Phan Nguyen

Brian R. Bartoldson, Yeping Hu, Amar Saini et al.

Data-driven modeling approaches can produce fast surrogates to study large-scale physics problems. Among them, graph neural networks (GNNs) that operate on mesh-based data are desirable because they possess inductive biases that promote physical faithfulness, but hardware limitations have precluded their application to large computational domains. We show that it is \textit{possible} to train a class of GNN surrogates on 3D meshes. We scale MeshGraphNets (MGN), a subclass of GNNs for mesh-based physics modeling, via our domain decomposition approach to facilitate training that is mathematically equivalent to training on the whole domain under certain conditions. With this, we were able to train MGN on meshes with \textit{millions} of nodes to generate computational fluid dynamics (CFD) simulations. Furthermore, we show how to enhance MGN via higher-order numerical integration, which can reduce MGN's error and training time. We validated our methods on an accompanying dataset of 3D $\text{CO}_2$-capture CFD simulations on a 3.1M-node mesh. This work presents a practical path to scaling MGN for real-world applications.

Tavish McDonald, Brian Tsan, Amar Saini et al.

Researchers produce thousands of scholarly documents containing valuable technical knowledge. The community faces the laborious task of reading these documents to identify, extract, and synthesize information. To automate information gathering, document-level question answering (QA) offers a flexible framework where human-posed questions can be adapted to extract diverse knowledge. Finetuning QA systems requires access to labeled data (tuples of context, question and answer). However, data curation for document QA is uniquely challenging because the context (i.e. answer evidence passage) needs to be retrieved from potentially long, ill-formatted documents. Existing QA datasets sidestep this challenge by providing short, well-defined contexts that are unrealistic in real-world applications. We present a three-stage document QA approach: (1) text extraction from PDF; (2) evidence retrieval from extracted texts to form well-posed contexts; (3) QA to extract knowledge from contexts to return high-quality answers -- extractive, abstractive, or Boolean. Using QASPER for evaluation, our detect-retrieve-comprehend (DRC) system achieves a +7.19 improvement in Answer-F1 over existing baselines while delivering superior context selection. Our results demonstrate that DRC holds tremendous promise as a flexible framework for practical scientific document QA.

Ta Duc Huy, Sen Kim Tran, Phan Nguyen et al.

The ability to interpret and intervene model decisions is important for the adoption of computer-aided diagnosis methods in clinical workflows. Recent concept-based methods link the model predictions with interpretable concepts and modify their activation scores to interact with the model. However, these concepts are at the image level, which hinders the model from pinpointing the exact patches the concepts are activated. Alternatively, prototype-based methods learn representations from training image patches and compare these with test image patches, using the similarity scores for final class prediction. However, interpreting the underlying concepts of these patches can be challenging and often necessitates post-hoc guesswork. To address this issue, this paper introduces the novel Concept-based Similarity Reasoning network (CSR), which offers (i) patch-level prototype with intrinsic concept interpretation, and (ii) spatial interactivity. First, the proposed CSR provides localized explanation by grounding prototypes of each concept on image regions. Second, our model introduces novel spatial-level interaction, allowing doctors to engage directly with specific image areas, making it an intuitive and transparent tool for medical imaging. CSR improves upon prior state-of-the-art interpretable methods by up to 4.5\% across three biomedical datasets. Our code is released at https://github.com/tadeephuy/InteractCSR.

Phan Nguyen, Dat Cao, Quang Hien Kha et al.

Skin lesion classification is essential for early dermatological diagnosis, yet many existing computer-aided systems rely primarily on dermoscopic images and underutilize the multimodal evidence routinely available in clinical practice. To address this gap, we propose \textbf{JI-ADF}, a trimodal deep learning framework that integrates dermoscopic images, clinical photographs, and structured patient metadata for clinically grounded skin lesion classification. The proposed architecture combines joint multimodal representation learning with modality-specific auxiliary supervision and an adaptive decision fusion mechanism that dynamically calibrates modality contributions on a per-sample basis. To enhance cross-modal reasoning while preserving modality-specific evidence, we further introduce a multimodal fusion attention (MMFA) module. We evaluate JI-ADF on the large-scale MILK10k benchmark, which reflects real-world clinical acquisition conditions and severe class imbalance. The proposed method demonstrates strong and well-balanced performance across lesion categories, improving sensitivity and Dice score while maintaining high specificity and good calibration. Extensive analyses, including modality ablation, calibration evaluation, and Grad-CAM visualization, further confirm the robustness and clinically meaningful behavior of the model. These results indicate that JI-ADF provides a reliable and practical foundation for multimodal skin lesion classification in real-world clinical settings.

Clifford Anderson-Bergman, Phan Nguyen, Jose Cadena Pico

Latent Euclidean embedding models a given network by representing each node in a Euclidean space, where the probability of two nodes sharing an edge is a function of the distances between the nodes. This implies that for two nodes to share an edge with high probability, they must be relatively close in all dimensions. This constraint may be overly restrictive for describing modern networks, in which having similarities in at least one area may be sufficient for having a high edge probability. We introduce a new model, which we call Latent Channel Networks, which allows for such features of a network. We present an EM algorithm for fitting the model, for which the computational complexity is linear in the number of edges and number of channels and apply the algorithm to both synthetic and classic network datasets.