Rui Wang

Yuta Hozumi, Rui Wang, Guo-Wei Wei

Most dimensionality reduction methods employ frequency domain representations obtained from matrix diagonalization and may not be efficient for large datasets with relatively high intrinsic dimensions. To address this challenge, Correlated Clustering and Projection (CCP) offers a novel data domain strategy that does not need to solve any matrix. CCP partitions high-dimensional features into correlated clusters and then projects correlated features in each cluster into a one-dimensional representation based on sample correlations. Residue-Similarity (R-S) scores and indexes, the shape of data in Riemannian manifolds, and algebraic topology-based persistent Laplacian are introduced for visualization and analysis. Proposed methods are validated with benchmark datasets associated with various machine learning algorithms.

Rui Wang, Hongsong Feng, Guo-Wei Wei

The birth of ChatGPT, a cutting-edge language model-based chatbot developed by OpenAI, ushered in a new era in AI. However, due to potential pitfalls, its role in rigorous scientific research is not clear yet. This paper vividly showcases its innovative application within the field of drug discovery. Focused specifically on developing anti-cocaine addiction drugs, the study employs GPT-4 as a virtual guide, offering strategic and methodological insights to researchers working on generative models for drug candidates. The primary objective is to generate optimal drug-like molecules with desired properties. By leveraging the capabilities of ChatGPT, the study introduces a novel approach to the drug discovery process. This symbiotic partnership between AI and researchers transforms how drug development is approached. Chatbots become facilitators, steering researchers towards innovative methodologies and productive paths for creating effective drug candidates. This research sheds light on the collaborative synergy between human expertise and AI assistance, wherein ChatGPT's cognitive abilities enhance the design and development of potential pharmaceutical solutions. This paper not only explores the integration of advanced AI in drug discovery but also reimagines the landscape by advocating for AI-powered chatbots as trailblazers in revolutionizing therapeutic innovation.

Hongsong Feng, Rui Wang, Chang-Guo Zhan et al.

Opioid Use Disorder (OUD) has emerged as a significant global public health issue, with complex multifaceted conditions. Due to the lack of effective treatment options for various conditions, there is a pressing need for the discovery of new medications. In this study, we propose a deep generative model that combines a stochastic differential equation (SDE)-based diffusion modeling with the latent space of a pretrained autoencoder model. The molecular generator enables efficient generation of molecules that are effective on multiple targets, specifically the mu, kappa, and delta opioid receptors. Furthermore, we assess the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the generated molecules to identify drug-like compounds. To enhance the pharmacokinetic properties of some lead compounds, we employ a molecular optimization approach. We obtain a diverse set of drug-like molecules. We construct binding affinity predictors by integrating molecular fingerprints derived from autoencoder embeddings, transformer embeddings, and topological Laplacians with advanced machine learning algorithms. Further experimental studies are needed to evaluate the pharmacological effects of these drug-like compounds for OUD treatment. Our machine learning platform serves as a valuable tool in designing and optimizing effective molecules for addressing OUD.

ZhengZhao Feng, Rui Wang, TianXing Wang et al.

Dynamic Graph Neural Networks (GNNs) combine temporal information with GNNs to capture structural, temporal, and contextual relationships in dynamic graphs simultaneously, leading to enhanced performance in various applications. As the demand for dynamic GNNs continues to grow, numerous models and frameworks have emerged to cater to different application needs. There is a pressing need for a comprehensive survey that evaluates the performance, strengths, and limitations of various approaches in this domain. This paper aims to fill this gap by offering a thorough comparative analysis and experimental evaluation of dynamic GNNs. It covers 81 dynamic GNN models with a novel taxonomy, 12 dynamic GNN training frameworks, and commonly used benchmarks. We also conduct experimental results from testing representative nine dynamic GNN models and three frameworks on six standard graph datasets. Evaluation metrics focus on convergence accuracy, training efficiency, and GPU memory usage, enabling a thorough comparison of performance across various models and frameworks. From the analysis and evaluation results, we identify key challenges and offer principles for future research to enhance the design of models and frameworks in the dynamic GNNs field.

Cheng Yuan, Jian Jiang, Kunyi Yang et al.

Surgical video segmentation is critical for AI to interpret spatial-temporal dynamics in surgery, yet model performance is constrained by limited annotated data. The SAM2 model, pretrained on natural videos, offers potential for zero-shot surgical segmentation, but its applicability in complex surgical environments, with challenges like tissue deformation and instrument variability, remains unexplored. We present the first comprehensive evaluation of the zero-shot capability of SAM2 in 9 surgical datasets (17 surgery types), covering laparoscopic, endoscopic, and robotic procedures. We analyze various prompting (points, boxes, mask) and {finetuning (dense, sparse) strategies}, robustness to surgical challenges, and generalization across procedures and anatomies. Key findings reveal that while SAM2 demonstrates notable zero-shot adaptability in structured scenarios (e.g., instrument segmentation, {multi-organ segmentation}, and scene segmentation), its performance varies under dynamic surgical conditions, highlighting gaps in handling temporal coherence and domain-specific artifacts. These results highlight future pathways to adaptive data-efficient solutions for the surgical data science field.

Chendong Wang, Donglin Bai, Yifan Yang et al.

We present \emph{Video-in-the-Loop} (ViTL), a two-stage long-video QA framework that preserves a fixed token budget by first \emph{localizing} question-relevant interval(s) with a low-fps skim and then \emph{answering} via span-aware reallocation of visual tokens at higher effective frame rate, emitting an interleaved output with both spans and the final option for direct attribution. We also introduce \dataname{}, which converts description based event graphs into \emph{span-grounded} multiple-choice QA by pairing each question with \emph{ground-truth} time span(s) and related reasoning. ViTL is trained end-to-end with an interleaved group-relative objective that couples temporal IoU for localization with answer correctness, allowing credit to flow from answers back to spans without increasing compute. Under fixed token budgets, ViTL attains up to 8.6% with 50% less frame input on long-video QA and temporal grounding (e.g., Charades-STA, ActivityNet-Captions) and ablations show that span-aware token reallocation consistently surpasses uniform sampling. Together, \dataname{} and ViTL provide an interpretable, compute-efficient recipe for scalable long-video QA.

Ewerton R. Vieira, Daniel Nakhimovich, Kai Gao et al.

This work explores the use of topological tools for achieving effective non-prehensile manipulation in cluttered, constrained workspaces. In particular, it proposes the use of persistent homology as a guiding principle in identifying the appropriate non-prehensile actions, such as pushing, to clean a cluttered space with a robotic arm so as to allow the retrieval of a target object. Persistent homology enables the automatic identification of connected components of blocking objects in the space without the need for manual input or tuning of parameters. The proposed algorithm uses this information to push groups of cylindrical objects together and aims to minimize the number of pushing actions needed to reach to the target. Simulated experiments in a physics engine using a model of the Baxter robot show that the proposed topology-driven solution is achieving significantly higher success rate in solving such constrained problems relatively to state-of-the-art alternatives from the literature. It manages to keep the number of pushing actions low, is computationally efficient and the resulting decisions and motion appear natural for effectively solving such tasks.