Related papers: This before That: Causal Precedence in the Biomedi…

This article studies the estimation of the causal effect of a time-varying treatment on time-to-an-event or on some other continuously distributed outcome. The paper applies to the situation where treatment is repeatedly adapted to…

Prescriptions, or actionable recommendations, are commonly generated across various fields to influence key outcomes such as improving public health, enhancing economic policies, or increasing business efficiency. While traditional…

Predicting the effects of chemical and genetic perturbations on quantitative cell states is a central challenge in computational biology, molecular medicine and drug discovery. Recent work has leveraged large-scale single-cell data and…

Causal inference is a critical research topic across many domains, such as statistics, computer science, education, public policy and economics, for decades. Nowadays, estimating causal effect from observational data has become an appealing…

Proximal causal inference was recently proposed as a framework to identify causal effects from observational data in the presence of hidden confounders for which proxies are available. In this paper, we extend the proximal causal inference…

Causal inference and model interpretability research are gaining increasing attention, especially in the domains of healthcare and bioinformatics. Despite recent successes in this field, decorrelating features under nonlinear environments…

We present a constraint-based algorithm for learning causal structures from observational time-series data, in the presence of latent confounders. We assume a discrete-time, stationary structural vector autoregressive process, with both…

Explainable recommendation systems leverage transparent reasoning to foster user trust and improve decision-making processes. Current approaches typically decouple recommendation generation from explanation creation, violating causal…

Pre-trained language models (PLMs) have been the de facto paradigm for most natural language processing (NLP) tasks. This also benefits biomedical domain: researchers from informatics, medicine, and computer science (CS) communities propose…

Recent years have seen rapid progress at the intersection between causality and machine learning. Motivated by scientific applications involving high-dimensional data, in particular in biomedicine, we propose a deep neural architecture for…

Foundation models for tabular data, such as the Tabular Prior-data Fitted Network (TabPFN), are pre-trained on a massive number of synthetic datasets generated by structural causal models (SCM). They leverage in-context learning to offer…

The notion of causality assumes a paramount position within the realm of human cognition. Over the past few decades, there has been significant advancement in the domain of causal effect estimation across various disciplines, including but…

Recent empirical evidence indicates that transformer based in-context learning performs better when using a prefix language model (prefixLM), in which in-context samples can all attend to each other, compared to causal language models…

Extracting biomedical relations from large corpora of scientific documents is a challenging natural language processing task. Existing approaches usually focus on identifying a relation either in a single sentence (mention-level) or across…

The notion of causal effect is fundamental across many scientific disciplines. Traditionally, quantitative researchers have studied causal effects at the level of variables; for example, how a certain drug dose (W) causally affects a…

Revealing novel insights from the relationship between molecular measurements and pathology remains a very impactful application of machine learning in biomedicine. Data in this domain typically contain only a few observations but thousands…

This paper discusses causal independence models and a generalization of these models called causal interaction models. Causal interaction models are models that have independent mechanisms where a mechanism can have several causes. In…

We address the common yet often-overlooked selection bias in interventional studies, where subjects are selectively enrolled into experiments. For instance, participants in a drug trial are usually patients of the relevant disease; A/B…

Interventional causal discovery seeks to identify causal relations by leveraging distributional changes introduced by interventions, even in the presence of latent confounders. Beyond the spurious dependencies induced by latent confounders,…

Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using…