31 accepted papers
Understanding the functions of DNAs, RNAs, and proteins is fundamental to advancing life science research and enabling translational applications such as drug discovery and precision medicine. While deep learning methods have shown promise in biomolecular function prediction, they typically constrai…
Model editing aims to correct errors in large, pretrained models without altering unrelated behaviors. While some recent works have edited vision–language models (VLMs), no existing editors tackle reasoning-heavy tasks, which typically require humans and models to reason about images. We therefore p…
Ensuring model calibration is critical for reliable prediction, yet popular distribution-free methods such as histogram binning and isotonic regression offer only asymptotic guarantees. We introduce a unified framework for Venn and Venn-Abers calibration that extends Vovk's approach beyond binary cl…
Knowledge editing is a promising way to improve factuality in large language models, but recent studies have shown significant model degradation during sequential editing. In this paper, we formalize the popular locate-then-edit methods as a two-step fine-tuning process, allowing us to precisely ide
Large language models (LLMs) have revolutionized natural language processing, yet their practical utility is often limited by persistent issues of hallucinations and outdated parametric knowledge. Although post-training model editing offers a pathway for dynamic updates, existing methods frequently…
Medical large language models (LLMs) research often makes bold claims, from encoding clinical knowledge to reasoning like a physician. These claims are usually backed by evaluation on competitive benchmarks—a tradition inherited from mainstream machine learning. But how do we separate real progress…
Machine Translation errors in high-stakes settings like healthcare pose unique risks that could lead to clinical harm. The challenges are even more pronounced for low-resourced languages where human translators are scarce and MT tools perform poorly. In this work, we provide a taxonomy of Machine Tr
Recent advances in generative diffusion models have enabled text-controlled synthesis of realistic and diverse images with impressive quality. Despite these remarkable advances, the application of text-to-image generative models in computer vision for standard visual recognition tasks remains limite…
In this paper, we introduce a new class of score-based generative models (SGMs) designed to handle high-cardinality data distributions by leveraging concepts from mean-field theory. We present mean-field chaos diffusion models (MF-CDMs), which address the curse of dimensionality inherent in high-car…
A digital twin is a virtual replica of a real-world physical phenomena that uses mathematical modeling to characterize and simulate its defining features. By constructing digital twins for disease processes, we can perform in-silico simulations that mimic patients' health conditions and counterfactu…
Causal inferences from a randomized controlled trial (RCT) may not pertain to a *target* population where some effect modifiers have a different distribution. Prior work studies *generalizing* the results of a trial to a target population with no outcome but covariate data available. We show how the…
In machine learning, model calibration and predictive inference are essential for producing reliable predictions and quantifying uncertainty to support decision-making. Recognizing the complementary roles of point and interval predictions, we introduce Self-Calibrating Conformal Prediction, a method…
Generative models capable of precisely capturing nuanced clinical features in medical images hold great promise for facilitating clinical data sharing, enhancing rare disease datasets, and efficiently synthesizing (annotated) medical images at scale. Despite their potential, assessing the quality of…
We investigate the problem of machine learning-based (ML) predictive inference on individual treatment effects (ITEs). Previous work has focused primarily on developing ML-based “meta-learners” that can provide point estimates of the conditional average treatment effect (CATE)—these are model-agnost…
We present DiffInfinite, a hierarchical diffusion model that generates arbitrarily large histological images while preserving long-range correlation structural information. Our approach first generates synthetic segmentation masks, subsequently used as conditions for the high-fidelity generative dif…
Echocardiography is one of the most commonly used diagnostic imaging modalities in cardiology. Application of deep learning models to echocardiograms can enable automated identification of cardiac structures, estimation of cardiac function, and prediction of clinical outcomes. However, a major hindr…
Devising domain- and model-agnostic evaluation metrics for generative models is an important and as yet unresolved problem. Most existing metrics, which were tailored solely to the image synthesis setup, exhibit a limited capacity for diagnosing the different modes of failure of generative models ac…
Current approaches for multi-horizon time series forecasting using recurrent neural networks (RNNs) focus on issuing point estimates, which is insufficient for decision-making in critical application domains where an uncertainty estimate is also required. Existing approaches for uncertainty quantifi…
Generating synthetic time-series data is crucial in various application domains, such as medical prognosis, wherein research is hamstrung by the lack of access to data due to concerns over privacy. Most of the recently proposed methods for generating synthetic time-series rely on implicit likelihood…
Organ transplantation can improve life expectancy for recipients, but the probability of a successful transplant depends on the compatibility between donor and recipient features. Current medical practice relies on coarse rules for donor-recipient matching, but is short of domain knowledge regarding…
Organ transplantation is often the last resort for treating end-stage illnesses, but managing transplant wait-lists is challenging because of organ scarcity and the complexity of assessing donor-recipient compatibility. In this paper, we develop a data-driven model for (real-time) organ allocation u…
Deep learning models achieve high predictive accuracy across a broad spectrum of tasks, but rigorously quantifying their predictive uncertainty remains challenging. Usable estimates of predictive uncertainty should (1) cover the true prediction targets with high probability, and (2) discriminate bet…
Recurrent neural networks (RNNs) are instrumental in modelling sequential and time-series data. Yet, when using RNNs to inform decision-making, predictions by themselves are not sufficient {—} we also need estimates of predictive uncertainty. Existing approaches for uncertainty quantification in RNN…
Comorbid diseases co-occur and progress via complex temporal patterns that vary among individuals. In electronic medical records, we only observe onsets of diseases, but not their triggering comorbidities — i.e., the mechanisms underlying temporal relations between diseases need to be inferred. Lear…
The estimation of treatment effects is a pervasive problem in medicine. Existing methods for estimating treatment effects from longitudinal observational data assume that there are no hidden confounders, an assumption that is not testable in practice and, if it does not hold, leads to biased estimat…
Modern neural networks have proven to be powerful function approximators, providing state-of-the-art performance in a multitude of applications. They however fall short in their ability to quantify confidence in their predictions — this is crucial in high-stakes applications that involve critical de…
The importance of survival analysis in many disciplines (especially in medicine) has led to the development of a variety of approaches to modeling the survival function. Models constructed via various approaches offer different strengths and weaknesses in terms of discriminative performance and cali…
The problem of estimating causal effects of treatments from observational data falls beyond the realm of supervised learning {—} because counterfactual data is inaccessible, we can never observe the true causal effects. In the absence of "supervision", how can we evaluate the performance of causal i…
Clinical prognostic models derived from largescale healthcare data can inform critical diagnostic and therapeutic decisions. To enable off-theshelf usage of machine learning (ML) in prognostic research, we developed AUTOPROGNOSIS: a system for automating the design of predictive modeling pipelines t…
Estimating heterogeneous treatment effects from observational data is a central problem in many domains. Because counterfactual data is inaccessible, the problem differs fundamentally from supervised learning, and entails a more complex set of modeling choices. Despite a variety of recently proposed…
We develop ForecastICU: a prognostic decision support system that monitors hospitalized patients and prompts alarms for intensive care unit (ICU) admissions. ForecastICU is first trained in an offline stage by constructing a Bayesian belief system that corresponds to its belief about how trajectorie…