success rate but often lack diversity. Generation-based methods that generate grasping postures conditioned on the object can often produce diverse grasping, but they are insufficient for high grasping success due to lack of discriminative information. To mitigate, we introduce a unified diffusion-based dexterous grasp generation model, dubbed the name UGG, which operates within the object point cloud and hand parameter spaces. Our all-transformer architecture unifies the information from the object, the hand, and the contacts, introducing a novel representation of contact points for improved contact modeling. The flexibility and quality of our model enable the integration of a lightweight discriminator, benefiting from simulated discriminative data, which pushes for a high success rate while preserving high diversity. Beyond grasp generation, our model can also generate objects based on hand information, offering valuable insights into object design and studying how the generative model perceives objects. Our model achieves state-of-the-art dexterous grasping on the large-scale DexGraspNet dataset while facilitating human-centric object design, marking a significant advancement in dexterous grasping research. Our project page is https://jiaxin-lu.github.io/ugg/ .

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.

Flexible Visual Recognition by Evidential Modeling of Confusion and Ignorance

In real-world scenarios, typical visual recognition systems could fail under two major causes, i.e., the misclassification between known classes and the excusable misbehavior on unknown-class images. To tackle these deficiencies, flexible visual recognition should dynamically predict multiple classes when they are unconfident between choices and reject making predictions when the input is entirely out of the training distribution. Two challenges emerge along with this novel task. First, prediction uncertainty should be separately quantified as confusion depicting inter-class uncertainties and ignorance identifying out-of-distribution samples. Second, both confusion and ignorance should be comparable between samples to enable effective decision-making. In this paper, we propose to model these two sources of uncertainty explicitly with the theory of Subjective Logic. Regarding recognition as an evidence-collecting process, confusion is then defined as conflicting evidence, while ignorance is the absence of evidence. By predicting Dirichlet concentration parameters for singletons, comprehensive subjective opinions, including confusion and ignorance, could be achieved via further evidence combinations. Through a series of experiments on synthetic data analysis, visual recognition, and open-set detection, we demonstrate the effectiveness of our methods in quantifying two sources of uncertainties and dealing with flexible recognition.

SAM-Deblur: Let Segment Anything Boost Image Deblurring

Image deblurring is a critical task in the field of image restoration, aiming to eliminate blurring artifacts. However, the challenge of addressing non-uniform blurring leads to an ill-posed problem, which limits the generalization performance of existing deblurring models. To solve the problem, we propose a framework SAM-Deblur, integrating prior knowledge from the Segment Anything Model (SAM) into the deblurring task for the first time. In particular, SAM-Deblur is divided into three stages. First, We preprocess the blurred images, obtain image masks via SAM, and propose a mask dropout method for training to enhance model robustness. Then, to fully leverage the structural priors generated by SAM, we propose a Mask Average Pooling (MAP) unit specifically designed to average SAM-generated segmented areas, serving as a plug-and-play component which can be seamlessly integrated into existing deblurring networks. Finally, we feed the fused features generated by the MAP Unit into the deblurring model to obtain a sharp image. Experimental results on the RealBlurJ, ReloBlur, and REDS datasets reveal that incorporating our methods improves NAFNet's PSNR by 0.05, 0.96, and 7.03, respectively. Code will be available at \href{https://github.com/HPLQAQ/SAM-Deblur}{SAM-Deblur}.

DDM-NET: End-to-end learning of keypoint feature Detection, Description and Matching for 3D localization

In this paper, we propose an end-to-end framework that jointly learns keypoint detection, descriptor representation and cross-frame matching for the task of image-based 3D localization. Prior art has tackled each of these components individually, purportedly aiming to alleviate difficulties in effectively train a holistic network. We design a self-supervised image warping correspondence loss for both feature detection and matching, a weakly-supervised epipolar constraints loss on relative camera pose learning, and a directional matching scheme that detects key-point features in a source image and performs coarse-to-fine correspondence search on the target image. We leverage this framework to enforce cycle consistency in our matching module. In addition, we propose a new loss to robustly handle both definite inlier/outlier matches and less-certain matches. The integration of these learning mechanisms enables end-to-end training of a single network performing all three localization components. Bench-marking our approach on public data-sets, exemplifies how such an end-to-end framework is able to yield more accurate localization that out-performs both traditional methods as well as state-of-the-art weakly supervised methods.