Duc Duy Nguyen

Md Masud Rana, Duc Duy Nguyen

Understanding and accurately predicting protein-ligand binding affinity are essential in the drug design and discovery process. At present, machine learning-based methodologies are gaining popularity as a means of predicting binding affinity due to their efficiency and accuracy, as well as the increasing availability of structural and binding affinity data for protein-ligand complexes. In biomolecular studies, graph theory has been widely applied since graphs can be used to model molecules or molecular complexes in a natural manner. In the present work, we upgrade the graph-based learners for the study of protein-ligand interactions by integrating extensive atom types such as SYBYL and extended connectivity interactive features (ECIF) into multiscale weighted colored graphs (MWCG). By pairing with the gradient boosting decision tree (GBDT) machine learning algorithm, our approach results in two different methods, namely $^\text{sybyl}\text{GGL}$-Score and $^\text{ecif}\text{GGL}$-Score. Both of our models are extensively validated in their scoring power using three commonly used benchmark datasets in the drug design area, namely CASF-2007, CASF-2013, and CASF-2016. The performance of our best model $^\text{sybyl}\text{GGL}$-Score is compared with other state-of-the-art models in the binding affinity prediction for each benchmark. While both of our models achieve state-of-the-art results, the SYBYL atom-type model $^\text{sybyl}\text{GGL}$-Score outperforms other methods by a wide margin in all benchmarks.

Duc Duy Nguyen, Tat-Jun Chin, Minh Hoai

We aim to learn a joint representation between inertial measurement unit (IMU) signals and 2D pose sequences extracted from video, enabling accurate cross-modal retrieval, temporal synchronization, subject and body-part localization, and action recognition. To this end, we introduce MoBind, a hierarchical contrastive learning framework designed to address three challenges: (1) filtering out irrelevant visual background, (2) modeling structured multi-sensor IMU configurations, and (3) achieving fine-grained, sub-second temporal alignment. To isolate motion-relevant cues, MoBind aligns IMU signals with skeletal motion sequences rather than raw pixels. We further decompose full-body motion into local body-part trajectories, pairing each with its corresponding IMU to enable semantically grounded multi-sensor alignment. To capture detailed temporal correspondence, MoBind employs a hierarchical contrastive strategy that first aligns token-level temporal segments, then fuses local (body-part) alignment with global (body-wide) motion aggregation. Evaluated on mRi, TotalCapture, and EgoHumans, MoBind consistently outperforms strong baselines across all four tasks, demonstrating robust fine-grained temporal alignment while preserving coarse semantic consistency across modalities. Code is available at https://github.com/bbvisual/ MoBind.

Yifeng Huang, Duc Duy Nguyen, Lam Nguyen et al.

This paper addresses the task of counting human actions of interest using sensor data from wearable devices. We propose a novel exemplar-based framework, allowing users to provide exemplars of the actions they want to count by vocalizing predefined sounds ''one'', ''two'', and ''three''. Our method first localizes temporal positions of these utterances from the audio sequence. These positions serve as the basis for identifying exemplars representing the action class of interest. A similarity map is then computed between the exemplars and the entire sensor data sequence, which is further fed into a density estimation module to generate a sequence of estimated density values. Summing these density values provides the final count. To develop and evaluate our approach, we introduce a diverse and realistic dataset consisting of real-world data from 37 subjects and 50 action categories, encompassing both sensor and audio data. The experiments on this dataset demonstrate the viability of the proposed method in counting instances of actions from new classes and subjects that were not part of the training data. On average, the discrepancy between the predicted count and the ground truth value is 7.47, significantly lower than the errors of the frequency-based and transformer-based methods. Our project, code and dataset can be found at https://github.com/cvlab-stonybrook/ExRAC.

Trung Nguyen, Md Masud Rana, Farjana Tasnim Mukta et al.

Accurate prediction of blood-brain barrier permeability (BBBP) is essential for central nervous system (CNS) drug development. While graph neural networks (GNNs) have advanced molecular property prediction, they often rely on molecular topology and neglect the three-dimensional geometric information crucial for modeling transport mechanisms. This paper introduces the geometric multi-color message-passing graph neural network (GMC-MPNN), a novel framework that enhances standard message-passing architectures by explicitly incorporating atomic-level geometric features and long-range interactions. Our model constructs weighted colored subgraphs based on atom types to capture the spatial relationships and chemical context that govern BBB permeability. We evaluated GMC-MPNN on three benchmark datasets for both classification and regression tasks, using rigorous scaffold-based splitting to ensure a robust assessment of generalization. The results demonstrate that GMC-MPNN consistently outperforms existing state-of-the-art models, achieving superior performance in both classifying compounds as permeable/non-permeable (AUC-ROC of 0.9704 and 0.9685) and in regressing continuous permeability values (RMSE of 0.4609, Pearson correlation of 0.7759). An ablation study further quantified the impact of specific atom-pair interactions, revealing that the model's predictive power derives from its ability to learn from both common and rare, but chemically significant, functional motifs. By integrating spatial geometry into the graph representation, GMC-MPNN sets a new performance benchmark and offers a more accurate and generalizable tool for drug discovery pipelines.

Quang Vinh Nguyen, Vo Hoang Thanh Son, Chau Truong Vinh Hoang et al.

Naturalistic driving action localization task aims to recognize and comprehend human behaviors and actions from video data captured during real-world driving scenarios. Previous studies have shown great action localization performance by applying a recognition model followed by probability-based post-processing. Nevertheless, the probabilities provided by the recognition model frequently contain confused information causing challenge for post-processing. In this work, we adopt an action recognition model based on self-supervise learning to detect distracted activities and give potential action probabilities. Subsequently, a constraint ensemble strategy takes advantages of multi-camera views to provide robust predictions. Finally, we introduce a conditional post-processing operation to locate distracted behaviours and action temporal boundaries precisely. Experimenting on test set A2, our method obtains the sixth position on the public leaderboard of track 3 of the 2024 AI City Challenge.

Ekaterina Merkurjev, Duc DUy Nguyen, Guo-Wei Wei

Machine learning methods have greatly changed science, engineering, finance, business, and other fields. Despite the tremendous accomplishments of machine learning and deep learning methods, many challenges still remain. In particular, the performance of machine learning methods is often severely affected in case of diverse data, usually associated with smaller data sets or data related to areas of study where the size of the data sets is constrained by the complexity and/or high cost of experiments. Moreover, data with limited labeled samples is a challenge to most learning approaches. In this paper, the aforementioned challenges are addressed by integrating graph-based frameworks, multiscale structure, modified and adapted optimization procedures and semi-supervised techniques. This results in two innovative multiscale Laplacian learning (MLL) approaches for machine learning tasks, such as data classification, and for tackling diverse data, data with limited samples and smaller data sets. The first approach, called multikernel manifold learning (MML), integrates manifold learning with multikernel information and solves a regularization problem consisting of a loss function and a warped kernel regularizer using multiscale graph Laplacians. The second approach, called the multiscale MBO (MMBO) method, introduces multiscale Laplacians to a modification of the famous classical Merriman-Bence-Osher (MBO) scheme, and makes use of fast solvers for finding the approximations to the extremal eigenvectors of the graph Laplacian. We demonstrate the performance of our methods experimentally on a variety of data sets, such as biological, text and image data, and compare them favorably to existing approaches.