Author name cluster

Dat Nguyen

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7 papers

2 author rows

ICML Conference 2025 Conference Paper

KinDEL: DNA-Encoded Library Dataset for Kinase Inhibitors

Benson Chen
Tomasz Danel
Gabriel H. S. Dreiman
Patrick J. McEnaney
Nikhil Jain
Kirill Novikov
Spurti Umesh Akki
Joshua L. Turnbull

DNA-Encoded Libraries (DELs) represent a transformative technology in drug discovery, facilitating the high-throughput exploration of vast chemical spaces. Despite their potential, the scarcity of publicly available DEL datasets presents a bottleneck for the advancement of machine learning methodologies in this domain. To address this gap, we introduce KinDEL, one of the largest publicly accessible DEL datasets and the first one that includes binding poses from molecular docking experiments. Focused on two kinases, Mitogen-Activated Protein Kinase 14 (MAPK14) and Discoidin Domain Receptor Tyrosine Kinase 1 (DDR1), KinDEL includes 81 million compounds, offering a rich resource for computational exploration. Additionally, we provide comprehensive biophysical assay validation data, encompassing both on-DNA and off-DNA measurements, which we use to evaluate a suite of machine learning techniques, including novel structure-based probabilistic models. We hope that our benchmark, encompassing both 2D and 3D structures, will help advance the development of machine learning models for data-driven hit identification using DELs.

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IJCAI Conference 2025 Conference Paper

TRIKOP: Exploring Visual Prompting Paradigms for Multi-Grade Knee Osteoarthritis Classification on MRI Images

Hieu Phan
Hung Pham
Dat Nguyen
Khoa Le
Tuan Nguyen
Triet Tran
Tho Quan

Knee osteoarthritis (KOA) is a degenerative joint disease that significantly impacts quality of life. While transfer learning shows promise in medical imaging, its application to KOA diagnosis remains challenging due to medical data's unique characteristics. To address this, we propose TRIKOP, a framework leveraging Visual Prompting for KOA diagnosis on MRI. Our approach explores three prompt-generating strategies that extract clinically relevant information from input images. Each prompt type is encoded using a tailored method to integrate effectively into the Vision Transformer for optimal representation. Among them, the contrastive embedding prompting strategy achieves 63. 04% accuracy on the OAI dataset, surpassing prior studies. Moreover, TRIKOP produces attention maps highlighting diagnostically significant regions, improving model interpretability. This work highlights TRIKOP’s potential to improve AI-driven KOA diagnosis and clinical support.

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TMLR Journal 2025 Journal Article

VirDA: Reusing Backbone for Unsupervised Domain Adaptation with Visual Reprogramming

Duc-Duy Nguyen
Dat Nguyen

Image classification is among the pillars of computer-vision pipelines. While state-of-the-art models excel within their training domains, their performance often deteriorates when transferred to a new, unlabeled setting. Unsupervised domain adaptation (UDA) addresses this challenge by repurposing a well-trained source classifier for the target domain, enabling strong downstream results without the need for additional labeled data. Existing UDA pipelines fine-tune already well-trained backbone parameters for every new source-and-target pair, resulting in the number of training parameters and storage memory growing linearly with each new pair, and also preventing the reuse of these well-trained backbone parameters. Inspired by recent implications that existing backbones have textural biases, we propose making use of domain-specific textural bias for domain adaptation via visual reprogramming, namely VirDA. Instead of fine-tuning the full backbone, VirDA prepends a domain-specific visual reprogramming layer to the backbone. This layer produces visual prompts that act as an added textural bias to the input image, adapting its ``style'' to a target domain. To optimize these visual reprogramming layers, we use multiple objective functions that optimize the intra- and inter-domain distribution differences when domain-adapting visual prompts are applied. This process does not require modifying the backbone parameters, allowing the same backbone to be reused across different domains. We evaluate VirDA on Office-31 and obtain 92.8% mean accuracy with only 1.5M trainable parameters. VirDA surpasses PDA, the state-of-the-art parameter-efficient UDA baseline, by +1.6% accuracy while using just 46% of its parameters. Compared with full-backbone fine-tuning, VirDA outperforms CDTrans and FixBi by +0.2% and +1.4%, respectively, while requiring only 1.7% and 2.8% of their trainable parameters. Relative to the strongest current methods (PMTrans and TVT), VirDA uses ~1.7% of their parameters and trades off only 2.2% and 1.1% accuracy, respectively.

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NeurIPS Conference 2023 Conference Paper

Learning Probabilistic Symmetrization for Architecture Agnostic Equivariance

Jinwoo Kim
Dat Nguyen
Ayhan Suleymanzade
Hyeokjun An
Seunghoon Hong

We present a novel framework to overcome the limitations of equivariant architectures in learning functions with group symmetries. In contrary to equivariant architectures, we use an arbitrary base model such as an MLP or a transformer and symmetrize it to be equivariant to the given group by employing a small equivariant network that parameterizes the probabilistic distribution underlying the symmetrization. The distribution is end-to-end trained with the base model which can maximize performance while reducing sample complexity of symmetrization. We show that this approach ensures not only equivariance to given group but also universal approximation capability in expectation. We implement our method on various base models, including patch-based transformers that can be initialized from pretrained vision transformers, and test them for a wide range of symmetry groups including permutation and Euclidean groups and their combinations. Empirical tests show competitive results against tailored equivariant architectures, suggesting the potential for learning equivariant functions for diverse groups using a non-equivariant universal base architecture. We further show evidence of enhanced learning in symmetric modalities, like graphs, when pretrained from non-symmetric modalities, like vision. Code is available at https: //github. com/jw9730/lps.

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NeurIPS Conference 2022 Conference Paper

Active Learning Helps Pretrained Models Learn the Intended Task

Alex Tamkin
Dat Nguyen
Salil Deshpande
Jesse Mu
Noah Goodman

Models can fail in unpredictable ways during deployment due to task ambiguity, when multiple behaviors are consistent with the provided training data. An example is an object classifier trained on red squares and blue circles: when encountering blue squares, the intended behavior is undefined. We investigate whether pretrained models are better active learners, capable of disambiguating between the possible tasks a user may be trying to specify. Intriguingly, we find that better active learning is an emergent property of the pretraining process: pretrained models require up to 5 times fewer labels when using uncertainty-based active learning, while non-pretrained models see no or even negative benefit. We find these gains come from an ability to select examples with attributes that disambiguate the intended behavior, such as rare product categories or atypical backgrounds. These attributes are far more linearly separable in pretrained model's representation spaces vs non-pretrained models, suggesting a possible mechanism for this behavior.

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NeurIPS Conference 2022 Conference Paper

Pure Transformers are Powerful Graph Learners

Jinwoo Kim
Dat Nguyen
Seonwoo Min
Sungjun Cho
Moontae Lee
Honglak Lee
Seunghoon Hong

We show that standard Transformers without graph-specific modifications can lead to promising results in graph learning both in theory and practice. Given a graph, we simply treat all nodes and edges as independent tokens, augment them with token embeddings, and feed them to a Transformer. With an appropriate choice of token embeddings, we prove that this approach is theoretically at least as expressive as an invariant graph network (2-IGN) composed of equivariant linear layers, which is already more expressive than all message-passing Graph Neural Networks (GNN). When trained on a large-scale graph dataset (PCQM4Mv2), our method coined Tokenized Graph Transformer (TokenGT) achieves significantly better results compared to GNN baselines and competitive results compared to Transformer variants with sophisticated graph-specific inductive bias. Our implementation is available at https: //github. com/jw9730/tokengt.

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ICML Conference 2021 Conference Paper

HoroPCA: Hyperbolic Dimensionality Reduction via Horospherical Projections

Ines Chami
Albert Gu
Dat Nguyen
Christopher Ré

This paper studies Principal Component Analysis (PCA) for data lying in hyperbolic spaces. Given directions, PCA relies on: (1) a parameterization of subspaces spanned by these directions, (2) a method of projection onto subspaces that preserves information in these directions, and (3) an objective to optimize, namely the variance explained by projections. We generalize each of these concepts to the hyperbolic space and propose HoroPCA, a method for hyperbolic dimensionality reduction. By focusing on the core problem of extracting principal directions, HoroPCA theoretically better preserves information in the original data such as distances, compared to previous generalizations of PCA. Empirically, we validate that HoroPCA outperforms existing dimensionality reduction methods, significantly reducing error in distance preservation. As a data whitening method, it improves downstream classification by up to 3. 9% compared to methods that don’t use whitening. Finally, we show that HoroPCA can be used to visualize hyperbolic data in two dimensions.

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