Controllable Edge-Type-Specific Interpretation in Multi-Relational Graph Neural Networks for Drug Response Prediction

Graph Neural Networks have been widely applied in critical decision-making areas that demand interpretable predictions, leading to the flourishing development of interpretability algorithms. However, current graph interpretability algorithms tend to emphasize generality and often overlook biological significance, thereby limiting their applicability in predicting cancer drug responses. In this paper, we propose a novel post-hoc interpretability algorithm for cancer drug response prediction, CETExplainer, which incorporates a controllable edge-type-specific weighting mechanism. It considers the mutual information between subgraphs and predictions, proposing a structural scoring approach to provide fine-grained, biologically meaningful explanations for predictive models. We also introduce a method for constructing ground truth based on real-world datasets to quantitatively evaluate the proposed interpretability algorithm. Empirical analysis on the real-world dataset demonstrates that CETExplainer achieves superior stability and improves explanation quality compared to leading algorithms, thereby offering a robust and insightful tool for cancer drug prediction.

DRExplainer: Quantifiable Interpretability in Drug Response Prediction with Directed Graph Convolutional Network

Predicting the response of a cancer cell line to a therapeutic drug is pivotal for personalized medicine. Despite numerous deep learning methods that have been developed for drug response prediction, integrating diverse information about biological entities and predicting the directional response remain major challenges. Here, we propose a novel interpretable predictive model, DRExplainer, which leverages a directed graph convolutional network to enhance the prediction in a directed bipartite network framework. DRExplainer constructs a directed bipartite network integrating multi-omics profiles of cell lines, the chemical structure of drugs and known drug response to achieve directed prediction. Then, DRExplainer identifies the most relevant subgraph to each prediction in this directed bipartite network by learning a mask, facilitating critical medical decision-making. Additionally, we introduce a quantifiable method for model interpretability that leverages a ground truth benchmark dataset curated from biological features. In computational experiments, DRExplainer outperforms state-of-the-art predictive methods and another graph-based explanation method under the same experimental setting. Finally, the case studies further validate the interpretability and the effectiveness of DRExplainer in predictive novel drug response. Our code is available at: https://github.com/vshy-dream/DRExplainer.

DoraemonGPT: Toward Understanding Dynamic Scenes with Large Language Models

The field of AI agents is advancing at an unprecedented rate due to the capabilities of large language models (LLMs). However, LLM-driven visual agents mainly focus on solving tasks for the image modality, which limits their ability to understand the dynamic nature of the real world, making it still far from real-life applications, e.g., guiding students in laboratory experiments and identifying their mistakes. Considering the video modality better reflects the ever-changing and perceptually intensive nature of real-world scenarios, we devise DoraemonGPT, a comprehensive and conceptually elegant system driven by LLMs to handle dynamic video tasks. Given a video with a question/task, DoraemonGPT begins by converting the input video with massive content into a symbolic memory that stores \textit{task-related} attributes. This structured representation allows for spatial-temporal querying and reasoning by sub-task tools, resulting in concise and relevant intermediate results. Recognizing that LLMs have limited internal knowledge when it comes to specialized domains (e.g., analyzing the scientific principles underlying experiments), we incorporate plug-and-play tools to assess external knowledge and address tasks across different domains. Moreover, we introduce a novel LLM-driven planner based on Monte Carlo Tree Search to efficiently explore the large planning space for scheduling various tools. The planner iteratively finds feasible solutions by backpropagating the result's reward, and multiple solutions can be summarized into an improved final answer. We extensively evaluate DoraemonGPT in dynamic scenes and provide in-the-wild showcases demonstrating its ability to handle more complex questions than previous studies.

Deep unrolling Shrinkage Network for Dynamic MR imaging

Deep unrolling networks that utilize sparsity priors have achieved great success in dynamic magnetic resonance (MR) imaging. The convolutional neural network (CNN) is usually utilized to extract the transformed domain, and then the soft thresholding (ST) operator is applied to the CNN-transformed data to enforce the sparsity priors. However, the ST operator is usually constrained to be the same across all channels of the CNN-transformed data. In this paper, we propose a novel operator, called soft thresholding with channel attention (AST), that learns the threshold for each channel. In particular, we put forward a novel deep unrolling shrinkage network (DUS-Net) by unrolling the alternating direction method of multipliers (ADMM) for optimizing the transformed $l_1$ norm dynamic MR reconstruction model. Experimental results on an open-access dynamic cine MR dataset demonstrate that the proposed DUS-Net outperforms the state-of-the-art methods. The source code is available at \url{https://github.com/yhao-z/DUS-Net}.

Segment and Track Anything

This report presents a framework called Segment And Track Anything (SAMTrack) that allows users to precisely and effectively segment and track any object in a video. Additionally, SAM-Track employs multimodal interaction methods that enable users to select multiple objects in videos for tracking, corresponding to their specific requirements. These interaction methods comprise click, stroke, and text, each possessing unique benefits and capable of being employed in combination. As a result, SAM-Track can be used across an array of fields, ranging from drone technology, autonomous driving, medical imaging, augmented reality, to biological analysis. SAM-Track amalgamates Segment Anything Model (SAM), an interactive key-frame segmentation model, with our proposed AOT-based tracking model (DeAOT), which secured 1st place in four tracks of the VOT 2022 challenge, to facilitate object tracking in video. In addition, SAM-Track incorporates Grounding-DINO, which enables the framework to support text-based interaction. We have demonstrated the remarkable capabilities of SAM-Track on DAVIS-2016 Val (92.0%), DAVIS-2017 Test (79.2%)and its practicability in diverse applications. The project page is available at: https://github.com/z-x-yang/Segment-and-Track-Anything.

An Automated Vulnerability Detection Framework for Smart Contracts

With the increase of the adoption of blockchain technology in providing decentralized solutions to various problems, smart contracts have become more popular to the point that billions of US Dollars are currently exchanged every day through such technology. Meanwhile, various vulnerabilities in smart contracts have been exploited by attackers to steal cryptocurrencies worth millions of dollars. The automatic detection of smart contract vulnerabilities therefore is an essential research problem. Existing solutions to this problem particularly rely on human experts to define features or different rules to detect vulnerabilities. However, this often causes many vulnerabilities to be ignored, and they are inefficient in detecting new vulnerabilities. In this study, to overcome such challenges, we propose a framework to automatically detect vulnerabilities in smart contracts on the blockchain. More specifically, first, we utilize novel feature vector generation techniques from bytecode of smart contract since the source code of smart contracts are rarely available in public. Next, the collected vectors are fed into our novel metric learning-based deep neural network(DNN) to get the detection result. We conduct comprehensive experiments on large-scale benchmarks, and the quantitative results demonstrate the effectiveness and efficiency of our approach.

DeepMLE: A Robust Deep Maximum Likelihood Estimator for Two-view Structure from Motion

Two-view structure from motion (SfM) is the cornerstone of 3D reconstruction and visual SLAM (vSLAM). Many existing end-to-end learning-based methods usually formulate it as a brute regression problem. However, the inadequate utilization of traditional geometry model makes the model not robust in unseen environments. To improve the generalization capability and robustness of end-to-end two-view SfM network, we formulate the two-view SfM problem as a maximum likelihood estimation (MLE) and solve it with the proposed framework, denoted as DeepMLE. First, we propose to take the deep multi-scale correlation maps to depict the visual similarities of 2D image matches decided by ego-motion. In addition, in order to increase the robustness of our framework, we formulate the likelihood function of the correlations of 2D image matches as a Gaussian and Uniform mixture distribution which takes the uncertainty caused by illumination changes, image noise and moving objects into account. Meanwhile, an uncertainty prediction module is presented to predict the pixel-wise distribution parameters. Finally, we iteratively refine the depth and relative camera pose using the gradient-like information to maximize the likelihood function of the correlations. Extensive experimental results on several datasets prove that our method significantly outperforms the state-of-the-art end-to-end two-view SfM approaches in accuracy and generalization capability.