Minh Tho Nguyen

Minh Nguyen, Gia H. Ngo, Mert R. Sabuncu

The Granger framework is useful for discovering causal relations in time-varying signals. However, most Granger causality (GC) methods are developed for densely sampled timeseries data. A substantially different setting, particularly common in medical imaging, is the longitudinal study design, where multiple subjects are followed and sparsely observed over time. Longitudinal studies commonly track several biomarkers, which are likely governed by nonlinear dynamics that might have subject-specific idiosyncrasies and exhibit both direct and indirect causes. Furthermore, real-world longitudinal data often suffer from widespread missingness. GC methods are not well-suited to handle these issues. In this paper, we propose an approach named GLACIAL (Granger and LeArning-based CausalIty Analysis for Longitudinal studies) to fill this methodological gap by marrying GC with a multi-task neural forecasting model. GLACIAL treats subjects as independent samples and uses the model's average prediction accuracy on hold-out subjects to probe causal links. Input dropout and model interpolation are used to efficiently learn nonlinear dynamic relationships between a large number of variables and to handle missing values respectively. Extensive simulations and experiments on a real longitudinal medical imaging dataset show GLACIAL beating competitive baselines and confirm its utility. Our code is available at https://github.com/mnhng/GLACIAL.

Rey Mendoza, Minh Nguyen, Judith Weng Zhu et al.

Computed tomography has propelled scientific advances in fields from biology to materials science. This technology allows for the elucidation of 3-dimensional internal structure by the attenuation of x-rays through an object at different rotations relative to the beam. By imaging 2-dimensional projections, a 3-dimensional object can be reconstructed through a computational algorithm. Imaging at a greater number of rotation angles allows for improved reconstruction. However, taking more measurements increases the x-ray dose and may cause sample damage. Deep neural networks have been used to transform sparse 2-D projection measurements to a 3-D reconstruction by training on a dataset of known similar objects. However, obtaining high-quality object reconstructions for the training dataset requires high x-ray dose measurements that can destroy or alter the specimen before imaging is complete. This becomes a chicken-and-egg problem: high-quality reconstructions cannot be generated without deep learning, and the deep neural network cannot be learned without the reconstructions. This work develops and validates a self-supervised probabilistic deep learning technique, the physics-informed variational autoencoder, to solve this problem. A dataset consisting solely of sparse projection measurements from each object is used to jointly reconstruct all objects of the set. This approach has the potential to allow visualization of fragile samples with x-ray computed tomography. We release our code for reproducing our results at: https://github.com/vganapati/CT_PVAE .

Minh Nguyen, Gia H. Ngo, Mert R. Sabuncu

Given sufficient pairs of resting-state and task-evoked fMRI scans from subjects, it is possible to train ML models to predict subject-specific task-evoked activity using resting-state functional MRI (rsfMRI) scans. However, while rsfMRI scans are relatively easy to collect, obtaining sufficient task fMRI scans is much harder as it involves more complex experimental designs and procedures. Thus, the reliance on scarce paired data limits the application of current techniques to only tasks seen during training. We show that this reliance can be reduced by leveraging group-average contrasts, enabling zero-shot predictions for novel tasks. Our approach, named OPIC (short for Omni-Task Prediction of Individual Contrasts), takes as input a subject's rsfMRI-derived connectome and a group-average contrast, to produce a prediction of the subject-specific contrast. Similar to zero-shot learning in large language models using special inputs to obtain answers for novel natural language processing tasks, inputting group-average contrasts guides the OPIC model to generalize to novel tasks unseen in training. Experimental results show that OPIC's predictions for novel tasks are not only better than simple group-averages, but are also competitive with a state-of-the-art model's in-domain predictions that was trained using in-domain tasks' data.

Chinh Ngo, Trieu H. Trinh, Long Phan et al.

We introduce MTet, the largest publicly available parallel corpus for English-Vietnamese translation. MTet consists of 4.2M high-quality training sentence pairs and a multi-domain test set refined by the Vietnamese research community. Combining with previous works on English-Vietnamese translation, we grow the existing parallel dataset to 6.2M sentence pairs. We also release the first pretrained model EnViT5 for English and Vietnamese languages. Combining both resources, our model significantly outperforms previous state-of-the-art results by up to 2 points in translation BLEU score, while being 1.6 times smaller.

Chandrajit Bajaj, Minh Nguyen, Conrad Li

In this paper, we present a novel reinforcement learning framework designed to optimize molecular dynamics by focusing on the entire trajectory rather than just the final molecular configuration. Leveraging a stochastic version of Pontryagin's Maximum Principle (PMP) and Soft Actor-Critic (SAC) algorithm, our framework effectively explores non-convex molecular energy landscapes, escaping local minima to stabilize in low-energy states. Our approach operates in continuous state and action spaces without relying on labeled data, making it applicable to a wide range of molecular systems. Through extensive experimentation on six distinct molecules, including Bradykinin and Oxytocin, we demonstrate competitive performance against other unsupervised physics-based methods, such as the Greedy and NEMO-based algorithms. Our method's adaptability and focus on dynamic trajectory optimization make it suitable for applications in areas such as drug discovery and molecular design.

Minh Nguyen, Nancy F. Chen

NLP models excel on tasks with clean inputs, but are less accurate with noisy inputs. In particular, character-level noise such as human-written typos and adversarially-engineered realistic-looking misspellings often appears in text and can easily trip up NLP models. Prior solutions to address character-level noise often alter the content of the inputs (low fidelity), thus inadvertently lowering model accuracy on clean inputs. We proposed FiRo, an approach to boost NLP model performance on noisy inputs without sacrificing performance on clean inputs. FiRo sanitizes the input text while preserving its fidelity by inferring the noise-free form for each token in the input. FiRo uses finite-context aggregation to obtain contextual embeddings which is then used to find the noise-free form within a restricted output space. The output space is restricted to a small cluster of probable candidates in order to predict the noise-free tokens more accurately. Although the clusters are small, FiRo's effective vocabulary (union of all clusters) can be scaled up to better preserve the input content. Experimental results show NLP models that use FiRo outperforming baselines on six classification tasks and one sequence labeling task at various degrees of noise.

Minh Nguyen, Chandrajit Bajaj

Reinforcement learning (RL) in continuous state-action spaces remains challenging in scientific computing due to poor sample efficiency and lack of pathwise physical consistency. We introduce Differential Reinforcement Learning (Differential RL), a novel framework that reformulates RL from a continuous-time control perspective via a differential dual formulation. This induces a Hamiltonian structure that embeds physics priors and ensures consistent trajectories without requiring explicit constraints. To implement Differential RL, we develop Differential Policy Optimization (DPO), a pointwise, stage-wise algorithm that refines local movement operators along the trajectory for improved sample efficiency and dynamic alignment. We establish pointwise convergence guarantees, a property not available in standard RL, and derive a competitive theoretical regret bound of $O(K^{5/6})$. Empirically, DPO outperforms standard RL baselines on representative scientific computing tasks, including surface modeling, grid control, and molecular dynamics, under low-data and physics-constrained conditions.

Chandrajit Bajaj, Minh Nguyen

Despite extensive research, time series classification and forecasting on noisy data remain highly challenging. The main difficulties lie in finding suitable mathematical concepts to describe time series and effectively separate noise from the true signals. Unlike traditional methods treating time series as static vectors or fixed sequences, we propose a novel framework that views each time series, regardless of length, as a realization of a continuous-time stochastic process. This mathematical approach captures dependencies across timestamps and detects hidden, time-varying signals within the noise. However, real-world data often involves multiple distinct dynamics, making it insufficient to model the entire process with a single stochastic model. To address this, we assign each dynamic a unique signature vector and introduce the concept of "most informative timestamps" to infer a sparse approximation of the individual dynamics from these vectors. The resulting model, called Motion Code, includes parameters that fully capture diverse underlying dynamics in an integrated manner, enabling simultaneous classification and forecasting of time series. Extensive experiments on noisy datasets, including real-world Parkinson's disease sensor tracking, demonstrate Motion Code's strong performance against established benchmarks for time series classification and forecasting.

Luke McLennan, Yi Wang, Ryan Farell et al.

We introduce a robust framework for learning various generalized Hamiltonian dynamics from noisy, sparse phase-space data and in an unsupervised manner based on variational Bayesian inference. Although conservative, dissipative, and port-Hamiltonian systems might share the same initial total energy of a closed system, it is challenging for a single Hamiltonian network model to capture the distinctive and varying motion dynamics and physics of a phase space, from sampled observational phase space trajectories. To address this complicated Hamiltonian manifold learning challenge, we extend sparse symplectic, random Fourier Gaussian processes learning with predictive successive numerical estimations of the Hamiltonian landscape, using a generalized form of state and conjugate momentum Hamiltonian dynamics, appropriate to different classes of conservative, dissipative and port-Hamiltonian physical systems. In addition to the kernelized evidence lower bound (ELBO) loss for data fidelity, we incorporate stability and conservation constraints as additional hyper-parameter balanced loss terms to regularize the model's multi-gradients, enforcing physics correctness for improved prediction accuracy with bounded uncertainty.

Minh Nguyen, Gia H. Ngo, Nancy F. Chen

Spell check is a useful application which processes noisy human-generated text. Spell check for Chinese poses unresolved problems due to the large number of characters, the sparse distribution of errors, and the dearth of resources with sufficient coverage of heterogeneous and shifting error domains. For Chinese spell check, filtering using confusion sets narrows the search space and makes finding corrections easier. However, most, if not all, confusion sets used to date are fixed and thus do not include new, shifting error domains. We propose a scalable adaptable filter that exploits hierarchical character embeddings to (1) obviate the need to handcraft confusion sets, and (2) resolve sparsity problems related to infrequent errors. Our approach compares favorably with competitive baselines and obtains SOTA results on the 2014 and 2015 Chinese Spelling Check Bake-off datasets.