Bianca Dumitrascu

Soledad Villar, Weichi Yao, David W. Hogg et al.

Units equivariance (or units covariance) is the exact symmetry that follows from the requirement that relationships among measured quantities of physics relevance must obey self-consistent dimensional scalings. Here, we express this symmetry in terms of a (non-compact) group action, and we employ dimensional analysis and ideas from equivariant machine learning to provide a methodology for exactly units-equivariant machine learning: For any given learning task, we first construct a dimensionless version of its inputs using classic results from dimensional analysis, and then perform inference in the dimensionless space. Our approach can be used to impose units equivariance across a broad range of machine learning methods which are equivariant to rotations and other groups. We discuss the in-sample and out-of-sample prediction accuracy gains one can obtain in contexts like symbolic regression and emulation, where symmetry is important. We illustrate our approach with simple numerical examples involving dynamical systems in physics and ecology.

Nabeel Sarwar, Wilson Gregory, George A Kevrekidis et al.

Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and computationally intractable. Here we introduce MarkerMap, a generative model for selecting minimal gene sets which are maximally informative of cell type origin and enable whole transcriptome reconstruction. MarkerMap provides a scalable framework for both supervised marker selection, aimed at identifying specific cell type populations, and unsupervised marker selection, aimed at gene expression imputation and reconstruction. We benchmark MarkerMap's competitive performance against previously published approaches on real single cell gene expression data sets. MarkerMap is available as a pip installable package, as a community resource aimed at developing explainable machine learning techniques for enhancing interpretability in single-cell studies.

Weichi Yao, Bianca Dumitrascu, Bryan R. Goldsmith et al.

Active data acquisition is central to many learning and optimization tasks in deep neural networks, yet remains challenging because most approaches rely on predictive uncertainty estimates that are difficult to obtain reliably. To this end, we propose Goal-Oriented Influence- Maximizing Data Acquisition (GOIMDA), an active acquisition algorithm that avoids explicit posterior inference while remaining uncertainty-aware through inverse curvature. GOIMDA selects inputs by maximizing their expected influence on a user-specified goal functional, such as test loss, predictive entropy, or the value of an optimizer-recommended design. Leveraging first-order influence functions, we derive a tractable acquisition rule that combines the goal gradient, training-loss curvature, and candidate sensitivity to model parameters. We show theoretically that, for generalized linear models, GOIMDA approximates predictive-entropy minimization up to a correction term accounting for goal alignment and prediction bias, thereby, yielding uncertainty-aware behavior without maintaining a Bayesian posterior. Empirically, across learning tasks (including image and text classification) and optimization tasks (including noisy global optimization benchmarks and neural-network hyperparameter tuning), GOIMDA consistently reaches target performance with substantially fewer labeled samples or function evaluations than uncertainty-based active learning and Gaussian-process Bayesian optimization baselines.

Li-Fang Cheng, Gregory Darnell, Bianca Dumitrascu et al.

In the scenario of real-time monitoring of hospital patients, high-quality inference of patients' health status using all information available from clinical covariates and lab tests is essential to enable successful medical interventions and improve patient outcomes. Developing a computational framework that can learn from observational large-scale electronic health records (EHRs) and make accurate real-time predictions is a critical step. In this work, we develop and explore a Bayesian nonparametric model based on Gaussian process (GP) regression for hospital patient monitoring. We propose MedGP, a statistical framework that incorporates 24 clinical and lab covariates and supports a rich reference data set from which relationships between observed covariates may be inferred and exploited for high-quality inference of patient state over time. To do this, we develop a highly structured sparse GP kernel to enable tractable computation over tens of thousands of time points while estimating correlations among clinical covariates, patients, and periodicity in patient observations. MedGP has a number of benefits over current methods, including (i) not requiring an alignment of the time series data, (ii) quantifying confidence regions in the predictions, (iii) exploiting a vast and rich database of patients, and (iv) inferring interpretable relationships among clinical covariates. We evaluate and compare results from MedGP on the task of online prediction for three patient subgroups from two medical data sets across 8,043 patients. We found MedGP improves online prediction over baseline methods for nearly all covariates across different disease subgroups and studies. The publicly available code is at https://github.com/bee-hive/MedGP.

Yuli Slavutsky, Ozgur Beker, David Blei et al.

Disentangled representations enable models to separate factors of variation that are shared across experimental conditions from those that are condition-specific. This separation is essential in domains such as biomedical data analysis, where generalization to new treatments, patients, or species depends on isolating stable biological signals from context-dependent effects. While extensions of the variational autoencoder (VAE) framework have been proposed to address this problem, they frequently suffer from leakage between latent representations, limiting their ability to generalize to unseen conditions. Here, we introduce DISCoVeR, a new variational framework that explicitly separates condition-invariant and condition-specific factors. DISCoVeR integrates three key components: (i) a dual-latent architecture that models shared and specific factors separately; (ii) two parallel reconstructions that ensure both representations remain informative; and (iii) a novel max-min objective that encourages clean separation without relying on handcrafted priors, while making only minimal assumptions. Theoretically, we show that this objective maximizes data likelihood while promoting disentanglement, and that it admits a unique equilibrium. Empirically, we demonstrate that DISCoVeR achieves improved disentanglement on synthetic datasets, natural images, and single-cell RNA-seq data. Together, these results establish DISCoVeR as a principled approach for learning disentangled representations in multi-condition settings.

Jacob D. Moss, Felix L. Opolka, Bianca Dumitrascu et al.

Physically-inspired latent force models offer an interpretable alternative to purely data driven tools for inference in dynamical systems. They carry the structure of differential equations and the flexibility of Gaussian processes, yielding interpretable parameters and dynamics-imposed latent functions. However, the existing inference techniques associated with these models rely on the exact computation of posterior kernel terms which are seldom available in analytical form. Most applications relevant to practitioners, such as Hill equations or diffusion equations, are hence intractable. In this paper, we overcome these computational problems by proposing a variational solution to a general class of non-linear and parabolic partial differential equation latent force models. Further, we show that a neural operator approach can scale our model to thousands of instances, enabling fast, distributed computation. We demonstrate the efficacy and flexibility of our framework by achieving competitive performance on several tasks where the kernels are of varying degrees of tractability.

Li-Fang Cheng, Bianca Dumitrascu, Michael Zhang et al.

Multi-output Gaussian processes (GPs) are a flexible Bayesian nonparametric framework that has proven useful in jointly modeling the physiological states of patients in medical time series data. However, capturing the short-term effects of drugs and therapeutic interventions on patient physiological state remains challenging. We propose a novel approach that models the effect of interventions as a hybrid Gaussian process composed of a GP capturing patient physiology convolved with a latent force model capturing effects of treatments on specific physiological features. This convolution of a multi-output GP with a GP including a causal time-marked kernel leads to a well-characterized model of the patients' physiological state responding to interventions. We show that our model leads to analytically tractable cross-covariance functions, allowing scalable inference. Our hierarchical model includes estimates of patient-specific effects but allows sharing of support across patients. Our approach achieves competitive predictive performance on challenging hospital data, where we recover patient-specific response to the administration of three common drugs: one antihypertensive drug and two anticoagulants.

Michael Minyi Zhang, Bianca Dumitrascu, Sinead A. Williamson et al.

Many machine learning problems can be framed in the context of estimating functions, and often these are time-dependent functions that are estimated in real-time as observations arrive. Gaussian processes (GPs) are an attractive choice for modeling real-valued nonlinear functions due to their flexibility and uncertainty quantification. However, the typical GP regression model suffers from several drawbacks: 1) Conventional GP inference scales $O(N^{3})$ with respect to the number of observations; 2) Updating a GP model sequentially is not trivial; and 3) Covariance kernels typically enforce stationarity constraints on the function, while GPs with non-stationary covariance kernels are often intractable to use in practice. To overcome these issues, we propose a sequential Monte Carlo algorithm to fit infinite mixtures of GPs that capture non-stationary behavior while allowing for online, distributed inference. Our approach empirically improves performance over state-of-the-art methods for online GP estimation in the presence of non-stationarity in time-series data. To demonstrate the utility of our proposed online Gaussian process mixture-of-experts approach in applied settings, we show that we can sucessfully implement an optimization algorithm using online Gaussian process bandits.

Bianca Dumitrascu, Karen Feng, Barbara E Engelhardt

We address the problem of regret minimization in logistic contextual bandits, where a learner decides among sequential actions or arms given their respective contexts to maximize binary rewards. Using a fast inference procedure with Polya-Gamma distributed augmentation variables, we propose an improved version of Thompson Sampling, a Bayesian formulation of contextual bandits with near-optimal performance. Our approach, Polya-Gamma augmented Thompson Sampling (PG-TS), achieves state-of-the-art performance on simulated and real data. PG-TS explores the action space efficiently and exploits high-reward arms, quickly converging to solutions of low regret. Its explicit estimation of the posterior distribution of the context feature covariance leads to substantial empirical gains over approximate approaches. PG-TS is the first approach to demonstrate the benefits of Polya-Gamma augmentation in bandits and to propose an efficient Gibbs sampler for approximating the analytically unsolvable integral of logistic contextual bandits.