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Some patients benefit from a treatment while others may do so less or do not benefit at all. We have previously developed a two-stage network meta-regression prediction model that synthesized randomized trials and evaluates how treatment…

Repurposing existing drugs to treat new diseases is a cost-effective alternative to de novo drug development, but there are millions of potential drug-disease combinations to be considered with only a small fraction being viable. In silico…

Quantitative Methods · Quantitative Biology 2025-10-24 Austin Polanco , M. E. J. Newman

Polypharmacy, defined as the use of multiple drugs together, is a standard treatment method, especially for severe and chronic diseases. However, using multiple drugs together may cause interactions between drugs. Drug-drug interaction…

Machine Learning · Computer Science 2022-07-13 Farhan Tanvir , Khaled Mohammed Saifuddin , Esra Akbas

Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…

Quantitative Methods · Quantitative Biology 2020-04-13 Thomas Gaudelet , Noel Malod-Dognin , Jon Sanchez-Valle , Vera Pancaldi , Alfonso Valencia , Natasa Przulj

Drug combination refers to the use of two or more drugs to treat a specific disease at the same time. It is currently the mainstream way to treat complex diseases. Compared with single drugs, drug combinations have better efficacy and can…

Quantitative Methods · Quantitative Biology 2024-10-15 Xinxing Yang , Jiachen Li , Xiao Kang , Guojin Pei , Keyu Liu , Genke Yang , Jian Chu

In causal estimation problems, the parameter of interest is often only partially identified, implying that the parameter cannot be recovered exactly, even with infinite data. Here, we study Bayesian inference for partially identified…

Methodology · Statistics 2022-04-26 Jiajing Zheng , Alexander D'Amour , Alexander Franks

In pharmaceutical R&D, predicting the efficacy of a pharmaceutical in treating a particular disease prior to clinical testing or any real-world use has been challenging. In this paper, we propose a flexible and modular machine…

Machine Learning · Computer Science 2025-09-10 Adrien Couetoux , Thomas Devenyns , Lise Diagne , David Champagne , Pierre-Yves Mousset , Chris Anagnostopoulos

Randomized experiments are widely used to estimate the causal effects of a proposed treatment in many areas of science, from medicine and healthcare to the physical and biological sciences, from the social sciences to engineering, to public…

Methodology · Statistics 2022-11-30 Christina Lee Yu , Edoardo M Airoldi , Christian Borgs , Jennifer T Chayes

Drug recommendation (DR) systems aim to support healthcare professionals in selecting appropriate medications based on patients' medical conditions. State-of-the-art approaches utilize deep learning techniques for improving DR, but fall…

Information Retrieval · Computer Science 2025-11-03 Yu Lin , Zhen Jia , Philipp Christmann , Xu Zhang , Shengdong Du , Tianrui Li

Predicting medications is a crucial task in many intelligent healthcare systems. It can assist doctors in making informed medication decisions for patients according to electronic medical records (EMRs). However, medication prediction is a…

Artificial Intelligence · Computer Science 2022-05-02 Yang An , Bo Jin , Xiaopeng Wei

Throughout the different phases of a drug development program, randomized trials are used to establish the tolerability, safety, and efficacy of a candidate drug. At each stage one aims to optimize the design of future studies by…

Applications · Statistics 2021-02-08 Sebastian Weber , Andrew Gelman , Daniel Lee , Michael Betancourt , Aki Vehtari , Amy Racine

Detecting predictive biomarkers from multi-omics data is important for precision medicine, to improve diagnostics of complex diseases and for better treatments. This needs substantial experimental efforts that are made difficult by the…

Quantitative Methods · Quantitative Biology 2021-06-08 Betül Güvenç Paltun , Samuel Kaski , Hiroshi Mamitsuka

Causal inference is widely used in various fields, such as biology, psychology and economics, etc. In observational studies, we need to balance the covariates before estimating causal effect. This study extends the one-dimensional entropy…

Methodology · Statistics 2022-05-19 Juan Chen , Yingchun Zhou

Estimation of heterogeneous treatment effects is an active area of research. Most of the existing methods, however, focus on estimating the conditional average treatment effects of a single, binary treatment given a set of pre-treatment…

Methodology · Statistics 2025-05-30 Max Goplerud , Kosuke Imai , Nicole E. Pashley

The concept of personalised medicine in cancer therapy is becoming increasingly important. There already exist drugs administered specifically for patients with tumours presenting well-defined mutations. However, the field is still in its…

Biomolecules · Quantitative Biology 2024-08-26 Abbi Abdel-Rehim , Oghenejokpeme Orhobor , Gareth Griffiths , Larisa Soldatova , Ross D. King

Massively multitask neural architectures provide a learning framework for drug discovery that synthesizes information from many distinct biological sources. To train these architectures at scale, we gather large amounts of data from public…

Machine Learning · Statistics 2015-02-10 Bharath Ramsundar , Steven Kearnes , Patrick Riley , Dale Webster , David Konerding , Vijay Pande

Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the…

Genomics · Quantitative Biology 2015-04-09 Andrew L. Beam , Alison Motsinger-Reif , Jon Doyle

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the…

Machine Learning · Computer Science 2023-01-18 Zhihang Hu , Qinze Yu , Yucheng Guo , Taifeng Wang , Irwin King , Xin Gao , Le Song , Yu Li

Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…

Biomolecules · Quantitative Biology 2007-11-13 Jose C Nacher , Jean-Marc Schwartz

Drug target identification is of significant commercial interest to pharmaceutical companies, and there is a vast amount of research done related to the topic of therapeutic target identification. Interdisciplinary research in this area…

Molecular Networks · Quantitative Biology 2013-07-30 Reka Albert , Bhaskar DasGupta , Nasim Mobasheri