List of works - Marinka Žitnik

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

scientific article published on 16 November 2017

Building a knowledge graph to enable precision medicine

scientific article published in 2023

COLLECTIVE PAIRWISE CLASSIFICATION FOR MULTI-WAY ANALYSIS OF DISEASE AND DRUG DATA.

scientific article

Co-evolution based machine-learning for predicting functional interactions between human genes

scientific article published on 09 November 2021

Cross-type Biomedical Named Entity Recognition with Deep Multi-Task Learning

scientific article published on 01 May 2019

Data Fusion by Matrix Factorization

scientific article

Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion

scientific article

DeepPurpose: A Deep Learning Library for Drug-Target Interaction Prediction

scientific article published on 04 December 2020

Discovering Novel Cell Types across Heterogeneous Single-cell Experiments

scientific article

Discovering disease-disease associations by fusing systems-level molecular data

scientific article

Embedding Logical Queries on Knowledge Graphs ⬇️

article

Evolution of resilience in protein interactomes across the tree of life

scientific article

Fast optimization of non-negative matrix tri-factorization.

scientific article published on 11 June 2019

GNNExplainer: Generating Explanations for Graph Neural Networks ⬇️

scientific article published in January 2019

GNNGuard: Defending Graph Neural Networks against Adversarial Attacks ⬇️

Gene Prioritization by Compressive Data Fusion and Chaining

scientific article

Gene network inference by fusing data from diverse distributions

scientific article

Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.

scientific article published in June 2014

Graph Meta Learning via Local Subgraphs ⬇️

scientific article published in November 2020

Identification of disease treatment mechanisms through the multiscale interactome

scientific article

Identification of disease treatment mechanisms through the multiscale interactome

Jumping across biomedical contexts using compressive data fusion

scientific article

Large-scale analysis of disease pathways in the human interactome

scientific article published in January 2018

Leveraging the Cell Ontology to classify unseen cell types

scientific article

MARS: discovering novel cell types across heterogeneous single-cell experiments

scientific article published on 19 October 2020

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

scientific article published on 21 September 2018

Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold

scientific article

Modeling polypharmacy side effects with graph convolutional networks.

scientific article

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19

scientific article published on 15 April 2020

Network enhancement as a general method to denoise weighted biological networks

scientific article published in Nature Communications

Open Graph Benchmark: Datasets for Machine Learning on Graphs ⬇️

scholarly article by Weihua Hu et al published November 2020 in Advances in Neural Information Processing Systems 33

Orange: data mining toolbox in Python ⬇️

scholarly article by Janez Demšar et al published August 2013 in Journal of Machine Learning Research

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

scientific article published on 18 January 2016

Predicting multicellular function through multi-layer tissue networks

scientific article published in July 2017

Prioritizing network communities.

scientific article

Scalable non-negative matrix tri-factorization.

scientific article published on 29 December 2017

Scientific discovery in the age of artificial intelligence

scientific article published on 2 August 2023

List of works by Marinka Žitnik

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

Building a knowledge graph to enable precision medicine

COLLECTIVE PAIRWISE CLASSIFICATION FOR MULTI-WAY ANALYSIS OF DISEASE AND DRUG DATA.

Co-evolution based machine-learning for predicting functional interactions between human genes

Cross-type Biomedical Named Entity Recognition with Deep Multi-Task Learning

Data Fusion by Matrix Factorization

Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion

DeepPurpose: A Deep Learning Library for Drug-Target Interaction Prediction

Discovering Novel Cell Types across Heterogeneous Single-cell Experiments

Discovering disease-disease associations by fusing systems-level molecular data

Embedding Logical Queries on Knowledge Graphs ⬇️

Evolution of resilience in protein interactomes across the tree of life

Fast optimization of non-negative matrix tri-factorization.

GNNExplainer: Generating Explanations for Graph Neural Networks ⬇️

GNNGuard: Defending Graph Neural Networks against Adversarial Attacks ⬇️

Gene Prioritization by Compressive Data Fusion and Chaining

Gene network inference by fusing data from diverse distributions

Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.

Graph Meta Learning via Local Subgraphs ⬇️

Identification of disease treatment mechanisms through the multiscale interactome

Identification of disease treatment mechanisms through the multiscale interactome

Jumping across biomedical contexts using compressive data fusion

Large-scale analysis of disease pathways in the human interactome

Leveraging the Cell Ontology to classify unseen cell types

MARS: discovering novel cell types across heterogeneous single-cell experiments

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold

Modeling polypharmacy side effects with graph convolutional networks.

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19

Network enhancement as a general method to denoise weighted biological networks

Open Graph Benchmark: Datasets for Machine Learning on Graphs ⬇️

Orange: data mining toolbox in Python ⬇️

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

Predicting multicellular function through multi-layer tissue networks

Prioritizing network communities.

Scalable non-negative matrix tri-factorization.

Scientific discovery in the age of artificial intelligence

Sieve-based relation extraction of gene regulatory networks from biological literature

SkipGNN: predicting molecular interactions with skip-graph networks

Subgraph Neural Networks ⬇️

To Embed or Not: Network Embedding as a Paradigm in Computational Biology

Unifying single-cell annotations based on the Cell Ontology ⬇️

Unifying single-cell annotations based on the Cell Ontology