Related papers: PRESCRIBE: Predicting Single-Cell Responses with B…

Because large language models are expensive to pretrain on different datasets, using smaller-scale experiments to decide on data is crucial for reducing costs. Which benchmarks and methods of making decisions from observed performance at…

Simulation-based inference (SBI) methods such as approximate Bayesian computation (ABC), synthetic likelihood, and neural posterior estimation (NPE) rely on simulating statistics to infer parameters of intractable likelihood models.…

Learning individual-level causal effects from observational data, such as inferring the most effective medication for a specific patient, is a problem of growing importance for policy makers. The most important aspect of inferring causal…

Computational models support high-stakes decisions across engineering and science, and practitioners increasingly seek probabilistic predictions to quantify uncertainty in such models. Existing approaches generate predictions either by…

Differential expression (DE) plays a fundamental role toward illuminating the molecular mechanisms driving a difference between groups (e.g., due to treatment or disease). While any analysis is run on particular cells/samples, the intent is…

This paper demonstrates a methodology for examining the accuracy of uncertain inference systems (UIS), after their parameters have been optimized, and does so for several common UIS's. This methodology may be used to test the accuracy when…

Bayesian inference provides a principled framework for probabilistic reasoning. If inference is performed in two steps, uncertainty propagation plays a crucial role in accounting for all sources of uncertainty and variability. This becomes…

Causal inference is a vital aspect of multiple scientific disciplines and is routinely applied to high-impact applications such as medicine. However, evaluating the performance of causal inference methods in real-world environments is…

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data,…

Screening before model building is a reasonable strategy to reduce the dimension of regression problems. Sure independence screening is an efficient approach to this purpose. It applies the slope estimate of a simple linear regression as a…

In high-stakes domains like healthcare, users often expect that sharing personal information with machine learning systems will yield tangible benefits, such as more accurate diagnoses and clearer explanations of contributing factors.…

The prediction of cancer prognosis and metastatic potential immediately after the initial diagnoses is a major challenge in current clinical research. The relevance of such a signature is clear, as it will free many patients from the agony…

Undertaking causal inference with observational data is incredibly useful across a wide range of tasks including the development of medical treatments, advertisements and marketing, and policy making. There are two significant challenges…

Predicting the impact of genomic and drug perturbations in cellular function is crucial for understanding gene functions and drug effects, ultimately leading to improved therapies. To this end, Causal Representation Learning (CRL)…

We empirically show that Bayesian inference can be inconsistent under misspecification in simple linear regression problems, both in a model averaging/selection and in a Bayesian ridge regression setting. We use the standard linear model,…

Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…

Modeling uncertainty in deep neural networks, despite recent important advances, is still an open problem. Bayesian neural networks are a powerful solution, where the prior over network weights is a design choice, often a normal…

Most machine learning techniques are based upon statistical learning theory, often simplified for the sake of computing speed. This paper is focused on the uncertainty aspect of mathematical modeling in machine learning. Regression analysis…

Organic synthesis is one of the key stumbling blocks in medicinal chemistry. A necessary yet unsolved step in planning synthesis is solving the forward problem: given reactants and reagents, predict the products. Similar to other work, we…

A predictive model makes outcome predictions based on some given features, i.e., it estimates the conditional probability of the outcome given a feature vector. In general, a predictive model cannot estimate the causal effect of a feature…