List of works - Samuel Kaski

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

scientific article published on 3 October 2017

A community effort to assess and improve drug sensitivity prediction algorithms.

scientific article

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

scientific article from 2017

An information retrieval perspective on visualization of gene expression data with ontological annotation

article

Analysis and visualization of gene expression data using self-organizing maps

scientific article

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

scientific article

Associative clustering for exploring dependencies between functional genomics data sets

scientific article

BCI for Physiological Text Annotation

Bayesian Multi-view Tensor Factorization

Bayesian metabolic flux analysis reveals intracellular flux couplings

scientific article published on 01 July 2019

Bayesian multi-tensor factorization ⬇️

Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data

scientific article published on 01 July 2019

Clustering Based on Conditional Distributions in an Auxiliary Space ⬇️

scientific article published on January 1, 2002

Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

scientific article published on 14 January 2009

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

scientific article

Cross-Species Translation of Multi-way Biomarkers

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

scientific article published on 23 August 2016

Data Visualization and Analysis with Self-Organizing Maps in Learning Metrics

scholarly article by Samuel Kaski et al published 2001 in Lecture Notes in Computer Science

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma

scientific article

Dependencies between stimuli and spatially independent fMRI sources: towards brain correlates of natural stimuli.

scientific article

Depression, depressive symptoms and treatments in women who have recently given birth: UK cohort study

scientific article published on 24 October 2018

Developing a Symbiotic System for Scientific Information Seeking: The MindSee Project

Differentially private Bayesian learning on distributed data ⬇️

Dimensionality Reduction for Data Visualization [Applications Corner]

Directing exploratory search

Directing exploratory search with interactive intent modeling

Discovering heritable modes of MEG spectral power

scientific article published on 01 January 2019

Discriminative clustering

Discriminative components of data

scientific article

Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

scientific article published on September 2016

Efficient differentially private learning improves drug sensitivity prediction

scientific article

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

scientific article published on 10 October 2016

Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data

scientific article

Exploration and retrieval of whole-metagenome sequencing samples

scientific article

Exploratory Clustering of Gene Expression Profiles of Mutated Yeast Strains

article

Exploratory modeling of yeast stress response and its regulation with gCCA and associative clustering

scientific article published on 01 August 2005

Exploring Peripheral Physiology as a Predictor of Perceived Relevance in Information Retrieval

Extracting relevance and affect information from physiological text annotation

Fast Semi-Supervised Discriminative Component Analysis

Fast dependent components for fMRI analysis

Focused Multi-task Learning Using Gaussian Processes

article

Focused multi-task learning in a Gaussian process framework

Fundamentals and Recent Developments in Approximate Bayesian Computation

scientific article published on January 2017

Gender-dependent progression of systemic metabolic states in early childhood

scientific article published on 3 June 2008

Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines

scientific article

Genome-wide association studies with high-dimensional phenotypes

scientific article published in August 2013

Global modeling of transcriptional responses in interaction networks

scientific article

Graph visualization with latent variable models

scholarly article published 2010

Graphical Multi-way Models

article

Group Factor Analysis

scientific article published on 18 December 2014

Hierarchical Generative Biclustering for MicroRNA Expression Analysis ⬇️

scientific article published on March 1, 2011

High density lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy

scientific article

Human Strategic Steering Improves Performance of Interactive Optimization

scientific article published on 7 July 2020

Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis.

scientific article

Identifying fragments of natural speech from the listener's MEG signals

scientific article published on 17 February 2012

Improved learning of Riemannian metrics for exploratory analysis

scientific article

Improved learning of Riemannian metrics for exploratory analysis [Neural Networks 17 (8–9) 1087–1100]

Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches

scientific article published on 15 December 2019

Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge.

scientific article

Infinite factorization of multiple non-parametric views

Integrating neurophysiologic relevance feedback in intent modeling for information retrieval

scientific article published on 12 March 2019

Integrative and personalized QSAR analysis in cancer by kernelized Bayesian matrix factorization

scientific article

Intentradar

Interactive Elicitation of Knowledge on Feature Relevance Improves Predictions in Small Data Sets

Interactive Intent Modeling for Exploratory Search

Interactive intent modeling: Information Discovery Beyond Search

scientific article (publication date: 23 December 2014)

Kernelized Bayesian Matrix Factorization

scientific article published on October 2014

Knowledge elicitation via sequential probabilistic inference for high-dimensional prediction

Learning More Accurate Metrics for Self-Organizing Maps

Learning from Relevant Tasks Only

Likelihood-free inference via classification

scientific article published on 13 March 2017

Likelihood-free inference with deep Gaussian processes

scientific article published in 2022

Local multidimensional scaling

scientific article published on 19 June 2006

Machine Teaching of Active Sequential Learners ⬇️

Machine learning for signal processing 2010

scholarly article by Jaakko Peltonen et al published March 2012 in Neurocomputing

Matching samples of multiple views

MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection

scientific article published on 13 September 2017

Metabolic regulation in progression to autoimmune diabetes

scientific article

Methods for estimating human endogenous retrovirus activities from EST databases

scientific article

Modelling G×E with historical weather information improves genomic prediction in new environments

scientific article published on 01 October 2019

Modelling-based experiment retrieval: a case study with gene expression clustering ⬇️

scientific article published on 6 January 2016

Multi-task and multi-view learning of user state

article

Multitask Learning Using Regularized Multiple Kernel Learning

Multivariate multi-way analysis of multi-source data

scientific article

Natural brain-information interfaces: Recommending information by relevance inferred from human brain signals ⬇️

scientific article

Non-Stationary Spectral Kernels ⬇️

scientific article published in January 2017

On the Identifiability of Transmission Dynamic Models for Infectious Diseases

scientific article

Parameter Inference for Computational Cognitive Models with Approximate Bayesian Computation

scientific article published on 01 June 2019

Phenotype-driven identification of epithelial signalling clusters

scientific article published on 5 March 2018

Predicting term-relevance from brain signals

Preliminary Studies on Personalized Preference Prediction from Gaze in Comparing Visualizations

scholarly article by Hamed R.-Tavakoli et al published 2016 in Lecture Notes in Computer Science

Privacy-preserving data sharing via probabilistic modeling

scientific article published in 2021

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays

scientific article published in January 2011

Probabilistic approach to detecting dependencies between data sets

Probabilistic drug connectivity mapping

scientific article

Probabilistic modeling and machine learning in structural and systems biology

scientific article published on 3 May 2007

Probabilistic retrieval and visualization of biologically relevant microarray experiments

scientific article published on June 2009

Probabilistic retrieval and visualization of biologically relevant microarray experiments

scientific article published on 19 October 2009

Probabilistic toxicogenomics studies in vitro

Relevant subtask learning by constrained mixture models

article by Jaakko Peltonen et al published 5 November 2010 in Intelligent Data Analysis

Representation transfer for differentially private drug sensitivity prediction

scientific article published on 01 July 2019

Rethinking pooling in graph neural networks ⬇️

scientific article published in November 2020

SciNet

SciNet: Interactive Intent Modeling for Information Discovery

scientific article (publication date: 2015)

Searching for functional gene modules with interaction component models

scientific article

Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups

scientific article published in June 2005

Sequential information bottleneck for finite data

Simple integrative preprocessing preserves what is shared in data sources

scientific article

Sparse group factor analysis for biclustering of multiple data sources ⬇️

scientific article

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations

scientific article published on September 2014

Stronger findings from mass spectral data through multi-peak modeling

scientific article

Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods

scientific article published on 04 November 2020

Supervised nonlinear dimensionality reduction by Neighbor Retrieval

Supporting exploratory search tasks with interactive user modeling

Targeted retrieval of gene expression measurements using regulatory models

scientific article published on 27 June 2012

The rocky road to personalized medicine: computational and statistical challenges

Toward computational cumulative biology by combining models of biological datasets ⬇️

scientific article

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures

scientific article from 2015

Towards brain-activity-controlled information retrieval: Decoding image relevance from MEG signals

scientific article published on 13 January 2015

Trustworthiness and metrics in visualizing similarity of gene expression

scientific article

Two-way analysis of high-dimensional collinear data

article

Using dependencies to pair samples for multi-view learning

Visualizations for Assessing Convergence and Mixing of MCMC

scholarly article by Jarkko Venna et al published 2003 in Lecture Notes in Computer Science

Visualizations for assessing convergence and mixing of Markov chain Monte Carlo simulations

scholarly article by Jaakko Peltonen et al published October 2009 in Computational Statistics & Data Analysis

Winner-take-all networks for physiological models of competitive learning

scientific article published in 1994

d3p - A Python Package for Differentially-Private Probabilistic Programming

scientific article published on 05 March 2022

List of works by Samuel Kaski

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

A community effort to assess and improve drug sensitivity prediction algorithms.

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

An information retrieval perspective on visualization of gene expression data with ontological annotation

Analysis and visualization of gene expression data using self-organizing maps

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

Associative clustering for exploring dependencies between functional genomics data sets

BCI for Physiological Text Annotation

Bayesian Multi-view Tensor Factorization

Bayesian metabolic flux analysis reveals intracellular flux couplings

Bayesian multi-tensor factorization ⬇️

Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data

Clustering Based on Conditional Distributions in an Auxiliary Space ⬇️

Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

Cross-Species Translation of Multi-way Biomarkers

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Data Visualization and Analysis with Self-Organizing Maps in Learning Metrics

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma

Dependencies between stimuli and spatially independent fMRI sources: towards brain correlates of natural stimuli.

Depression, depressive symptoms and treatments in women who have recently given birth: UK cohort study

Developing a Symbiotic System for Scientific Information Seeking: The MindSee Project

Differentially private Bayesian learning on distributed data ⬇️

Dimensionality Reduction for Data Visualization [Applications Corner]

Directing exploratory search

Directing exploratory search with interactive intent modeling

Discovering heritable modes of MEG spectral power

Discriminative clustering

Discriminative components of data

Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

Efficient differentially private learning improves drug sensitivity prediction

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data

Exploration and retrieval of whole-metagenome sequencing samples

Exploratory Clustering of Gene Expression Profiles of Mutated Yeast Strains

Exploratory modeling of yeast stress response and its regulation with gCCA and associative clustering

Exploring Peripheral Physiology as a Predictor of Perceived Relevance in Information Retrieval

Extracting relevance and affect information from physiological text annotation

Fast Semi-Supervised Discriminative Component Analysis

Fast dependent components for fMRI analysis

Focused Multi-task Learning Using Gaussian Processes

Focused multi-task learning in a Gaussian process framework

Fundamentals and Recent Developments in Approximate Bayesian Computation

Gender-dependent progression of systemic metabolic states in early childhood

Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines

Genome-wide association studies with high-dimensional phenotypes

Global modeling of transcriptional responses in interaction networks

Graph visualization with latent variable models

Graphical Multi-way Models

Group Factor Analysis

Hierarchical Generative Biclustering for MicroRNA Expression Analysis ⬇️

High density lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy

Human Strategic Steering Improves Performance of Interactive Optimization

Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis.

Identifying fragments of natural speech from the listener's MEG signals

Improved learning of Riemannian metrics for exploratory analysis

Improved learning of Riemannian metrics for exploratory analysis [Neural Networks 17 (8–9) 1087–1100]

Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches

Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge.

Infinite factorization of multiple non-parametric views

Integrating neurophysiologic relevance feedback in intent modeling for information retrieval

Integrative and personalized QSAR analysis in cancer by kernelized Bayesian matrix factorization

Intentradar

Interactive Elicitation of Knowledge on Feature Relevance Improves Predictions in Small Data Sets

Interactive Intent Modeling for Exploratory Search

Interactive intent modeling: Information Discovery Beyond Search

Kernelized Bayesian Matrix Factorization

Knowledge elicitation via sequential probabilistic inference for high-dimensional prediction

Learning More Accurate Metrics for Self-Organizing Maps

Learning from Relevant Tasks Only

Likelihood-free inference via classification

Likelihood-free inference with deep Gaussian processes

Local multidimensional scaling

Machine Teaching of Active Sequential Learners ⬇️

Machine learning for signal processing 2010

Matching samples of multiple views

MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection

Metabolic regulation in progression to autoimmune diabetes

Methods for estimating human endogenous retrovirus activities from EST databases