Nathan M. Urban

A N M Nafiz Abeer, Nathan Urban, M Ryan Weil et al.

Molecular design based on generative models, such as variational autoencoders (VAEs), has become increasingly popular in recent years due to its efficiency for exploring high-dimensional molecular space to identify molecules with desired properties. While the efficacy of the initial model strongly depends on the training data, the sampling efficiency of the model for suggesting novel molecules with enhanced properties can be further enhanced via latent space optimization. In this paper, we propose a multi-objective latent space optimization (LSO) method that can significantly enhance the performance of generative molecular design (GMD). The proposed method adopts an iterative weighted retraining approach, where the respective weights of the molecules in the training data are determined by their Pareto efficiency. We demonstrate that our multi-objective GMD LSO method can significantly improve the performance of GMD for jointly optimizing multiple molecular properties.

Sanket Jantre, Nathan M. Urban, Xiaoning Qian et al.

Bayesian inference for neural networks, or Bayesian deep learning, has the potential to provide well-calibrated predictions with quantified uncertainty and robustness. However, the main hurdle for Bayesian deep learning is its computational complexity due to the high dimensionality of the parameter space. In this work, we propose a novel scheme that addresses this limitation by constructing a low-dimensional subspace of the neural network parameters-referred to as an active subspace-by identifying the parameter directions that have the most significant influence on the output of the neural network. We demonstrate that the significantly reduced active subspace enables effective and scalable Bayesian inference via either Monte Carlo (MC) sampling methods, otherwise computationally intractable, or variational inference. Empirically, our approach provides reliable predictions with robust uncertainty estimates for various regression tasks.

Amir Hossein Rahmati, Mingzhou Fan, Ruida Zhou et al.

Instead of randomly acquiring training data points, Uncertainty-based Active Learning (UAL) operates by querying the label(s) of pivotal samples from an unlabeled pool selected based on the prediction uncertainty, thereby aiming at minimizing the labeling cost for model training. The efficacy of UAL critically depends on the model capacity as well as the adopted uncertainty-based acquisition function. Within the context of this study, our analytical focus is directed toward comprehending how the capacity of the machine learning model may affect UAL efficacy. Through theoretical analysis, comprehensive simulations, and empirical studies, we conclusively demonstrate that UAL can lead to worse performance in comparison with random sampling when the machine learning model class has low capacity and is unable to cover the underlying ground truth. In such situations, adopting acquisition functions that directly target estimating the prediction performance may be beneficial for improving the performance of UAL.

Alif Bin Abdul Qayyum, Xihaier Luo, Nathan M. Urban et al.

The world is moving towards clean and renewable energy sources, such as wind energy, in an attempt to reduce greenhouse gas emissions that contribute to global warming. To enhance the analysis and storage of wind data, we introduce a deep learning framework designed to simultaneously enable effective dimensionality reduction and continuous representation of multi-altitude wind data from discrete observations. The framework consists of three key components: dimensionality reduction, cross-modal prediction, and super-resolution. We aim to: (1) improve data resolution across diverse climatic conditions to recover high-resolution details; (2) reduce data dimensionality for more efficient storage of large climate datasets; and (3) enable cross-prediction between wind data measured at different heights. Comprehensive testing confirms that our approach surpasses existing methods in both super-resolution quality and compression efficiency.

A N M Nafiz Abeer, Sanket Jantre, Nathan M Urban et al.

Deep generative models have been accelerating the inverse design process in material and drug design. Unlike their counterpart property predictors in typical molecular design frameworks, generative molecular design models have seen fewer efforts on uncertainty quantification (UQ) due to computational challenges in Bayesian inference posed by their large number of parameters. In this work, we focus on the junction-tree variational autoencoder (JT-VAE), a popular model for generative molecular design, and address this issue by leveraging the low dimensional active subspace to capture the uncertainty in the model parameters. Specifically, we approximate the posterior distribution over the active subspace parameters to estimate the epistemic model uncertainty in an extremely high dimensional parameter space. The proposed UQ scheme does not require alteration of the model architecture, making it readily applicable to any pre-trained model. Our experiments demonstrate the efficacy of the AS-based UQ and its potential impact on molecular optimization by exploring the model diversity under epistemic uncertainty.

Sanket Jantre, Tianle Wang, Gilchan Park et al.

Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language Models (LLMs) have demonstrated remarkable potential in predicting protein structures and interactions via automated mining of vast biomedical literature; yet their inherent uncertainty remains a key challenge for deriving reproducible findings, critical for biomedical applications. In this study, we present an uncertainty-aware adaptation of LLMs for PPI analysis, leveraging fine-tuned LLaMA-3 and BioMedGPT models. To enhance prediction reliability, we integrate LoRA ensembles and Bayesian LoRA models for uncertainty quantification (UQ), ensuring confidence-calibrated insights into protein behavior. Our approach achieves competitive performance in PPI identification across diverse disease contexts while addressing model uncertainty, thereby enhancing trustworthiness and reproducibility in computational biology. These findings underscore the potential of uncertainty-aware LLM adaptation for advancing precision medicine and biomedical research.

Fernando Llorente, Daniel Waxman, Sanket Jantre et al.

Gaussian processes (GPs) offer a flexible, uncertainty-aware framework for modeling complex signals, but scale cubically with data, assume static targets, and are brittle to outliers, limiting their applicability in large-scale problems with dynamic and noisy environments. Recent work introduced decentralized random Fourier feature Gaussian processes (DRFGP), an online and distributed algorithm that casts GPs in an information-filter form, enabling exact sequential inference and fully distributed computation without reliance on a fusion center. In this paper, we extend DRFGP along two key directions: first, by introducing a robust-filtering update that downweights the impact of atypical observations; and second, by incorporating a dynamic adaptation mechanism that adapts to time-varying functions. The resulting algorithm retains the recursive information-filter structure while enhancing stability and accuracy. We demonstrate its effectiveness on a large-scale Earth system application, underscoring its potential for in-situ modeling.

Sanket Jantre, Deepak Akhare, Zhiyuan Wang et al.

Partial differential equations (PDEs) underpin the modeling of many natural and engineered systems. It can be convenient to express such models as neural PDEs rather than using traditional numerical PDE solvers by replacing part or all of the PDE's governing equations with a neural network representation. Neural PDEs are often easier to differentiate, linearize, reduce, or use for uncertainty quantification than the original numerical solver. They are usually trained on solution trajectories obtained by long-horizon rollout of the PDE solver. Here we propose a more sample-efficient data-augmentation strategy for generating neural PDE training data from a computer model by space-filling sampling of local "stencil" states. This approach removes a large degree of spatiotemporal redundancy present in trajectory data and oversamples states that may be rarely visited but help the neural PDE generalize across the state space. We demonstrate that accurate neural PDE stencil operators can be learned from synthetic training data generated by the computational equivalent of 10 timesteps' worth of numerical simulation. Accuracy is further improved if we assume access to a single full-trajectory simulation from the computer model, which is typically available in practice. Across several PDE systems, we show that our data-augmented stencil data yield better trained neural stencil operators, with clear performance gains compared with naively sampled stencil data from simulation trajectories. Finally, with only 10 solver steps' worth of augmented stencil data, our approach outperforms traditional ML emulators trained on thousands of trajectories in long-horizon rollout accuracy and stability.

Amir Hossein Rahmati, Nathan M. Urban, Byung-Jun Yoon et al.

Machine Learning surrogates have been developed to accelerate solving systems dynamics of complex processes in different science and engineering applications. To faithfully capture governing systems dynamics, these methods rely on large training datasets, hence restricting their applicability in real-world problems. In this work, we propose BayPOD-AL, an active learning framework based on an uncertainty-aware Bayesian proper orthogonal decomposition (POD) approach, which aims to effectively learn reduced-order models from high-fidelity full-order models representing complex systems. Experimental results on predicting the temperature evolution over a rod demonstrate BayPOD-AL's effectiveness in suggesting the informative data and reducing computational cost related to constructing a training dataset compared to other uncertainty-guided active learning strategies. Furthermore, we demonstrate BayPOD-AL's generalizability and efficiency by evaluating its performance on a dataset of higher temporal resolution than the training dataset.

Alif Bin Abdul Qayyum, Susan D. Mertins, Amanda K. Paulson et al.

The data-driven drug design problem can be formulated as an optimization task of a potentially expensive black-box objective function over a huge high-dimensional and structured molecular space. The junction tree variational autoencoder (JTVAE) has been shown to be an efficient generative model that can be used for suggesting legitimate novel drug-like small molecules with improved properties. While the performance of the generative molecular design (GMD) scheme strongly depends on the initial training data, one can improve its sampling efficiency for suggesting better molecules with enhanced properties by optimizing the latent space. In this work, we propose how mechanistic models - such as pathway models described by differential equations - can be used for effective latent space optimization(LSO) of JTVAEs and other similar models for GMD. To demonstrate the potential of our proposed approach, we show how a pharmacodynamic model, assessing the therapeutic efficacy of a drug-like small molecule by predicting how it modulates a cancer pathway, can be incorporated for effective LSO of data-driven models for GMD.

Alif Bin Abdul Qayyum, Xihaier Luo, Nathan M. Urban et al.

World is looking for clean and renewable energy sources that do not pollute the environment, in an attempt to reduce greenhouse gas emissions that contribute to global warming. Wind energy has significant potential to not only reduce greenhouse emission, but also meet the ever increasing demand for energy. To enable the effective utilization of wind energy, addressing the following three challenges in wind data analysis is crucial. Firstly, improving data resolution in various climate conditions to ensure an ample supply of information for assessing potential energy resources. Secondly, implementing dimensionality reduction techniques for data collected from sensors/simulations to efficiently manage and store large datasets. Thirdly, extrapolating wind data from one spatial specification to another, particularly in cases where data acquisition may be impractical or costly. We propose a deep learning based approach to achieve multi-modal continuous resolution wind data prediction from discontinuous wind data, along with data dimensionality reduction.