Related papers: Drug response prediction by inferring pathway-resp…

High-dimensional deep neural network representations of images and concepts can be aligned to predict human annotations of diverse stimuli. However, such alignment requires the costly collection of behavioral responses, such that, in…

Predicting cancer dynamics under treatment is challenging due to high inter-patient heterogeneity, lack of predictive biomarkers, and sparse and noisy longitudinal data. Mathematical models can summarize cancer dynamics by a few…

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic…

Early identification of sensitive cancer cell lines is essential for accelerating biomarker discovery and elucidating drug mechanism of action. Given the efficiency and low cost of small-scale drug screens relative to extensive omics…

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…

The goal of personalized decision making is to map a unit's characteristics to an action tailored to maximize the expected outcome for that unit. Obtaining high-quality mappings of this type is the goal of the dynamic regime literature. In…

Learning by integrating multiple heterogeneous data sources is a common requirement in many tasks. Collective Matrix Factorization (CMF) is a technique to learn shared latent representations from arbitrary collections of matrices. It can be…

Drug combinations are frequently used for the treatment of cancer patients in order to increase efficacy, decrease adverse side effects, or overcome drug resistance. Given the enormous number of drug combinations, it is cost- and…

We propose a unified framework for adaptive routing in multitask, multimodal prediction settings where data heterogeneity and task interactions vary across samples. Motivated by applications in psychotherapy where structured assessments and…

Learning representations of nodes in a low dimensional space is a crucial task with numerous interesting applications in network analysis, including link prediction, node classification, and visualization. Two popular approaches for this…

One of the promising methods for the treatment of complex diseases such as cancer is combinational therapy. Due to the combinatorial complexity, machine learning models can be useful in this field, where significant improvements have…

The understanding of the type of inhibitory interaction plays an important role in drug design. Therefore, researchers are interested to know whether a drug has competitive or non-competitive interaction to particular protein targets.…

Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently…

We present a novel method to improve pharmacokinetics modeling, an essential step of drug development. Conventional models frequently fail to fully represent the intricacies of drug absorption and distribution, which limits their predictive…

Accurate identification of synergistic treatment combinations and their underlying biological mechanisms is critical across many disease domains, especially cancer. In translational oncology research, preclinical systems such as…

Accurate prediction of drug target interactions is critical for accelerating drug discovery and elucidating complex biological mechanisms. In this work, we frame drug target prediction as a link prediction task on heterogeneous biomedical…

Cancer drug response varies widely across tumors due to multi-layer molecular heterogeneity, motivating computational decision support for precision oncology. Despite recent progress in deep CDR models, robust alignment between…

The idea of "stratified medicine" is an important driver of methodological research on the identification of predictive biomarkers. Most methods proposed so far for this purpose have been developed for the use on randomized data only.…

We investigate the learning of quantitative structure activity relationships (QSARs) as a case-study of meta-learning. This application area is of the highest societal importance, as it is a key step in the development of new medicines. The…

A comprehensive pharmaceutical recommendation system was designed based on the patients and drugs features extracted from Drugs.com and Druglib.com. First, data from these databases were combined, and a dataset of patients and drug…