Samuel Kaski

Balancing Imbalanced Toxicity Models : Using MolBERT with Focal Loss

Muhammad Arslan Masood, Samuel Kaski, Hugo Ceulemans, Dorota Herman, Markus Heinonen 2025 AI in Drug Discovery - 1st International Workshop, AIDD 2024, Held in Conjunction with ICANN 2024, Proceedings

Towards Interpretable Models of Chemist Preferences for Human-in-the-Loop Assisted Drug Discovery

Yasmine Nahal, Markus Heinonen, Mikhail Kabeshov, Jon Paul Janet, Eva Nittinger, Ola Engkvist, Samuel Kaski 2025 AI in Drug Discovery - 1st International Workshop, AIDD 2024, Held in Conjunction with ICANN 2024, Proceedings

Likelihood-free inference in state-space models with unknown dynamics

Alexander Aushev, Thong Tran, Henri Pesonen, Andrew Howes, Samuel Kaski 2024 STATISTICS AND COMPUTING

Embarrassingly Parallel GFlowNets

Tiago da Silva, Luis Max Carvalho, Amauri Souza, Samuel Kaski, Diego Mesquita 2024 Proceedings of the 41st International Conference on Machine Learning

Compositional Sculpting of Iterative Generative Processes

Timur Garipov, Sebastiaan De Peuter, Ge Yang, Vikas Garg, Samuel Kaski, Tommi Jaakkola 2024 Advances in Neural Information Processing Systems 36 - 37th Conference on Neural Information Processing Systems, NeurIPS 2023

Bayesian reduced rank regression models generalizable neural fingerprints that differentiate between individuals in magnetoencephalography data

Joonas Haakana, Susanne Merz, Samuel Kaski, Hanna Renvall, Riitta Salmelin 2024 European Journal of Neuroscience

Intelligent digital tools for screening of brain connectivity and dementia risk estimation in people affected by mild cognitive impairment: the AI-Mind clinical study protocol

Ira H. Haraldsen, Christoffer Hatlestad-Hall, Camillo Marra, Hanna Renvall, Fernando Maestu, Jorge Acosta-Hernandez, Soraya Alfonsin, Vebjorn Andersson, Abhilash Anand, Victor Ayllon, Aleksandar Babic, Asma Belhadi, Cindy Birck, Ricardo Bruna, Naike Caraglia, Claudia Carrarini, Erik Christensen, Americo Cicchetti, Signe Daugbjerg, Rossella Di Bidino, Ana Diaz-Ponce, Ainar Drews, Guido Maria Giuffre, Jean Georges, Pedro Gil-Gregorio, Dianne Gove, Tim M. Govers, Harry Hallock, Marja Hietanen, Lone Holmen, Jaakko Hotta, Samuel Kaski, Rabindra Khadka, Antti S. Kinnunen, Anne M. Koivisto, Shrikanth Kulashekhar, Denis Larsen, Mia Liljeström, Pedro G. Lind, Alberto Marcos Dolado, Serena Marshall, Susanne Merz, Francesca Miraglia, Juha Montonen, Ville Mäntynen, Anne Rita Oksengard, Javier Olazaran, Teemu Paajanen, Jose M. Pena, Luis Pena, Daniel lrabien Peniche, Ana S. Perez, Mohamed Radwan, Federico Ramirez-Torano, Andrea Rodriguez-Pedrero, Timo Saarinen, Mario Salas-Carrillo, Riitta Salmelin, Sonia Sousa, Abdillah Suyuthi, Mathias Toft, Pablo Toharia, Thomas Tveitstol, Mats Tveter, Ramesh Upreti, Robin J. Vermeulen, Fabrizio Vecchio, Anis Yazidi, Paolo Maria Rossini 2024 Frontiers in Neurorobotics

Estimating treatment effects from single-arm trials via latent-variable modeling

Manuel Haussmann, Tran Minh Son Le, Viivi Halla-aho, Samu Kurki, Jussi Leinonen, Miika Koskinen, Samuel Kaski, Harri Lähdesmäki 2024 Proceedings of the 27th International Conference on Artificial Intelligence and Statistics

Learning Robust Statistics for Simulation-based Inference under Model Misspecification

Daolang Huang, Ayush Bharti, Amauri Holanda De Souza Junior, Luigi Acerbi, Samuel Kaski 2024 Advances in Neural Information Processing Systems 36 - 37th Conference on Neural Information Processing Systems, NeurIPS 2023

Practical Equivariances via Relational Conditional Neural Processes

Daolang Huang, Manuel Haussmann, Ulpu Remes, Ti John, Grégoire Clarté, Kevin Sebastian Luck, Samuel Kaski, Luigi Acerbi 2024 Advances in Neural Information Processing Systems 36 - 37th Conference on Neural Information Processing Systems, NeurIPS 2023

Virtual laboratories : Transforming research with AI

Arto Klami, Theo Damoulas, Ola Engkvist, Patrick Rinke, Samuel Kaski 2024 Data-Centric Engineering

Uncoupled Learning of Differential Stackelberg Equilibria with Commitments

Robert Loftin, Mustafa Mert Çelikok, Herke van Hoof, Samuel Kaski, Frans A. Oliehoek 2024 AAMAS '24: Proceedings of the 23rd International Conference on Autonomous Agents and Multiagent Systems

Deep Bayesian Experimental Design for Drug Discovery

Muhammad Arslan Masood, Tianyu Cui, Samuel Kaski 2024 AI in Drug Discovery - 1st International Workshop, AIDD 2024, Held in Conjunction with ICANN 2024, Proceedings

Metis : a Python-based user interface to collect expert feedback for generative chemistry models

Janosch Menke, Yasmine Nahal, Esben Jannik Bjerrum, Mikhail Kabeshov, Samuel Kaski, Ola Engkvist 2024 Journal of Cheminformatics

Collaborative learning from distributed data with differentially private synthetic data

Lukas Prediger, Joonas Jälkö, Antti Honkela, Samuel Kaski 2024 BMC Medical Informatics and Decision Making

Entity Footprinting: Modeling Contextual User States via Digital Activity Monitoring

Zeinab Rezaei Yousefi, Tung Vuong, Marie Al-Ghossein, Tuukka Ruotsalo, Giulio Jacucci, Samuel Kaski 2024 ACM Transactions on Interactive Intelligent Systems

Input-gradient space particle inference for neural network ensembles

Trung Trinh, Markus Heinonen, Luigi Acerbi, Samuel Kaski 2024 The Twelfth International Conference on Learning Representations

Open Ad Hoc Teamwork with Cooperative Game Theory

Jianhong Wang, Yang Li, Yuan Zhang, Wei Pan, Samuel Kaski 2024 Proceedings of the 41st International Conference on Machine Learning

Online Simulator-Based Experimental Design for Cognitive Model Selection

Alexander Aushev, Aini Putkonen, Grégoire Clarté, Suyog Chandramouli, Luigi Acerbi, Samuel Kaski, Andrew Howes 2023 Computational Brain and Behavior

Optimally-weighted Estimators of the Maximum Mean Discrepancy for Likelihood-Free Inference

Ayush Bharti, Masha Naslidnyk, Oscar Key, Samuel Kaski, Francois Xavier Briol 2023 Proceedings of the 40th International Conference on Machine Learning

Modeling needs user modeling

Mustafa Mert Çelikok, Pierre Alexandre Murena, Samuel Kaski 2023 Frontiers in Artificial Intelligence

Teaching to Learn

Mustafa Mert Çelikok, Pierre Alexandre Murena, Samuel Kaski 2023 AAAI-23 Technical Tracks 5

Toward AI assistants that let designers design

Sebastiaan De Peuter, Antti Oulasvirta, Samuel Kaski 2023 AI Magazine

Zero-Shot Assistance in Sequential Decision Problems

Sebastiaan De Peuter, Samuel Kaski 2023 AAAI-23 Technical Tracks 10

Differentiable user models

Alex Hämäläinen, Mustafa Mert Celikok, Samuel Kaski 2023 Proceedings of the 39th Conference on Uncertainty in Artificial Intelligence (UAI 2023)

DPVIm: Differentially Private Variational Inference Improved

Joonas Jälkö, Lukas Prediger, Antti Honkela, Samuel Kaski 2023 Transactions on Machine Learning Research

Cooperative Bayesian Optimization for Imperfect Agents

Ali Khoshvishkaie, Petrus Mikkola, Pierre Alexandre Murena, Samuel Kaski 2023 Machine Learning and Knowledge Discovery in Databases : Research Track - European Conference, ECML PKDD 2023, Proceedings

Multi-Fidelity Bayesian Optimization with Unreliable Information Sources

Petrus Mikkola, Julien Martinelli, Louis Filstroff, Samuel Kaski 2023 Proceedings of the 26th International Conference on Artificial Intelligence and Statistics

Prior knowledge elicitation: The past, present, and future

Petrus Mikkola, Osvaldo Martin, Suyog Halasinamara Chandramouli, Marcelo Hartmann, Oriol Abril Pla, Owen Thomas, Henri Pesonen, Jukka Corander, Aki Vehtari, Samuel Kaski, Paul-Christian Burkner, Arto Klami 2023 Bayesian Analysis

Chemistry-Based Modeling on Phenotype-Based Drug-Induced Liver Injury Annotation : From Public to Proprietary Data

Mohammad Moein, Markus Heinonen, Natalie Mesens, Ronnie Chamanza, Chidozie Amuzie, Yvonne Will, Hugo Ceulemans, Samuel Kaski, Dorota Herman 2023 Chemical Research in Toxicology

ABC of the future

Henri Pesonen, Umberto Simola, Alvaro Köhn-Luque, Henri Vuollekoski, Xiaoran Lai, Arnoldo Frigessi, Samuel Kaski, David T. Frazier, Worapree Maneesoonthorn, Gael M. Martin, Jukka Corander 2023 International Statistical Review

Noise-Aware Statistical Inference with Differentially Private Synthetic Data

Ossi Räisä, Joonas Jälkö, Samuel Kaski, Antti Honkela 2023 Proceedings of The 26th International Conference on Artificial Intelligence and Statistics (AISTATS) 2023

A fast method to generate hundreds of thousands of synthetic genomes and phenotypes

Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Rahul Gupta, Remo Monti, Ying Wang, Pier Francesco Palamara, Samuel Kaski, Andrea Ganna, Christoph Lippert, Pekka Marttinen 2023 European Journal of Human Genetics

Characterizing personalized effects of family information on disease risk using graph representation learning

Sophie Wharrie, Zhiyu Yang, Andrea Ganna, Samuel Kaski 2023 Proceedings of the 8th Machine Learning for Healthcare Conference

HAPNEST : efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes

Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Remo Monti, Rahul Gupta, Ying Wang, Alicia Martin, Luke J. O'Connor, Samuel Kaski, Pekka Marttinen, Pier Francesco Palamara, Christoph Lippert, Andrea Ganna 2023 Bioinformatics (Oxford, England)

The influence of inter-regional delays in generating large-scale brain networks of phase synchronization

N. Williams, A. Ojanperä, F. Siebenhühner, B. Toselli, S. Palva, G. Arnulfo, S. Kaski, J. M. Palva 2023 NeuroImage

Stochastic cluster embedding

Zhirong Yang, Yuwei Chen, Denis Sedov, Samuel Kaski, Jukka Corander 2023 STATISTICS AND COMPUTING

Imitation-guided Multimodal Policy Generation from Behaviourally Diverse Demonstrations

Shibei Zhu, Rituraj Kaushik, Samuel Kaski, Ville Kyrki 2023 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)

Parallel MCMC Without Embarrassing Failures

Daniel Augusto de Souza, Diego Parente Paiva Mesquita, Samuel Kaski, Luigi Acerbi 2022 Proceedings of The 25th International Conference on Artificial Intelligence and Statistics

Likelihood-Free Inference with Deep Gaussian Processes

Alexander Aushev, Henri Pesonen, Markus Heinonen, Jukka Corander, Samuel Kaski 2022 Computational Statistics & Data Analysis

Approximate Bayesian Computation with Domain Expert in the Loop

Ayush Bharti, Louis Filstroff, Samuel Kaski 2022 Proceedings of the 39th International Conference on Machine Learning

Best-Response Bayesian Reinforcement Learning with Bayes-adaptive POMDPs for Centaurs

Mustafa Mert Çelikok, Frans A. Oliehoek, Samuel Kaski 2022 International Conference on Autonomous Agents and Multiagent Systems, AAMAS 2022

Deconfounded Representation Similarity for Comparison of Neural Networks

Tianyu Cui, Yogesh Kumar, Pekka Marttinen, Samuel Kaski 2022 Advances in Neural Information Processing Systems 35 (NeurIPS 2022)

Gene–gene interaction detection with deep learning

Tianyu Cui, Khaoula El Mekkaoui, Jaakko Reinvall, Aki S. Havulinna, Pekka Marttinen, Samuel Kaski 2022 Communications Biology

DIVERSE: Bayesian Data IntegratiVE learning for precise drug ResponSE prediction

Betul Guvencpaltun, Samuel Kaski, Hiroshi Mamitsuka 2022 IEEE/ACM Transactions on Computational Biology and Bioinformatics

Variational multiple shooting for Bayesian ODEs with Gaussian processes

Pashupati Hedge, Cagatay Yildiz, Harri Lähdesmäki, Samuel Kaski, Markus Heinonen 2022 Proceedings of the 38th Conference on Uncertainty in Artificial Intelligence (UAI 2022), PMLR

Targeted Causal Elicitation

Nazaal Ibrahim, Ti John, Zhigao Guo, Samuel Kaski 2022

Identification of multiplicatively acting modulatory mutational signatures in cancer

Dovydas Kičiatovas, Qingli Guo, Miika Kailas, Henri Pesonen, Jukka Corander, Samuel Kaski, Esa Pitkänen, Ville Mustonen 2022 BMC Bioinformatics

The relationship between electrophysiological and hemodynamic measures of neural activity varies across picture naming tasks: A multimodal magnetoencephalography-functional magnetic resonance imaging study

Tommi Mononen, Jan Kujala, Mia Liljeström, Eemeli Leppäaho, Samuel Kaski, Riitta Salmelin 2022 Frontiers in Neuroscience

Human-in-the-Loop Large-Scale Predictive Maintenance of Workstations

Alexander Nikitin, Samuel Kaski 2022 KDD '22: Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

Non-separable spatio-temporal graph kernels via SPDEs

Alexander Nikitin, ST John, Arno Solin, Samuel Kaski 2022 Proceedings of The 25th International Conference on Artificial Intelligence and Statistics

d3p - A Python Package for Differentially-Private Probabilistic Programming

Lukas Prediger, Niki Loppi, Samuel Kaski, Antti Honkela 2022 Proceedings of Privacy Enhancing Technologies

Accounting for stellar activity signals in radial-velocity data by using change point detection techniques star

U. Simola, A. Bonfanti, X. Dumusque, J. Cisewski-Kehe, S. Kaski, J. Corander 2022 Astronomy & Astrophysics

Provably expressive temporal graph networks

Amauri H. Souza, Diego Mesquita, Samuel Kaski, Vikas Garg 2022 Advances in Neural Information Processing Systems 35 (NeurIPS 2022)

Human-in-the-loop assisted de novo molecular design

Iiris Sundin, Alexey Voronov, Haoping Xiao, Kostas Papadopoulos, Esben Jannik Bjerrum, Markus Heinonen, Atanas Patronov, Samuel Kaski, Ola Engkvist 2022 Journal of Cheminformatics

Likelihood-free inference by ratio estimation

Owen M. Thomas, Ritabrata Dutta, Jukka Corander, Samuel Kaski, Michael Gutmann 2022 Bayesian Analysis

Tackling covariate shift with node-based Bayesian neural networks

Trung Q Trinh, Markus Heinonen, Luigi Acerbi, Samuel Kaski 2022 Proceedings of the 39th International Conference on Machine Learning

Modular Flows: Differential Molecular Generation

Yogesh Verma, Samuel Kaski, Markus Heinonen, Vikas Garg 2022 Advances in Neural Information Processing Systems 35 (NeurIPS 2022)

EntityBot : Actionable Entity Recommendations for Everyday Digital Task

Tung Vuong, Salvatore Andolina, Giulio Jacucci, Pedram Daee, Khalil Klouche, Mats Sjöberg, Tuukka Ruotsalo, Samuel Kaski 2022 CHI 2022 - Extended Abstracts of the 2022 CHI Conference on Human Factors in Computing Systems

HAPNEST: an efficient tool for generating large-scale genetics datasets from limited training data

Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Remo Monti, Rahul Gupta, Ying Wang, Alicia Martin, Luke J O'Connor, Samuel Kaski, Pekka Marttinen, Pier Francesco Palamara, Christoph Lippert, Andrea Ganna 2022

Informative Bayesian Neural Network Priors for Weak Signals

Tianyu Cui, Aki S. Havulinna, Pekka Marttinen, Samuel Kaski 2021 Bayesian Analysis

Federated Stochastic Gradient Langevin Dynamics

Khaoula El Mekkaoui, Diego Parente Paiva Mesquita, Paul Blomstedt, Samuel Kaski 2021 Proceedings of the Thirty-Seventh Conference on Uncertainty in Artificial Intelligence

Machine learning approaches for drug combination therapies

Betul Guvenc, Samuel Kaski, Hiroshi Mamitsuka 2021 Briefings in Bioinformatics

Bayesian inference of ODEs with Gaussian processes

Pashupati Hegde, Çağatay Yıldız, Harri Lähdesmäki, Samuel Kaski, Markus Heinonen 2021 arXiv.org

Entity Recommendation for Everyday Digital Tasks

Giulio Jacucci, Pedram Daee, Tung Vuong, Salvatore Andolina, Khalil Klouche, Mats Sjöberg, Tuukka Ruotsalo, Samuel Kaski 2021 ACM Transactions on Computer-Human Interaction

Privacy-preserving data sharing via probabilistic modeling

Joonas Jälkö, Eemil Lagerspetz, Jari Haukka, Sasu Tarkoma, Antti Honkela, Samuel Kaski 2021 Patterns

Behaviour-Conditioned Policies for Cooperative Reinforcement Learning Tasks

Antti Keurulainen, Isak Westerlund, Ariel Kwiatkowski, Samuel Kaski, Alexander Ilin 2021 Artificial Neural Networks and Machine Learning – ICANN 2021 - 30th International Conference on Artificial Neural Networks, Proceedings

Learning to Assist Agents by Observing Them

Antti Keurulainen, Isak Westerlund, Samuel Kaski, Alexander Ilin 2021 Artificial Neural Networks and Machine Learning – ICANN 2021 - 30th International Conference on Artificial Neural Networks, Proceedings

Differentially Private Bayesian Inference for Generalized Linear Models

Tejas Kulkarni, Joonas Jälkö, Antti Koskela, Samuel Kaski, Antti Honkela 2021 Proceedings of the 38th International Conference on Machine Learning

Bayesian Inference for Optimal Transport with Stochastic Cost

Anton Mallasto, Markus Heinonen, Samuel Kaski 2021 Proceedings of Asian Conference on Machine Learning

Is this company a lead customer? Estimating stages of B2B buying journey

Neda B. Marvasti, Juho-Petteri Huhtala, Zeinab R. Yousefi, Iiro Vaniala, Bikesh Upreti, Pekka Malo, Samuel Kaski, Henrikki Tikkanen 2021 Industrial Marketing Management

Decision Rule Elicitation for Domain Adaptation

Alexander Nikitin, Samuel Kaski 2021 26th International Conference on Intelligent User Interfaces, IUI 2021

De-randomizing MCMC dynamics with the diffusion Stein operator

Zheyang Shen, Markus Heinonen, Samuel Kaski 2021 Advances in Neural Information Processing Systems 34 - 35th Conference on Neural Information Processing Systems, NeurIPS 2021

Online content match-making in B2B markets

Bikesh Raj Upreti, Juho-Petteri Huhtala, Henrikki Tikkanen, Pekka Malo, Neda Marvasti, Samuel Kaski, Iiro Vaniala, Pekka Mattila 2021 Industrial Marketing Management

EntityBot

Tung Vuong, Salvatore Andolina, Giulio Jacucci, Pedram Daee, Khalil Klouche, Mats Sjöberg, Tuukka Ruotsalo, Samuel Kaski 2021 RecSys 2021 - 15th ACM Conference on Recommender Systems

A decision-theoretic approach for model interpretability in Bayesian framework

Homayun Afrabandpey, Tomi Peltola, Juho Piironen, Aki Vehtari, Samuel Kaski 2020 Machine Learning

Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium

Sergio Arredondo-Alonso, Janetta Top, Alan McNally, Santeri Puranen, Maiju Pesonen, Johan Pensar, Pekka Marttinen, Johanna Braat, Malbert Rogers, Willem van Schaik, Samuel Kaski, Rob J L Willems, Jukka Corander, Anita Schürch 2020 MBIO

Deep Convolutional Gaussian Processes

Kenneth Blomqvist, Samuel Kaski, Markus Heinonen 2020 Machine Learning and Knowledge Discovery in Databases - European Conference, ECML PKDD 2019, Proceedings

Human Strategic Steering Improves Performance of Interactive Optimization

Fabio Colella, Pedram Daee, Jussi Jokinen, Antti Oulasvirta, Samuel Kaski 2020 UMAP 2020 - Proceedings of the 28th ACM Conference on User Modeling, Adaptation and Personalization

Learning Global Pairwise Interactions with Bayesian Neural Networks

Tianyu Cui, Pekka Marttinen, Samuel Kaski 2020 ECAI 2020 - 24th European Conference on Artificial Intelligence, including 10th Conference on Prestigious Applications of Artificial Intelligence, PAIS 2020 - Proceedings

Rethinking pooling in graph neural networks

Diego Mesquita, Amauri Souza, Samuel Kaski 2020 Advances in Neural Information Processing Systems 33 pre-proceedings (NeurIPS 2020)

Projective Preferential Bayesian Optimization

Petrus Mikkola, Milica Todorovic, Jari Järvi, Patrick Rinke, Samuel Kaski 2020 37th International Conference on Machine Learning, ICML 2020

Interactive faceted query suggestion for exploratory search

Tuukka Ruotsalo, Giulio Jacucci, Samuel Kaski 2020 JOURNAL OF THE ASSOCIATION FOR INFORMATION SCIENCE AND TECHNOLOGY

Learning spectrograms with convolutional spectral kernels

Zheyang Shen, Markus Heinonen, Samuel Kaski 2020 The 23rd International Conference on Artificial Intelligence and Statistics

Scalable Probabilistic Matrix Factorization with Graph-Based Priors

Jonathan Strahl, Jaakko Peltonen, Hiroshi Mamitsuka, Samuel Kaski 2020 Proceedings of AAAI-20, AAAI Conference on Artificial Intelligence

A high-performance implementation of Bayesian matrix factorization with limited communication

Tom Vander Aa, Xiangju Qin, Paul Blomstedt, Roel Wuyts, Wilfried Verachtert, Samuel Kaski 2020 Computational Science – ICCS 2020 - 20th International Conference, Proceedings

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

Sanni Voutilainen, Markus Heinonen, Martina Andberg, Emmi Jokinen, Hannu Maaheimo, Johan Pääkkönen, Nina Hakulinen, Juha Rouvinen, Harri Lähdesmäki, Samuel Kaski, Juho Rousu, Merja Penttilä, Anu Koivula 2020 Applied Microbiology and Biotechnology

Human-in-the-loop Active Covariance Learning for Improving Prediction in Small Data Sets

Homayun Afrabandpey, Tomi Peltola, Samuel Kaski 2019 Proceedings of the 28th International Joint Conference on Artificial Intelligence, IJCAI 2019

Is the potential B2B buyer interested or ready to buy? Estimating the stage of the B2B buying behavior

Neda Barzegar Marvasti, Juho-Petteri Huhtala, Zeinab Rezaei Yousefi, Bikesh Upreti, Pekka Malo, Samuel Kaski, Henrikki Tikkanen 2019

Interactive AI with a Theory of Mind

Mustafa Mert Çelikok, Tomi Peltola, Pedram Daee, Samuel Kaski 2019

Block HSIC Lasso

Héctor Climente-González, Chloé Agathe Azencott, Samuel Kaski, Makoto Yamada 2019 Bioinformatics

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

Jussi Gillberg, Pekka Marttinen, Hiroshi Mamitsuka, Samuel Kaski 2019 Bioinformatics (Oxford, England)

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

Betul Guvenc, Hiroshi Mamitsuka, Samuel Kaski 2019 Briefings in Bioinformatics

Deep learning with differential Gaussian process flows

Pashupati Hegde, Markus Heinonen, Harri Lähdesmäki, Samuel Kaski 2019 The 22nd International Conference on Artificial Intelligence and Statistic

Bayesian metabolic flux analysis reveals intracellular flux couplings

Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki 2019 Bioinformatics

Aaltovaikutus = The Aalto Effect

Minna Hölttä, Andrew Flowers, Riikka Hopiavaara, Riitta Särkisilta-Lundberg, Annamari Tolonen, Helena Seppälä, Niina Norjamäki, Susanna Rosin, Terhi Ollikainen, Krista Kinnunen, Tiina Aulanko-Jokirinne, Sanna Syri, Mari Lundström, Teemu Malmi, Tuukka Saarimaa, Susanna Helke, Samuel Kaski, Markus Mäkelä, Milos Mladenovic, Heikki Remes 2019

Integrating neurophysiologic relevance feedback in intent modeling for information retrieval

Giulio Jacucci, Oswald Barral, Pedram Daee, Markus Wenzel, Baris Serim, Tuukka Ruotsalo, Patrik Pluchino, Jonathan Freeman, Luciano Gamberini, Samuel Kaski, Benjamin Blankertz 2019 JOURNAL OF THE ASSOCIATION FOR INFORMATION SCIENCE AND TECHNOLOGY

Parameter Inference for Computational Cognitive Models with Approximate Bayesian Computation

Antti Kangasrääsiö, Jussi P.P. Jokinen, Antti Oulasvirta, Andrew Howes, Samuel Kaski 2019 Cognitive Science

Discovering heritable modes of MEG spectral power

Eemeli Leppäaho, Hanna Renvall, Elina Salmela, Juha Kere, Riitta Salmelin, Samuel Kaski 2019 Human Brain Mapping

Resolving outbreak dynamics using approximate bayesian computation for stochastic birth–death models

Jarno Lintusaari, Paul Blomstedt, Brittany Rose, Tuomas Sivula, Michael U. Gutmann, Samuel Kaski, Jukka Corander 2019 Wellcome Open Research

Learning Image Relations with Contrast Association Networks

Yao Lu, Zhirong Yang, Juho Kannala, Samuel Kaski 2019 2019 International Joint Conference on Neural Networks, IJCNN 2019

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, Jordi Abante, Barbara Schmitz Abecassis, Nanne Aben, Delasa Aghamirzaie, Tero Aittokallio, Farida S. Akhtari, Bissan Al-lazikani, Tanvir Alam, Amin Allam, Chad Allen, Mariana Pelicano de Almeida, Doaa Altarawy, Vinicius Alves, Alicia Amadoz, Benedict Anchang, Albert A. Antolin, Jeremy R. Ash, Victoria Romeo Aznar, Wail Ba-alawi, Moeen Bagheri, Vladimir Bajic, Gordon Ball, Pedro J. Ballester, Delora Baptista, Christopher Bare, Mathilde Bateson, Andreas Bender, Denis Bertrand, Bhagya Wijayawardena, Keith A. Boroevich, Evert Bosdriesz, Mehmet Gonen, Samuel Kaski, Suleiman Ali Khan, Hiroshi Mamitsuka, Pekka Marttinen, Xin Wang, Alexey Zakharov 2019 Nature Communications

Embarrassingly parallel MCMC using deep invertible transformations

Diego Mesquita, Paul Blomstedt, Samuel Kaski 2019 Proceedings of The 35th Uncertainty in Artificial Intelligence Conference

Representation transfer for differentially private drug sensitivity prediction

Teppo Niinimäki, Mikko A. Heikkilä, Antti Honkela, Samuel Kaski 2019 Bioinformatics

Machine Teaching of Active Sequential Learners

Tomi Peltola, Mustafa Mert Çelikok, Pedram Daee, Samuel Kaski 2019 33rd Conference on Neural Information Processing Systems

Distributed Bayesian matrix factorization with limited communication

Xiangju Qin, Paul Blomstedt, Eemeli Leppäaho, Pekka Parviainen, Samuel Kaski 2019 Machine Learning

Scalable Bayesian non-linear matrix completion

Xiangju Qin, Paul Blomstedt, Samuel Kaski 2019 Proceedings of the 28th International Joint Conference on Artificial Intelligence, IJCAI 2019

Harmonizable mixture kernels with variational Fourier features

Zheyang Shen, Markus Heinonen, Samuel Kaski 2019 The 22nd International Conference on Artificial Intelligence and Statistics

Local dimension reduction of summary statistics for likelihood-free inference

Jukka Siren, Samuel Kaski 2019 STATISTICS AND COMPUTING

Active Learning for Decision-Making from Imbalanced Observational Data

Iiris Sundin, Peter Schulam, Eero Siivola, Aki Vehtari, Suchi Saria, Samuel Kaski 2019 36th International Conference on Machine Learning, ICML 2019

User Modelling for Avoiding Overfitting in Interactive Knowledge Elicitation for Prediction

Pedram Daee, Tomi Peltola, Aki Vehtari, Samuel Kaski 2018 IUI 2018 - Proceedings of the 23rd International Conference on Intelligent User Interfaces

Likelihood-free inference via classification

Michael U. Gutmann, Ritabrata Dutta, Samuel Kaski, Jukka Corander 2018 STATISTICS AND COMPUTING

Variational zero-inflated Gaussian processes with sparse kernels

Pashupati Hegde, Markus Heinonen, Samuel Kaski 2018 34th Conference on Uncertainty in Artificial Intelligence 2018, UAI 2018

Efficient differentially private learning improves drug sensitivity prediction

Antti Honkela, Mrinal Das, Arttu Nieminen, Onur Dikmen, Samuel Kaski 2018 Biology Direct

Inverse reinforcement learning from summary data

Antti Kangasrääsiö, Samuel Kaski 2018 Machine Learning

AI is far from ready

Samuel Kaski 2018

ELFI: Engine for likelihood-free inference

Jarno Lintusaari, Henri Vuollekoski, Antti Kangasrääsiö, Kusti Skytén, Marko Järvenpää, Pekka Marttinen, Michael U. Gutmann, Aki Vehtari, Jukka Corander, Samuel Kaski 2018 Journal of Machine Learning Research

Phenotype-driven identification of epithelial signalling clusters

Elsa Marques, Tomi Peltola, Samuel Kaski, Juha Klefström 2018 Scientific Reports

Deep Transfer Learning of Representations for Differentially Private Learning

Teppo Niinimäki, Mikko A. Heikkilä, Samuel Kaski, Antti Honkela 2018

Probabilistic Formulation of the Take The Best Heuristic

Tomi Peltola, Jussi Jokinen, Samuel Kaski 2018 CogSci 2018 Proceedings

Depression, depressive symptoms and treatments in women who have recently given birth

Irene Petersen, Tomi Peltola, Samuel Kaski, Kate R Walters, Sarah Hardoon 2018 BMJ Open

Interactive Intent Modeling for Exploratory Search

Tuukka Ruotsalo, Jaakko Peltonen, Manuel JA Eugster, Dorota Glowacka, Patrik Floréen, Petri Myllymäki, Giulio Jacucci, Samuel Kaski 2018 ACM Transactions on Information Systems

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

Iiris Sundin, Tomi Peltola, Luana Micallef, Homayun Afrabandpey, Marta Soare, Muntasir Mamun Majumder, Pedram Daee, Chen He, Baris Serim, Aki Havulinna, Caroline Heckman, Giulio Jacucci, Pekka Marttinen, Samuel Kaski 2018 Bioinformatics

Using counterfactual queries to improve models for decision-support

Iiris Sundin, Peter Schulam, Eero Siivola, Aki Vehtari, Suchi Saria, Samuel Kaski 2018

Interactive Prior Elicitation of Feature Similarities for Small Sample Size Prediction

Homayun Afrabandpey, Tomi Peltola, Samuel Kaski 2017 Proceedings of the 25th Conference on User Modeling, Adaptation and Personalization

The inconvenience of data of convenience

Chloé Agathe Azencott, Tero Aittokallio, Sushmita Roy, Thea Norman, Stephen Friend, Gustavo Stolovitzky, Anna Goldenberg, Ankit Agrawal, Emmanuel Barillot, Nikolai Bessonov, Deborah Chasman, Urszula Czerwinska, Alireza Fotuhi Siahpirani, Jan Greenberg, Manuel Huber, Samuel Kaski, Christoph Kurz, Marsha Mailick, Michael Merzenich, Nadya Morozova, Arezoo Movaghar, Mor Nahum, Torbjörn E.M. Nordling, Robert Penner, Krishanu Saha, Asif Salim, Siamak Sorooshyari, Vassili Soumelis, Alit Stark-Inbar, Audra Sterling, S. S. Shiju, Jing Tang, Alen Tosenberger, Thomas Van Vieet, Krister Wennerberg, Andrey Zinovyev 2017 Nature Methods

BCI for physiological text annotation

Oswald Barral, Ilkka Kosunen, Tuukka Ruotsalo, Michiel M. Spapé, Manuel J A Eugster, Niklas Ravaja, Samuel Kaski, Giulio Jacucci 2017 BCIforReal 2017 - Proceedings of the 2017 ACM Workshop on An Application-Oriented Approach to BCI Out of the Laboratory, co-located with IUI 2017

Multi-view kernel completion

Sahely Bhadra, Samuel Kaski, Juho Rousu 2017 Machine Learning

Knowledge elicitation via sequential probabilistic inference for high-dimensional prediction

Pedram Daee, Tomi Peltola, Marta Soare, Samuel Kaski 2017 Machine Learning

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

Mehmet Gönen, Barbara A. Weir, Glenn S. Cowley, Francisca Vazquez, Yuanfang Guan, Alok Jaiswal, Masayuki Karasuyama, Vladislav Uzunangelov, Tao Wang, Aviad Tsherniak, Sara Howell, Daniel Marbach, Bruce Hoff, Thea C. Norman, Antti Airola, Adrian Bivol, Kerstin Bunte, Daniel Carlin, Sahil Chopra, Alden Deran, Kyle Ellrott, Peddinti Gopalacharyulu, Kiley Graim, Samuel Kaski, Suleiman A. Khan, Yulia Newton, Sam Ng, Tapio Pahikkala, Evan Paull, Artem Sokolov, Hao Tang, Jing Tang, Krister Wennerberg, Yang Xie, Xiaowei Zhan, Fan Zhu, Tero Aittokallio, Hiroshi Mamitsuka, Joshua M. Stuart, Jesse S. Boehm, David E. Root, Guanghua Xiao, Gustavo Stolovitzky, William C. Hahn, Adam A. Margolin 2017 Cell Systems

MediSyn

Chen He, Luana Micallef, Zia-Ur-Rehman Tanoli, Samuel Kaski, Tero Aittokallio, Giulio Jacucci 2017 BMC Bioinformatics

Differentially Private Bayesian Learning on Distributed Data

Mikko A. Heikkilä, Eemil Lagerspetz, Samuel Kaski, Kana Shimizu, Sasu Tarkoma, Antti Honkela 2017 Advances in Neural Information Processing Systems 30

Inference of Strategic Behavior based on Incomplete Observation Data

Antti Kangasrääsiö, Samuel Kaski 2017 NIPS17 Workshop: Learning in the Presence of Strategic Behavior

Inferring Cognitive Models from Data using Approximate Bayesian Computation

Antti Kangasrääsiö, Kumaripaba Athukorala, Andrew Howes, Jukka Corander, Samuel Kaski, Antti Oulasvirta 2017 Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems

Modelling Human Decision-making based on Aggregate Observation Data

Antti Kangasrääsiö, Samuel Kaski 2017 Human In The Loop-ML Workshop at ICML

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

Pekka Kohonen, Juuso A. Parkkinen, Egon L. Willighagen, Rebecca Ceder, Krister Wennerberg, Samuel Kaski, Roland C. Grafström 2017 Nature Communications

GFA

Eemeli Leppäaho, Muhammad Ammad-ud-din, Samuel Kaski 2017 Journal of Machine Learning Research

ELFI, a software package for likelihood-free inference

Jarno Lintusaari, Henri Vuollekoski, Antti Kangasrääsiö, Kusti Skyten, Marko Järvenpää, Michael Gutmann, Aki Vehtari, Jukka Corander, Samuel Kaski 2017

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

Luana Micallef, Iiris Sundin, Pekka Marttinen, Muhammad Ammad-Ud-Din, Tomi Peltola, Marta Soare, Giulio Jacucci, Samuel Kaski 2017 IUI 2017 - Proceedings of the 22nd International Conference on Intelligent User Interfaces

Learning structures of Bayesian networks for variable groups

Pekka Parviainen, Samuel Kaski 2017 International Journal of Approximate Reasoning

A Mutually-Dependent Hadamard Kernel for Modelling Latent Variable Couplings

Sami Remes, Markus Heinonen, Samuel Kaski 2017 Proceedings of the 9th Asian Conference on Machine Learning

Non-Stationary Spectral Kernels

Sami Remes, Markus Heinonen, Samuel Kaski 2017 Advances in Neural Information Processing Systems 30

Low-dimensional information discovery and presentation system, apparatus and method

Tuukka Ruotsalo, Jaakko Peltonen, Manuel Eugster, Petri Myllymäki, Giulio Jacucci, Samuel Kaski, Dorota Glowacka 2017

Regression with n → 1 by expert knowledge elicitation

Marta Soare, Muhammad Ammad-Ud-din, Samuel Kaski 2017 Proceedings - 2016 15th IEEE International Conference on Machine Learning and Applications, ICMLA 2016

Convex factorization machine for toxicogenomics prediction

Makoto Yamada, Wenzhao Lian, Amit Goyal, Jianhui Chen, Kishan Wimalawarne, Suleiman A. Khan, Samuel Kaski, Hiroshi Mamitsuka, Yi Chang 2017 KDD 2017 - Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

Localized Lasso for High-Dimensional Regression

Makoto Yamada, Takeuchi Koh, Tomoharu Iwata, John Shawe-Taylor, Samuel Kaski 2017 Proceedings of the 20th International Conference on Artificial Intelligence and Statistics

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

Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli Kallioniemi, Tero Aittokallio, Samuel Kaski 2016 Bioinformatics

Extracting relevance and affect information from physiological text annotation

Oswald Barral, Ilkka Kosunen, Tuukka Ruotsalo, Michiel M. Spapé, Manuel J A Eugster, Niklas Ravaja, Samuel Kaski, Giulio Jacucci 2016 User Modeling and User-Adapted Interaction

Modelling-based experiment retrieval

Paul Blomstedt, Ritabrata Dutta, Sohan Seth, Alvis Brazma, Samuel Kaski 2016 Bioinformatics

Sparse group factor analysis for biclustering of multiple data sources

Kerstin Bunte, Eemeli Leppäaho, Inka Saarinen, Samuel Kaski 2016 Bioinformatics

A Latent Feature Model Approach to Biclustering

José Caldas, Samuel Kaski 2016 International Journal of Knowledge Discovery in Bioinformatics

Interactive intent modeling from multiple feedback domains

Pedram Daee, Joel Pyykkö, Dorota Glowacka, Samuel Kaski 2016 International Conference on Intelligent User Interfaces, Proceedings IUI

Probabilistic Expert Knowledge Elicitation of Feature Relevances in Sparse Linear Regression

Pedram Daee, Tomi Peltola, Marta Soare, Samuel Kaski 2016

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

Manuel Eugster, Tuukka Ruotsalo, Michiel Spape, Oswald Barral, Niklas Ravaja, Giulio Jacucci, Samuel Kaski 2016 Scientific Reports

A Robust Convex Formulation for Ensemble Clustering

Junning Gao, Makoto Yamada, Samuel Kaski, Hiroshi Mamitsuka, Shanfeng Zhu 2016 Proceedings of the Twenty-Fifth International Joint Conference on Artificial Intelligence (IJCAI-16)

Multiple output regression with latent noise

Leo Gillberg, Pekka Marttinen, Matti Pirinen, Antti J. Kangas, Pasi Soininen, Mehreen Ali, Aki S. Havulinna, Marjo Riitta Järvelin, Mika Ala-Korpela, Samuel Kaski 2016 Journal of Machine Learning Research

Generating data to improve protein stability prediction

Markus Heinonen, Emmi Jokinen, Samuel Kaski, Juho Rousu, Harri Lähdesmäki 2016

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo

Markus Heinonen, Henrik Mannerström, Juho Rousu, Samuel Kaski, Harri Lähdesmäki 2016 Proceedings of the 19th International Conference on Artificial Intelligence and Statistics

Dealing with Concept Drift in Exploratory Search: An Interactive Bayesian Approach

Antti Kangasrääsiö, Yi Chen, Dorota Glowacka, Samuel Kaski 2016

ELFI: Engine for Likelihood-Free Inference

Antti Kangasrääsiö, Jarno Lintusaari, Kusti Skyten, Marko Järvenpää, Henri Vuollekoski, Michael Gutmann, Aki Vehtari, Jukka Corander, Samuel Kaski 2016

Interactive modeling of concept drift and errors in relevance feedback

Antti Kangasrääsiö, Yi Chen, Dorota Głowacka, Samuel Kaski 2016 UMAP 2016 - Proceedings of the 2016 Conference on User Modeling Adaptation and Personalization

Personalization of Search Results using Interactive Intent Modeling

Antti Kangasrääsiö, Dorota Głowacka, Samuel Kaski 2016 ICML 2016 Workshop on Computational Frameworks for Personalization

Bayesian multi-tensor factorization

Suleiman Khan, Eemeli Leppäaho, Samuel Kaski 2016 Machine Learning

Fundamentals and Recent Developments in Approximate Bayesian Computation

Jarno Lintusaari, Michael Gutmann, Ritabrata Dutta, Samuel Kaski, Jukka Corander 2016 SYSTEMATIC BIOLOGY

On the identifiability of transmission dynamic models for infectious diseases

Jarno Lintusaari, Michaelu Gutmann, Samuel Kaski, Jukka Corander 2016 Genetics

Bayesian Networks for Variable Groups

Pekka Parviainen, Samuel Kaski 2016 JMLR: Workshop and Conference Proceedings

Classification of weak multi-view signals by sharing factors in a mixture of Bayesian group factor analyzers

Sami Remes, Tommi Mononen, Samuel Kaski 2016 Proceedings of the 5th Workshop on Machine Learning and Interpretation in Neuroimaging (MLINI) at NIPS 2015

Preliminary studies on personalized preference prediction from gaze in comparing visualizations

Hamed Rezazadegan Tavakoli, Hanieh Poostchimohammadabadi, Jaakko Peltonen, Jorma Laaksonen, Samuel Kaski 2016 Advances in Visual Computing

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

Solveig K. Sieberts, Fan Zhu, Javier García-García, Eli Stahl, Abhishek Pratap, Gaurav Pandey, Dimitrios Pappas, Daniel Aguilar, Bernat Anton, Jaume Bonet, Ridvan Eksi, Oriol Fornés, Emre Guney, Hongdong Li, Manuel Alejandro Marín, Bharat Panwar, Joan Planas-Iglesias, Daniel Poglayen, Jing Cui, Andre O. Falcao, Christine Suver, Bruce Hoff, Venkat S K Balagurusamy, Donna Dillenberger, Elias Chaibub Neto, Thea Norman, Tero Aittokallio, Muhammad Ammad-Ud-Din, Chloe Agathe Azencott, Víctor Bellón, Valentina Boeva, Kerstin Bunte, Himanshu Chheda, Lu Cheng, Jukka Corander, Michel Dumontier, Anna Goldenberg, Peddinti Gopalacharyulu, Mohsen Hajiloo, Daniel Hidru, Alok Jaiswal, Samuel Kaski, Beyrem Khalfaoui, Suleiman Ali Khan, Eric R. Kramer, Pekka Marttinen, Aziz M. Mezlini, Bhuvan Molparia, Matti Pirinen, Janna Saarela, Matthias Samwald, Véronique Stoven, Hao Tang, Jing Tang, Ali Torkamani, Jean Phillipe Vert, Bo Wang, Tao Wang, Krister Wennerberg, Nathan E. Wineinger, Guanghua Xiao, Yang Xie, Rae Yeung, Xiaowei Zhan, Cheng Zhao, Jeff Greenberg, Joel Kremer, Kaleb Michaud, Anne Barton, Marieke Coenen, Xavier Mariette, Corinne Miceli, Nancy Shadick, Michael Weinblatt, Niek De Vries, Paul P. Tak, Danielle Gerlag, Tom W J Huizinga, Fina Kurreeman, Cornelia F. Allaart, S. Louis Bridges, Lindsey Criswell, Larry Moreland, Lars Klareskog, Saedis Saevarsdottir, Leonid Padyukov, Peter K. Gregersen, Stephen Friend, Robert Plenge, Gustavo Stolovitzky, Baldo Oliva, Yuanfang Guan, Lara M. Mangravite 2016 Nature Communications

Interactive user intent modeling for eliciting priors of a normal linear model

Iiris Sundin, Luana Micallef, Pekka Marttinen, Muhammad Ammad-Ud-Din, Tomi Peltola, Marta Soare, Giulio Jacucci, Samuel Kaski 2016

Visualizations relevant to the user by multi-view latent variable factorization

Seppo Virtanen, Homayun Afrabandpey, Samuel Kaski 2016 ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings

Exploring peripheral physiology as a predictor of perceived relevance in information retrieval

Oswald Barral, Manuel J.A. Eugster, Tuukka Ruotsalo, Michiel Sovijärvi-Spape, Ilkka Kosunen, Niklas Ravaja, Samuel Kaski, Giulio Jacucci 2015 International Conference on Intelligent User Interfaces (IUI), Atlanta, USA, March 29 - April 1, 2015

Advances in Independent Component Analysis and Learning Machines

Ella Bingham, Samuel Kaski, Jorma Laaksonen, Jouko Lampinen 2015

Prediction of human population responses to toxic compounds by a collaborative competition

Federica Eduati, Lara M. Mangravite, Tao Wang, Hao Tang, J. Christopher Bare, Ruili Huang, Thea Norman, Mike Kellen, Michael P. Menden, Jichen Yang, Xiaowei Zhan, Rui Zhong, Guanghua Xiao, Menghang Xia, Nour Abdo, Oksana Kosyk, Stephen Friend, Allen Dearry, Anton Simeonov, Raymond R. Tice, Ivan Rusyn, Fred A. Wright, Gustavo Stolovitzky, Yang Xie, Julio Saez-Rodriguez, Tero Aittokallio, Salvatore Alaimo, Alicia Amadoz, Muhammad Ammad-ud-din, Chloé Agathe Azencott, Jaume Bacardit, Pelham Barron, Elsa Bernard, Andreas Beyer, Shao Bin, Alena van Bömmel, Karsten Borgwardt, April M. Brys, Brian Caffrey, Jeffrey Chang, Jungsoo Chang, Himanshu Chheda, Eleni G. Christodoulou, Mathieu Clément-Ziza, Trevor Cohen, Marianne Cowherd, Sofie Demeyer, Joaquin Dopazo, Joel D. Elhard, Samuel Kaski 2015 NATURE BIOTECHNOLOGY

Developing a Symbiotic System for Scientific Information Seeking

Luciano Gamberini, Anna Spagnolli, Benjamin Blankertz, Samuel Kaski, Jonathan Freeman, Laura Acqualagna, Oswald Barral, Maura Bellio, Luca Chech, Manuel Eugster, Eva Ferrari, Paolo Negri, Valeria Orso, Patrik Pluchino, Filippo Minelle, Baris Serim, Markus Wenzel, Giulio Jacucci 2015 Symbiotic Interaction. Symbiotic 2015

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

Roland C. Grafström, Penny Nymark, Vesa Hongisto, Ola Spjuth, Rebecca Ceder, Egon Willighagen, Barry Hardy, Samuel Kaski, Pekka Kohonen 2015 ATLA: Alternatives to Laboratory Animals

Improving Controllability and Predictability of Interactive Recommendation Interfaces for Exploratory Search

Antti Kangasrääsiö, Dorota Glowacka, Samuel Kaski 2015 International Conference on Intelligent User Interfaces (IUI'15), Atlanta, GA, 29.3.2015

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

Jukka-Pekka Kauppi, Melih Kandemir, Veli-Matti Saarinen, Lotta Hirvenkari, Lauri Parkkonen, Arto Klami, Riitta Hari, Samuel Kaski 2015 NeuroImage

Group Factor Analysis

Arto Klami, Seppo Virtanen, Eemeli Leppäaho, Samuel Kaski 2015 IEEE Transactions on Neural Networks

Interactive Intent Modeling: Information Discovery Beyond Search

Tuukka Ruotsalo, Giulio Jacucci, Petri Myllymaki, Samuel Kaski 2015 Communications of the ACM

Scinet: Interactive intent modeling for information discovery

Tuukka Ruotsalo, Jaakko Peltonen, Manuel J A Eugster, Dorota Glowacka, Aki Reijonen, Giulio Jacucci, Petri Myllymäki, Samuel Kaski 2015 SIGIR 2015 - Proceedings of the 38th International ACM SIGIR Conference on Research and Development in Information Retrieval

Majorization-Minimization for Manifold Embedding

Zhirong Yang, Jaakko Peltonen, Samuel Kaski 2015 The 18th International Conference on Artificial Intellgence and Statistics (AISTATS'15), San Diego, USA, May 9-12, 2015

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

Muhammad Ammad-ud-din, Elisabeth Georgii, Mehmet Gönen, Tuomo Laitinen, Olli Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski 2014 Journal of Chemical Information and Modeling

Optimal neighborhood preserving visualization by maximum satisfiability

Kerstin Bunte, Matti Järvisalo, Jeremias Berg, Petri Myllymäki, Jaakko Peltonen, Samuel Kaski 2014 Association for the advancement of artificial intelligence conference, AAAI-14, Québec, Canada, July 2014

A community effort to assess and improve drug sensitivity prediction algorithms

James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Muhammad Ammad-ud-din, Petteri Hintsanen, Suleiman A Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, NCI DREAM Community, James J Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray, Gustavo Stolovitzky 2014 NATURE BIOTECHNOLOGY

Predicting term-relevance from brain signals

Manuel J.A. Eugster, Tuukka Ruotsalo, Michiel Spapé, Ilkka Kosunen, Oswald Barral, Niklas Ravaja, Niklas Jacucci, Samuel Kaski 2014 Annual International ACM SIGIR Conference on Research & Development in Information Retrieval, (SIGIR 2014), Gold Coast, Australia, 6-11 July 2014

Toward Computational Cumulative Biology by Combining Models of Biological Datasets

Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, Samuel Kaski 2014 PloS one

Kernelized Bayesian Matrix Factorization

Mehmet Gönen, Samuel Kaski 2014 IEEE Transactions on Pattern Analysis and Machine Intelligence

Computational Statistics Approaches to Study Metabolic Syndrome

Ilkka Huopaniemi, Samuel Kaski 2014 A Systems Biology Approach to Study Metabolic Syndrome

Multi-task and multi-view learning of user state

Melih Kandemir, Akos Vetek, Mehmet Gönen, Arto Klami, Samuel Kaski 2014 Neurocomputing

Improving controllability and predictability of an interactive user model driven search interface

Antti Kangasrääsiö, Dorota Glowacka, Samuel Kaski 2014

Interactive Visualization of Search Intent for Exploratory Information Retrieval

Antti Kangasrääsiö, Dorota Glowacka, Tuukka Ruotsalo, Jaakko Peltonen, Manuel Eugster, Ksenia Konyushkova, Kumaripaba Athukorala, Ilkka Kosunen, Aki Reijonen, Petri Myllymäki, Giulio Jacucci, Samuel Kaski 2014

Preface

Samuel Kaski, Jukka Corander 2014 Journal of Machine Learning Research

Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, JMLR W&CP, Vol. 33

Samuel Kaski, Jukka Corander 2014

Bayesian Multi-View Tensor Factorization

Suleiman A. Khan, Samuel Kaski 2014 European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases, ECML'14, Nancy, September 15-19, 2014

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

Suleiman A. Khan, Seppo Virtanen, Olli P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski 2014 Bioinformatics

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

Pekka Marttinen, Matti Pirinen, Antti-Pekka Sarin, Jussi Gillberg, Johannes Kettunen, Ida Surakka, Antti J Kangas, Pasi Soininen, Paul "O'Reilly", Marika Kaakinen, Mika Kähönen, Terho Lehtimäki, Mika Ala-Korpela, Olli T Raitakari, Veikko Salomaa, Marjo-Riitta Järvelin, Samuli Ripatti, Samuel Kaski 2014 Bioinformatics

Probabilistic drug connectivity mapping

Juuso A. Parkkinen, Samuel Kaski 2014 BMC Bioinformatics

Toward computational cumulative biology by combining models of biological datasets

Jaakko Peltonen, Ali Faisal, Elisabeth Georgii, Johan Rung, Samuel Kaski 2014 Workshop on Machine Learning in Computational Biology, Neural Information Processing Systems, NIPS2014, 8-13 December, Montreal, Canada

Bayesian Optimization in Interactive Scientific Search

Tuukka Ruotsalo, Jaakko Peltonen, Manuel J.A. Eugster, Dorota Glowacka, Ksenia Konyushkova, Kumaripaba Athukorala, Ilkka Kosunen, Aki Reijonen, Petri Myllymäki, Giulio Jacucci, Samuel Kaski 2014 Workshop on Bayesian Optimization in Academia and Industry, Neural Information Processing Systems, NIPS2014, 8-13 December, Montreal, Canada

Intentradar: Search User Interface That Anticipates User's Search Intents

Tuukka Ruotsalo, Jaakko Peltonen, Manuel J.A. Eugster, Dorota Glowacka, Aki Reijonen, Giulio Jacucci, Petri Myllymäki, Samuel Kaski 2014 ACM CHI Conference on Human Factors in Computing Systems, CHI 2014, 26 April-1 May, Toronto, Canada

Exploration and retrieval of whole-metagenome sequencing samples

Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela 2014 Bioinformatics

Retrieval of experiments by efficient comparison of marginal likelihoods

Sohan Seth, John Shawe-Taylor, Samuel Kaski 2014 International conference on neural information processing, Kuching, Malaysia, November 3-6, 2014

Joint Workshop on Personalised Information Access-PIA 2014

Ben Steichen, Tuukka Ruotsalo, Maristella Agosti, Giulio Jacucci, Séamus Lawless, Peter Brusilovsky, Vincent Wade, Samuel Kaski, Oswald Barral 2014 UMAP 2014 Extended Proceedings

Cross-organism toxicogenomics with group factor analysis

Tommi Suvitaival, Juuso Parkkinen, Seppo Virtanen, Samuel Kaski 2014 Systems Biomedicine

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

Tommi Suvitaival, Simon Rogers, Samuel Kaski 2014 Bioinformatics

Stronger findings from mass spectral data through multi-peak modeling

Tommi Suvitaival, Simon Rogers, Samuel Kaski 2014 BMC Bioinformatics

Optimization equivalence of divergences improves neighbor embedding

Zhirong Yang, Jaakko Peltonen, Samuel Kaski 2014 International Conference on Machine Learning, ICML 2014, 21-26 June, Beijing, P. R. China

Adaptive timeline interface to personal history data

Antti Ajanki, Markus Koskela, Jorma Laaksonen, Samuel Kaski 2013 ICMI 2013 - Proceedings of the 2013 ACM International Conference on Multimodal Interaction

Directing Exploratory Search: Reinforcement Learning from User Interactions with Keywords

Dorota Glowacka, Tuukka Ruotsalo, Ksenia Konyushkova, Kumaripaba Athukorala, Samuel Kaski, Giulio Jacucci 2013 International Conference on Intelligent User Interfaces, Santa Monica, CA, March 19-22, 2013

SciNet: A System for Browsing Scientific Literature through Keyword Manipulation

Dorota Glowacka, Tuukka Ruotsalo, Ksenia Konyushkova, Kumaripaba Athukorala, Samuel Kaski, Giulio Jacucci 2013 International Conference on Intelligent User Interfaces, Santa Monica, CA, March 19-22, 2013

Kernelized Bayesian Matrix Factorization

Mehmet Gönen, Suleiman A. Khan, Samuel Kaski 2013 30th International Conference on Machine Learning ICML, Atlanta, Georgia, USA, June 16-21,2013

Bayesian Canonical Correlation Analysis

Arto Klami, Seppo Virtanen, Samuel Kaski 2013 Journal of Machine Learning Research

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

Miika Koskinen, Jaakko Viinikanoja, Mikko Kurimo, Arto Klami, Samuel Kaski, Riitta Hari 2013 Human Brain Mapping

Systematic use of computational methods allows stratification of treatment responders in glioblastoma multiforme

Riku Louhimo, Viljami Aittomäki, Ali Faisal, Marko Laakso, Ping Chen, Kristian Ovaska, Erkka Valo, Leo Lahti, Vladimir Rogojin, Samuel Kaski, Sampsa Hautaniemi 2013 Systems Biomedicine

Genome-wide association studies with high-dimensional phenotypes

P. Marttinen, Leo Gillberg, A. Havulinna, J. Corander, S. Kaski 2013 STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY

Information Retrieval Perspective to Interactive Data Visualization

Jaakko Peltonen, Max Sandholm, Samuel Kaski 2013 The Eurographics Conference on Visualization (Eurovis 2013), Leipzig, Germany, Leipzig, Germany, 2013

Directing exploratory search with interactive intent modeling

Tuukka Ruotsalo, Jaakko Peltonen, Manuel Eugster, Dorota Glowacka, Ksenia Konyushkova, Kumaripaba Athukorala, Ilkka Kosunen, Aki Reijonen, Petri Myllymäki, Giulio Jacucci, Samuel Kaski 2013 Proceedings of the 22nd ACM international conference on Conference on information & knowledge management

Supporting Exploratory Search Tasks with Interactive User Modelling

Tuukka Ruotsalo, Kumaripaba Athukorala, Dorota Glowacka, Ksenia Konyushkova, Antti Oulasvirta, Samuli Kaipiainen, Samuel Kaski, Giulio Jacucci 2013 ASIST 2013, the 76th ASIS&T Annual Meeting

Scalable Optimization of Neighbor Embedding for Visualization

Zhirong Yang, Jaakko Peltonen, Samuel Kaski 2013 30th International Conference on Machine Learning, Atlanta, GA, June 16-21, 2013

Data-Driven Information Retrieval in Heterogeneous Collections of Transcriptomics Data Links SIM2s to Malignant Pleural Mesothelioma

José Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew G. Nicholson, Sakari Knuutila, Alvis Brazma, Samuel Kaski 2012 Bioinformatics

The rocky road to personalized medicine: computational and statistical challenges

Jukka Corander, Tero Aittokallio, Samuli Ripatti, Samuel Kaski 2012 PERSONALIZED MEDICINE

Sparse Nonparametric Topic Model for Transfer Learning

Ali Faisal, Leo Gillberg, Jaakko Peltonen, Gayle Leen, Samuel Kaski 2012 ESANN 20th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning ESANN, Bruges, Belgium, April 25-27, 2012

Targeted Retrieval of Gene Expression Measurements Using Regulatory Models

Elisabeth Georgii, Jarkko Salojärvi, Mikael Brosché, Jaakko Kangasjärvi, Samuel Kaski 2012 Bioinformatics

Learning Relevance from Natural Eye Movements in Pervasive Interfaces

Melih Kandemir, Samuel Kaski 2012 14th ACM International Conference on Multimodal Interaction, Santa Monica, CA, USA, Octover 22-26, 2012

Unsupervised inference of auditory attention from biosensors

Melih Kandemir, Arto Klami, Akos Vetek, Samuel Kaski 2012 ECML PKDD European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2012) ECML PKDD, Bristol, UK, September 24-28, 2012

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

Suleiman A. Khan, Ali Faisal, John Patrick Mpindi, Juuso A. Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P. Kallioniemi, Krister Wennerberg, Samuel Kaski 2012 BMC Bioinformatics

Focused multi-task learning in a Gaussian process framework

Gayle Leen, Jaakko Peltonen, Samuel Kaski 2012 Machine Learning

Neurocomputing, Special Issue on Machine Learning for Signal Processing 2010, 80:1-128

Jaakko Peltonen, Tapani Raiko, Samuel Kaski 2012

Bayesian Group Factor Analysis

Seppo Virtanen, Arto Klami, Suleiman A. Khan, Samuel Kaski 2012 AISTAT AISTATS Fifteenth International Conference on Artificial Intelligence and Statistics (AISTAT 2012) AISTATS AISTAT, La Palma, Canary Islands, April 21-23, 2012

An Augmented Reality Interface to Contextual Information

Antti Ajanki, Mark Billinghurst, Hannes Gamper, Toni Järvenpää, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, Teemu Ruokolainen, Timo Tossavainen 2011 VIRTUAL REALITY

Probabilistic proactive timeline browser

Antti Ajanki, Samuel Kaski 2011 ICANN The 21st International Conference on Artificial Neural Networks (ICANN) ICANN, Part II

Hierarchical generative biclustering for MicroRNA Expression Analysis

José Caldas, Samuel Kaski 2011 Journal of Computational Biology

Multitask Learning Using Regularized Multiple Kernel Learning

Mehmet Gönen, Melih Kandemir, Samuel Kaski 2011 18th International Conference on Neural Information Processing (ICONIP)

Artificial Neural Networks and Machine Learning Research - ICANN 2011, Part I

Timo Honkela, Wodzisaw Duch, Mark Girolami, Samuel Kaski 2011

Artificial Neural Networks and Machine Learning Research - ICANN 2011, Part II

Timo Honkela, Wodzisaw Duch, Mark Girolami, Samuel Kaski 2011

Dimensionality Reduction for Data Visualization

Samuel Kaski, Jaakko Peltonen 2011 IEEE Signal Processing Magazine

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

Leo Lahti, Laura L. Elo, Tero Aittokallio, Samuel Kaski 2011 IEEE-ACM Transactions on Computational Biology and Bioinformatics

Focused Multi-task Learning Using Gaussian Processes

Gayle Leen, Jaakko Peltonen, Samuel Kaski 2011 ECML PKDD Machine Learning and Knowledge Discovery in Databases

Systematic Use of Computational Methods Allows Stratifying Treatment Responders in Glioblastoma Multiforme

Riku Louhimo, Viljami Aittomäki, Ali Faisal, Marko Laakso, Ping Chen, Kristian Ovaska, Erkka Valo, Leo Lahti, Vladimir Rogojin, Samuel Kaski, Sampsa Hautaniemi 2011 CAMDA 2011 conference, Critical Assessment of Massive Data Analysis

Generative Modeling for Maximizing Precision and Recall in Information Visualization

Jaakko Peltonen, Samuel Kaski 2011 AISTAT AISTATS The Fourteenth International Conference on Artificial Intelligence and Statistics (AISTAT) AISTAT AISTATS

Cross-species translation of multi-way biomarkers

Tommi Suvitaival, Ilkka Huopaniemi, Matej Oresic, Samuel Kaski 2011 ICANN The 21st International Conference on Artificial Neural Networks (ICANN) ICANN, Part I

Metabolic regulation in progression to autoimmune diabetes

Marko Sysi-Aho, Andrey Ermolov, Peddinti V. Gopalacharyulu, Abhishek Tripathi, Tuulikki Seppänen-Laakso, Johanna Maukonen, Ismo Mattila, Suvi T. Ruohonen, Laura Vähätalo, Laxman Yetukuri, Taina Härkönen, Erno Lindfors, Janne Nikkilä, Jorma Ilonen, Olli Simell, Maria Saarela, Mikael Knip, Samuel Kaski, Eriika Savontaus, Matej Oresic 2011 PLoS computational biology

Matching samples of multiple views

Abhishek Tripathi, Arto Klami, Matej Oresic, Samuel Kaski 2011 Data Mining and Knowledge Discovery

Bayesian CCA via Group Sparsity

Seppo Virtanen, Arto Klami, Samuel Kaski 2011 ICML The 28th International Conference on Machine Learning (ICML-11) ICML

Introduction to the special issue on mining and learning with graphs

S. V N Vishwanathan, Samuel Kaski, Jennifer Neville, Stefan Wrobel 2011 Machine Learning

Machine Learning, Special Issue on Learning and Mining with Graphs, 82(2)

S.V.N. Vishwanathan, Samuel Kaski, Jennifer Neville, Stefan Wrobel 2011

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

Laxman Yetukuri, Ilkka Huopaniemi, Artturi Koivuniemi, Marianna Maranghi, Anne Hiukka, Heli Nygren, Samuel Kaski, Marja-Riitta Taskinen, Ilpo Vattulainen, Matti Jauhiainen, Matej Oresic 2011 PloS one

Contextual Information Access with Augmented Reality

Antti Ajanki, Mark Billinghurst, Toni Järvenpää, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, Teemu Ruokolainen, Timo Tossavainen 2010 MLSP 2010, IEEE International Workshop on Machine Learning for Signal Processing (MLSP)

Ubiquitous Contextual Information Access with Proactive Retrieval and Augmentation

Antti Ajanki, Mark Billinghurst, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, Timo Tossavainen 2010 The fourth International Workshop on Ubiquitous Virtual Reality (IWUVR2010)

Pinview: Implicit Feedback in Content-Based Image Retrieval

Peter Auer, Zakria Hussain, Samuel Kaski, Arto Klami, Jussi Kujala, Jorma Laaksonen, Alex P. Leung, Kitsuchart Pasupa, John Shawe-Taylor 2010 ICML Workshop on Reinforcement Learning and Search in Very Large Spaces

Pinview: Implicit Feedback in Content-Based Image Retrieval

Peter Auer, Zakria Hussain, Samuel Kaski, Arto Klami, Jussi Kujala, Jorma Laaksonen, Alex P. Leung, Kitsuchart Pasupa, John Shawe-Taylor 2010 Workshop on Applications of Pattern Analysis

Hierarchical generative biclustering for microRNA expression analysis

José Caldas, Samuel Kaski 2010 Research in Computational Molecular Biology, 14th Annual International Conference RECOMB 2010, Lisbon, Portugal, April 25-28

Graphical Multi-Way Models

Ilkka Huopaniemi, Tommi Suvitaival, Matej Oresic, Samuel Kaski 2010 Machine Learning and Knowledge Discovery in Databases. European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010

Multivariate multi-way analysis of multi-source data

Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Oresic, Samuel Kaski 2010 Bioinformatics

Inferring Object Relevance from Gaze in Dynamic Scenes

Melih Kandemir, Veli-Matti Saarinen, Samuel Kaski 2010 ETRA 2010, ACM Symposium on Eye Tracking Research & Applications, Austin, TX, USA, March 22-24 (ETRA)

Proceedings of the 2010 IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010)

Samuel Kaski, David J. Miller, Erkki Oja, Antti Honkela 2010

Three Paths to Relevance

Samuel Kaski 2010 Brain-Inspired Information Technology

Bayesian exponential family projections for coupled data sources

Arto Klami, Seppo Virtanen, Samuel Kaski 2010 The Twenty-Sixth Conference on Uncertainty in Artificial Intelligence (2010)

Global modeling of transcriptional responses in interaction networks

Leo Lahti, Juha E.A. Knuuttila, Samuel Kaski 2010 Bioinformatics

Graph Visualization With Latent Variable Models

Juuso Parkkinen, Kristian Nybo, Jaakko Peltonen, Samuel Kaski 2010 MLG-2010, the Eighth Workshop on Mining and Learning with Graphs

Searching for functional gene modules with interaction component models

Juuso Parkkinen, Samuel Kaski 2010 BMC Systems Biology

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

Jaakko Peltonen, Helena Aidos, Nils Gehlenborg, Alvis Brazma, Samuel Kaski 2010 ICASSP 2010, IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)

Generative Modeling for Maximizing Precision and Recall in Information Visualization

Jaakko Peltonen, Samuel Kaski 2010

Relevant subtask learning by constrained mixture models

Jaakko Peltonen, Yusuf Yaslan, Samuel Kaski 2010 Intelligent Data Analysis

Infinite factorization of multiple non-parametric views

Simon Rogers, Arto Klami, Janne Sinkkonen, Mark Girolami, Samuel Kaski 2010 Machine Learning

Information retrieval perspective to nonlinear dimensionality reduction for data visualization

Jarkko Venna, Jaakko Peltonen, Kristian Nybo, Helena Aidos, Samuel Kaski 2010 Journal of Machine Learning Research

Variational Bayesian mixture of robust CCA models

Jaakko Viinikanoja, Arto Klami, Samuel Kaski 2010 Machine Learning and Knowledge Discovery in Databases. European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010

Can Eyes Reveal Interest? Implicit Queries from Gaze Patterns

Antti Ajanki, David R. Hardoon, Samuel Kaski, Kai Puolamäki, John Shawe-Taylor 2009 User Modeling and User-Adapted Interaction: The Journal of Personalization Research

Ubiquitous Contextual Information Access with Proactive Retrieval and Augmentation

Antti Ajanki, Mark Billinghurst, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, Timo Tossavainen 2009

Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data

Farid Benachenhou, Patric Jern, Merja Oja, Göran Sperber, Vidar Blikstad, Panu Somervuo, Samuel Kaski, Jonas Blomberg 2009 PloS one

Probabilistic retrieval and visualization of biologically relevant microarray experiments

José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski 2009 Bioinformatics

Multi-Way, Multi-View Learning

Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Oresic, Samuel Kaski 2009 NIPS 2009 workshop on Learning from Multiple Sources with Applications to Robotics

Two-Way Analysis of High-Dimensional Collinear Data

Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Oresic, Samuel Kaski 2009 Data Mining and Knowledge Discovery

GaZIR: Gaze-based Zooming Interface for Image Retrieval

László Kozma, Arto Klami, Samuel Kaski 2009 Proc. ICMI-MLMI 2009, The Eleventh International Conference on Multimodal Interfaces and The Sixth Workshop on Machine Learning for Multimodal Interaction

Dependency detection with similarity constraints

Leo Lahti, Samuel Myllykangas, Sakari Knuutila, Samuel Kaski 2009 Proc. MLSP 2009, IEEE International Workshop on Machine Learning for Signal Processing

Automatic Choice of Control Measurements

Gayle Leen, David R. Hardoon, Samuel Kaski 2009 Advances in Machine Learning (Proc. ACML'09, The 1st Asian Conference on Machine Learning)

Graph Visualization With Latent Variable Models

Kristian Nybo, Juuso Parkkinen, Samuel Kaski 2009

A Block Model Suitable for Sparse Graphs

Juuso Parkkinen, Janne Sinkkonen, Adam Gyenge, Samuel Kaski 2009

Learning to Rank Images from Eye movements

Kitsuchart Pasupa, Craig Saunders, Sandor Szedmak, Arto Klami, Samuel Kaski, Steve Gunn 2009 IEEE International Workshop on Human-Computer Interaction (HCI2009), October 4, 2009, Kyoto, Japan

Supervised Nonlinear Dimensionality Reduction by Neighbor Retrieval

Jaakko Peltonen, Helena Aidos, Samuel Kaski 2009 ICASSP 2009, the IEEE International Conference on Acoustics, Speech, and Signal Processing

Visualizations for Assessing Convergence and Mixing of Markov Chain Monte Carlo Simulations

Jaakko Peltonen, Jarkko Venna, Samuel Kaski 2009 Computational Statistics and Data Analysis

Bayesian Solutions to the Label Switching Problem

Kai Puolamäki, Samuel Kaski 2009 Advances in Intelligent Data Analysis VIII, Proceedings of the 8th International Symposium on Intelligent Data Analysis, IDA 2009

Fast Dependent Components for fMRI Analysis

Eerika Savia, Arto Klami, Samuel Kaski 2009 ICASSP 09, the International Conference on Acoustics, Speech, and Signal Processing

Latent Grouping Models for User Preference Prediction

Eerika Savia, Kai Puolamäki, Samuel Kaski 2009 Machine Learning

On Two-Way Grouping by One-Way Topic Models

Eerika Savia, Kai Puolamäki, Samuel Kaski 2009

Two-Way Grouping by One-Way Topic Models

Eerika Savia, Kai Puolamäki, Samuel Kaski 2009 IDA 2009, The 8th International Symposium on Intelligent Data Analysis, Advances in Intelligent Data Analysis VIII

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

Suvi Savola, Arto Klami, Abhishek Tripathi, Tarja Niini, Massimo Serra, Piero Picci, Samuel Kaski, Diana Zambelli, Katia Scotlandi, Sakari Knuutila 2009 BMC Cancer

Using Dependencies to Pair Samples for Multi-View Learning

Abhishek Tripathi, Arto Klami, Samuel Kaski 2009 ICASSP 09, the International Conference on Acoustics, Speech, and Signal Processing

An Analysis of Generalization Error in Relevant Subtask Learning

Keisuke Yamazaki, Samuel Kaski 2009 Advances in Neuro-Information Processing, 15th International Conference, ICONIP 2008

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

Jarkko Ylipaavalniemi, Eerika Savia, Sanna Malinen, Riitta Hari, Ricardo Vigário, Samuel Kaski 2009 NeuroImage

Bayesian Biclustering with the Plaid Model

José Caldas, Samuel Kaski 2008 The IEEE International Workshop on Machine Learning for Signal Processing XVIII

Can relevance of images be inferred from eye movements?

Arto Klami, Craig Saunders, Teófilo de Campos, Samuel Kaski 2008 MIR '08: Proceeding of the 1st ACM International Conference on Multimedia Information Retrieval

Probabilistic approach to detecting dependencies between data sets

Arto Klami, Samuel Kaski 2008 Neurocomputing

Gender dependent progression of systemic metabolic states in early childhood

Janne Nikkilä, Marko Sysi-Aho, Andrey Ermolov, Tuulikki Seppänen-Laakso, Olli Simell, Samuel Kaski, Matej Oresic 2008 MOLECULAR SYSTEMS BIOLOGY

Variational Bayes Learning from Relevant Tasks Only

Jaakko Peltonen, Yusuf Yaslan, Samuel Kaski 2008 Learning from Multiple Sources Workshop, 13 December 2008, Whistler Canada

Bayesian Solutions to the Label Switching Problem

Kai Puolamäki, Samuel Kaski 2008

Learning to learn implicit queries from gaze patterns

Kai Puolamäki, Antti Ajanki, Samuel Kaski 2008 ICML 2008, Twenty-Fifth International Conference on Machine Learning

Macadamia: Master's Programme in Machine Learning and Data Mining

Tapani Raiko, Kai Puolamäki, Juha Karhunen, Jaakko Hollmén, Antti Honkela, Samuel Kaski, Heikki Mannila, Erkki Oja, Olli Simula 2008 Teaching Machine Learning - Workshop on Open Problems and New Directions

Two-level infinite mixture for multi-domain data

Simon Rogers, Janne Sinkkonen, Arto Klami, Mark Girolami, Samuel Kaski 2008 Learning from Multiple Sources Workshop, 13 December 2008, Whistler Canada

A simple infinite topic mixture for rich graphs and relational data

Janne Sinkkonen, Juuso Parkkinen, Janne Aukia, Samuel Kaski 2008 NIPS 2008 Workshop on Analyzing Graphs: Theory and Applications

Infinite mixtures for multi-relational categorical data

Janne Sinkkonen, Janne Aukia, Samuel Kaski 2008 6th International Workshop on Mining and Learning with Graphs (MLG 2008)

Simple integrative preprocessing preserves what is shared in data sources

Abhishek Tripathi, Arto Klami, Samuel Kaski 2008 BMC Bioinformatics

Using Dependencies to Pair Samples for Multi-View Learning

Abhishek Tripathi, Arto Klami, Samuel Kaski 2008

On asymmetric generalization error of asymmetric multitask learning

Keisuke Yamazaki, Samuel Kaski 2008 Learning from Multiple Sources Workshop, 13 December 2008, Whistler Canada

Discovering condition-dependent Bayesian networks for gene regulation

Antti Ajanki, Janne Nikkilä, Samuel Kaski 2007 Fifth IEEE International Workshop on Genomic Signal Processing and Statistics, Tuusula, Finland, 2007

Information Retrieval by Inferring Implicit Queries from Eye Movements

David R. Hardoon, John Shawe-Taylor, Antti Ajanki, Kai Puolamäki, Samuel Kaski 2007 Eleventh International Conference on Artificial Intelligence and Statistics, San Juan, Puerto Rico, 2007

Learning from relevant tasks only

Samuel Kaski, Jaakko Peltonen 2007 18th European Conference on Machine Learning, ECML 2007, Warsaw, Poland, September 17-21, 2007

Probabilistic modeling and machine learning in structural and systems biology

Samuel Kaski, Juho Rousu, Esko Ukkonen 2007 BMC Bioinformatics

Local Dependent Components

Arto Klami, Samuel Kaski 2007 24th International Conference on Machine Learning, Corwallis, Oregon, USA, June 20-24, 2007

The self-organizing map as a visual neighbor retrieval method

Kristian Nybo, Jarkko Venna, Samuel Kaski 2007 6th International Workshop on Self-Organizing Maps, Bielefeld, Germany, 2007

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

Penny Nymark, Pamela M. Lindholm, Mikko V. Korpela, Leo Lahti, Salla Ruosaari, Samuel Kaski, Jaakko Hollmen, Sisko Anttila, Vuokko L. Kinnula, Sakari Knuutila 2007 BMC Genomics

Methods for estimating human endogenous retrovirus activities from EST databases

Merja Oja, Jaakko Peltonen, Jonas Blomberg, Samuel Kaski 2007 BMC Bioinformatics

Fast Semi-Supervised Discriminative Component Analysis

Jaakko Peltonen, Jacob Goldberger, Samuel Kaski 2007 2007 IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2007), Thessaloniki, Greece, August 27-29, 2007

Inferring vertex properties from topology in large networks

Janne Sinkkonen, Janne Aukia, Samuel Kaski 2007 5th International Workshop on Mining and Learning with Graphs, MLG'07, Firenze, Italy, Aug 1-3, 2007

Comparison of visualization methods for an atlas of gene expression data sets

Jarkko Venna, Samuel Kaski 2007 Information Visualization

Nonlinear dimensionality reduction as information retrieval

Jarkko Venna, Samuel Kaski 2007 11th International Conference on International Conference on Artificial Intelligence and Statistics, AISTATS 2007, San Juan, Puerto Rico, March 19-22, 2007

Functional Elements and Networks in fMRI

J. Ylipaavalniemi, E. Savia, R. Vigário, S. Kaski 2007 15th European Symposium on Artificial Neural Networks (ESANN 2007)

Implicit feedback from eye movements for proactive information retrieval

Samuel Kaski 2006 NIPS 2006 Workshop on User Adaptive Systems, Whistler, Canada, December 8, 2006

Ydintehtävät kunniaan

Samuel Kaski 2006 Polysteekki

Generative models that discover dependencies between data sets

Arto Klami, Samuel Kaski 2006 2006 IEEE International Workshop on Machine Learning for Signal Processing, Maynooth, Ireland, Sept. 6-8, 2006

Generative Models That Discover Dependencies between Data Sets

Arto Klami, Samuel Kaski 2006

Asbestos-associated malignancies in the lung and pleura show distinct genetic aberrations

Pamela Lindholm, Penny Nymark, Harriet Wikman, K. Salmenkivi, A. Nicholson, Mikko Korpela, S. Kaski, Salla Ruosaari, J. Hollmen, E. Vanhala, A. Karjalainen, S. Anttila, V. Kinnula, S. Knuutila 2006 LUNG CANCER

Exploring the independence of gene regulatory modules

Janne Nikkilä, Antti Honkela, Samuel Kaski 2006 Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006),Tuusula, Finland, 17-18 June 2006

Estimation of human endogenous retrovirus activities from expressed sequence databases

Merja Oja, Jaakko Peltonen, Samuel Kaski 2006 Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006), Tuusula, Finland, June 17-18, 2006

Fast Discriminative Component Analysis for Comparing Examples

Jaakko Peltonen, Jacob Goldberger, Samuel Kaski 2006 NIPS 2006 workshop on Learning to Compare Examples, Whistler, Canada, December 8, 2006

Learning when only some of the training data are from the same distribution as test data

Jaakko Peltonen, Samuel Kaski 2006

Discriminative MCMC

Kai Puolamäki, Jarkko Salojärvi, Eerika Savia, Samuel Kaski 2006

Proceedings of the NIPS 2005 Workshop on Machine Learning for Implicit Feedback and User Modeling

Kai Puolamäki, Samuel Kaski 2006

Probabilistic Modeling and Machine Learning in Structural and Systems Biology

Juho Rousu, Samuel Kaski, Esko Ukkonen 2006

Neural Networks and Machine Learning in Bioinformatics - Theory and Applications

Udo Seiffert, Barbara Hammer, Samuel Kaski, Thomas Villmann 2006 ESANN'06, 14th European Symposium on Artificial Neural Networks, Bruges, Belgium, 2006

Local Multidimensional Scaling

Jarkko Venna, Samuel Kaski 2006 Neural Networks

Nonlinear Dimensionality Reduction as Information Retrieval

Jarkko Venna, Samuel Kaski 2006

Visualizing Gene Interaction Graphs with Local Multidimensional Scaling

Jarkko Venna, Samuel Kaski 2006 14th European Symposium on Artificial Neural Networks (ESANN'2006), Bruges, Belgium, April 26-28, 2006

Functional Elements and Networks in fMRI

Jarkko Ylipaavalniemi, Eerika Savia, Ricardo Vigário, Samuel Kaski 2006

Proceedings of KRBIO05, Symposium on Knowledge Representation in Bioinformatics, Espoo, Finland, June 15-17, 2005

C. Bounsaythip, J. Hollmén, S. Kaski, M. Oresic 2005

Associative Clustering for Exploring Dependencies between Functional Genomics Data Sets

S. Kaski, J. Nikkilä, J. Sinkkonen, L. Lahti, J. Knuuttila, C. Roos 2005 IEEE-ACM Transactions on Computational Biology and Bioinformatics

Discriminative Clustering

S. Kaski, J. Sinkkonen, A. Klami 2005 Neurocomputing

Discriminative Clustering of Yeast Stress Response

S. Kaski, J. Nikkilä, E. Savia, C. Roos 2005 Bioinformatics using Computational Intelligence Paradigms

From Learning Metrics Towards Dependency Exploration

S. Kaski 2005 5th Workshop On Self-Organizing Maps, WSOM'05, Paris, France, September 5-8, 2005

Proactive Information Retrieval by Monitoring Eye Movements

S. Kaski 2005 Abstracts of BrainIT, The Second International Conference on Brain-Inspired Information Technology, Kyushu Institute of Technology, Kitakuyshu, Japan, October 7-9, 2005

User models from implicit feedback for proactive information retrieval

S. Kaski, P. Myllymäki, Ilpo Kojo 2005 Proceedings of Workshop 4 of the 10th International Conference on User Modeling; Machine Learning for User Modeling: Challenges, Edinburgh, Scotland, July 24-25, 2005

User models from implicit feedback for proactive information retrieval

Samuel Kaski, Petri Myllymäki, Ilpo Kojo 2005

Non-Parametric Dependent Components

A. Klami, S. Kaski 2005 IEEE International Conference on Acoustis, Speech, and Signal Processing, ICASSP'05, Philadelphia, PA, USA, March 18-23, 2005

Explorative Modeling of Yeast Stress Response and its Regulation with gCCA and Associative Clustering

J. Nikkilä, C. Roos, E. Savia, S. Kaski 2005 International Journal of Neural Systems

Integration of Transcription Factor Binding and Gene Expression by Associative Custering

J. Nikkilä, C. Roos, S. Kaski 2005 Symposium of Knowledge Representation in Bioinformatics, KRBIO05, Espoo, Finland, June 15-17, 2005

Self-Organizing Map-Based Discovery and Visualization of Human Endogeneous Retroviral Sequence Groups

Merja Oja, G.O. Sperber, Jonas Blomberg, S. Kaski 2005 International Journal of Neural Systems

Discriminative Components of Data

J. Peltonen, S. Kaski 2005 IEEE Transactions on Neural Networks

Combining Eye Movements and Collaborative Filtering for Proactive Information Retrieval

K. Puolamäki, J. Salojärvi, Eerika Savia, Jaana Simola, S. Kaski 2005 SIGIR 2005: Proceedings of the 28th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, Salvador, Brasil, August 15-19, 2005

Expectation Maximization Algorithms for Conditional Likelihoods

J. Salojärvi, K. Puolamäki, S. Kaski 2005 22nd International Conference on Machine Learning (ICML 2005), Bonn, Germany, August 7-11, 2005

Expectation Maximization Algorithms for Conditional Likelihoods

J. Salojärvi, K. Puolamäki, S. Kaski 2005

Implicit Relevance Feedback From Eye Movements

J. Salojärvi, K. Puolamäki, S. Kaski 2005 Artificial Neural Networks: Biological Inspirations - ICANN 2005: 15th International Conference, Warsaw, Poland, 11-15 September, 2005, Lecture Notes in Computer Science 3696

Inferring Relevance from Eye Movements: Feature Extraction

Jarkko Salojärvi, Kai Puolamäki, Jaana Simola, L. Kovanen, Ilpo Kojo, Samuel Kaski 2005

On Discriminative Joint Density Modeling

J. Salojärvi, K. Puolamäki, S. Kaski 2005 Machine Learning: ECML 2005, Lecture Notes in Artificial Intelligence 3270, European Conference on Machine Learning, Porto, Portugal, October 3-7, 2005

Two-Way Latent Grouping Model for User Preference Prediction

E. Savia, K. Puolamäki, J. Sinkkonen, S. Kaski 2005 21st Conference on Uncertainty in Artificial Intelligence (UAI) 2005, Edinburgh, Scotland, July 26-29, 2005

Associative Clustering (AC): Technical Details

Janne Sinkkonen, S. Kaski, L. Nikkilä, L. Lahti 2005

Local Multidimensional Scaling with Controlled Tradeoff Between Trustworthiness and Continuity

J. Venna, S. Kaski 2005 WSOM'05, Paris, France September 5-8, 2005

Visualized Atlas of a Gene Expression Databank

J. Venna, S. Kaski 2005 Symposium of Knowledge Representation in Bioinformatics, KRBIO05, Espoo, Finland, June 15-17, 2005

Principle of Learning Metrics for Data Analysis

S. Kaski, J. Sinkkonen 2004 Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology

Mining Massive Document Collections by the WEBSOM Method

K. Lagus, S. Kaski, T. Kohonen 2004 Information Sciences

Exploring Dependencies Between Yeast Stress Genes and their Regulators

J. Nikkilä, C. Roos, S. Kaski 2004 International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2004), Exeter, UK, August 25-27, 2004

Grouping and Visualizing Human Endogenous Retroviruses by Bootstrapping Median Self-organizing Maps

Merja Oja, G. Sperber, Jonas Blomberg, S. Kaski 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, California, USA, October 7-8, 2004

Improved Learning of Riemannian Metrics for Exploratory Data Analysis

J. Peltonen, A. Klami, S. Kaski 2004 Neural Networks

Sequential Information Bottleneck for Finite Data

J. Peltonen, J. Sinkkonen, S. Kaski 2004 Twenty-First International Conference on Machine Learning (ICML 2004), Banff, Alberta, Canada, July 4-8, 2004

Two-Way Latent Grouping Model for User Preference Prediction

K. Puolamäki, E. Savia, J. Sinkkonen, S. Kaski 2004

Relevance Feedback from Eye Movements for Proactive Information Retrieval

J. Salojärvi, K. Puolamäki, S. Kaski 2004 Workshop on Processing Sensory Information for Proactive Systems (PSIPS 2004), Oulu, Finland, June 14-15, 2004

On Text-Based Estimation of Document Relevance

E. Savia, S. Kaski, V. Tuulos, P. Myllymäki 2004 International Joint Conference on Neural Networks 2004, Budapest, Hungary, July 25-29, 2004

Associative Clustering

J. Sinkkonen, J. Nikkilä, L. Lahti, S. Kaski 2004 15th European Conference on Machine Learning (ECML 2004), Pisa, Italy, Sept. 20-24, 2004

Discriminative Clustering

Samuel Kaski 2003 54th Session of the International Statistical Institute, Berlin, Germany, August 13-20, 2003

Discriminative Clustering: Vector Quantization in Learning Metrics

Samuel Kaski, J. Sinkkonen 2003 26th Annual Conference of the Gesellschaft für Klassifikation, Mannheim, Germany, July 22-24, 2002

Informative Discriminant Analysis

Samuel Kaski, J. Peltonen 2003 ICML-2003, the Twentieth International Conference on Machine Learning, Washington, D.C., USA, August 21-24, 2003

Methods for Exploratory Cluster Analysis

Samuel Kaski, J. Nikkilä, T. Kohonen 2003 Intelligent Exploration of the Web

Regularized Discriminative Clustering

Samuel Kaski, J. Sinkkonen, A. Klami 2003 2003 IEEE International Workshop on Neural Networks for Signal Processing, Toulouse, France, September 17-19, 2003

Trustworthiness and Metrics in Visualizing Similarity of Gene Expression

Samuel Kaski, J. Nikkilä, Merja Oja, J. Venna, P. Törrönen, E. Castrén 2003 BMC Bioinformatics

Associative Clustering to Find Dependencies Between Expression Profiles and Transcription Factor Binding

Janne Nikkilä, C. Roos, Janne Sinkkonen, S. Kaski 2003

Bibliography of Self-Organizing Map SOM) Papers: 1998-2001 Addendum

Merja Oja, S. Kaski, T. Kohonen 2003 Neural Computing Surveys

Clustering of Human Endogenous Retrovirus Sequences with Median Self-Organizing Map

Merja Oja, P. Somervuo, S. Kaski, T. Kohonen 2003 Workshop on Self-Organizing Maps (WSOM'03), Hibikino, Japan, September 11-14, 2003

Finite Sequential Information Bottleneck (fsIB)

Jaakko Peltonen, J. Sinkkonen, S. Kaski 2003

Learning Metrics for Information Visualization

Jaakko Peltonen, A. Klami, S. Kaski 2003 Workshop on Self-Organizing Maps (WSOM'03), Hibikino, Kitakyushu, Japan, September 2003

Can Relevance be Inferred from Eye Movements in Information Retrieval?

Jarkko Salojärvi, I. Kojo, J. Simola, S. Kaski 2003 Workshop on Self-Organizing Maps (WSOM'03), Hibikino, Kitakyushu, Japan, September 11-14, 2003

Discriminative Clustering in Fisher Metrics

Jarkko Salojärvi, S. Kaski, J. Sinkkonen 2003 Supplementary Proceedings ICANN/ICONIP 2003, Istanbul, Turkey, June 26-29, 2003

Relevance Feedback from Eye Movements for Proactive Information Retrieval

Jarkko Salojärvi, K. Puolamäki, S. Kaski 2003

Associative Clustering by Maximizing a Bayes Factor

J. Sinkkonen, J. Nikkilä, L. Lahti, S. Kaski 2003

Visualizations for Assessing Convergence and Mixing of MCMC

J. Venna, S. Kaski, J. Peltonen 2003 14th European Conference on Machine Learning (ECML 2003), Cavtat-Dubrovnik, Croatia, Sept. 22-26, 2003

Visualizing High-Dimensional Posterior Distributions in Bayesian Modeling

Jarkko Venna, S. Kaski 2003 Artificial Neural Networks and Neural Information Processing - Supplementary Proceedings ICANN/ICONIP, Istanbul, Turkey, June, 2003

STeP 2002 - Intelligence, the Art of Natural and Artificial.Proceedings of the 10th Finnish Artificial Intelligence Conference, Oulu, Finland, Sept. 15-17

P. Ala-Siuru, Samuel Kaski 2002

Neljännesvuosisata Hatutusta: Hahmontunnistustutkimus Suomessa 1977-2002

Jukka Iivarinen, S. Kaski, E. Oja 2002

Learning Metrics

Samuel Kaski 2002 3rd Conference of the International Society for Ecological Informatics, Grottaferrata, Italy, August 26-30, 2002

Regularized Discriminative Clustering

Samuel Kaski, J. Sinkkonen, A. Klami 2002

Accurate Self-Organizing Maps in Learning Metrics

Arto Klami, J. Peltonen, S. Kaski 2002 Suomen Tekoälytutkimuksen Päivät, STeP -2002, Finnish AI Conference, Oulu, Finland, December 15-17, 2002

Analysis and Visualization of Gene Expression Data Using Self-Organizing Maps

Janne Nikkilä, Petri Törönen, S. Kaski, J. Venna, E. Castrén, Garry Wong 2002 Neural Networks

Exploratory Clustering of Gene Expression Profiles of Mutated Yeast Strains

Merja Oja, J. Nikkilä, P. Törönen, G. Wong, E. Castrén, S. Kaski 2002 Computational and Statistical Approaches to Genomics

Learning Metrics for SOM-Based Clustering and Visualization of Yeast Gene Expression Data

Merja Oja, P. Törönen, J. Nikkilä, E. Castrén, S. Kaski 2002 Bioinformatics 2002, Bergen, Norway, April 4-7, 2002

Learning Metrics for Visualizing Gene Functional Similarities

Merja Oja, J. Nikkilä, P. Törönen, E. Castrén, S. Kaski 2002 Suomen Tekoälytutkimuksen Päivät, STeP -2002, Finnish AI Conference, Oulu, Finland, December 15-17, 2002

Electronic Editor: Automatic Content-based Sequential Compilation of Newspaper Articles

Ville Ollikainen, Christer Bäckström, Samuel Kaski 2002 Neurocomputing

Discriminative Clustering of Text Documents

Janne Peltonen, J. Sinkkonen, S. Kaski 2002 9th International Conference on Neural Information Processing (ICONIP'02), Singapore, November 18-22, 2002

Learning More Accurate Metrics for Self-Organizing Maps

Jaakko Peltonen, A. Klami, S. Kaski 2002 International Conference on Artificial Neural Networks - ICANN 2002, Madrid, Spain, August 27-31, 2002

Mixture Density from Autonomous Experts

Jarkko Salojärvi, Samuel Kaski 2002 International Journal of Knowledge Based and Intelligent Engineering Systems

Clustering Based on Conditional Distributions in an Auxiliary Space

Janne Sinkkonen, S. Kaski 2002 Neural Computation

Discriminative Clustering: Optimal Contingency Tables by Learning Metrics

Janne Sinkkonen, S. Kaski, J. Nikkilä 2002 13th European Conference on Machine Learning (ECML'02), Helsinki, Finland, August 19-23, 2002

Analysis and Visualization of Gene Expression Data Using Self-Organizing Maps

Samuel Kaski, J. Nikkilä, P. Törrönen, E. Castren, G. Wong 2001 NSIP-01, IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing, Baltimore, Maryland, USA, June 3-6, 2001

A Topography-Preserving Latent Variable Model with Learning Metrics

Samuel Kaski, J. Sinkkonen 2001 Advances in Self-Organizing Maps, Workshop on Self-Organizing Maps (WSOM'01), Lincoln, UK, June 13-15, 2001

Bankruptcy Analysis with Self-Organizing Maps in Learning Metrics

Samuel Kaski, J. Sinkkonen, J. Peltonen 2001 IEEE Transactions on Neural Networks

Clustering Gene Expression Data by Mutual Information with Gene Function

Samuel Kaski, J. Sinkkonen, J. Nikkilä 2001 International Conference on Artificial Neural Networks (ICANN 2001), Vienna, Austria, August 21-25, 2001

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

Samuel Kaski, J. Sinkkonen, J. Peltonen 2001 Third International Conference on Data Warehousing and Knowledge Discovery (DaWaK 2001), Munich, Germany, Sept. 5-7, 2001

Generative Mixture Modeling by Autonomous Estimators

Samuel Kaski, J. Salojärvi 2001 5th International Conference Knowledge-Based Intelligent Information Engineering Systems & Allied Technologies (KES'2001), Osaka, Japan, Sept. 6-8, 2001

Learning Metrics for Exploratory Data Analysis

Samuel Kaski 2001 2001 IEEE Signal Processing Society Workshop, Neural Networks for Signal Processing XI, Falmouth, Massach., USA, Sept. 10-12, 2001

Learning Metrics for Self-Organizing Maps

Samuel Kaski, J. Sinkkonen, J. Peltonen 2001 International Joint Conference on Neural Networks (IJCNN'01), Washington, D.C., July 15-19, 2001

SOM-Based Exploratory Analysis of Gene Expression Data

Samuel Kaski 2001 Advances in Self-Organizing Maps, Workshop on Self-Organizing Maps (WSOM'01), Lincoln, UK, June 13-15, 2001

Analysis of Gene Expression Data Using Semi-Supervised Clustering

Janne Nikkilä, P. Törönen, J. Sinkkonen, S. Kaski 2001

Neighborhood Preservation in Nonlinear Projection Methods: An Experimental Study

Jarkko Venna, Samuel Kaski 2001

Coloring that Reveals Cluster Structures in Multivariate Data

Samuel Kaski, J. Venna, T. Kohonen 2000 Australian Journal of Intelligent Information Processing Systems

Convergence of a Stochastic Semisupervised Clustering Algorithm

Samuel Kaski 2000

Kohti uutta luovan ajattelun opettamista

Samuel Kaski 2000 OPE2, Dokumentoitua opetuksen kehittämistä Teknillisessä korkeakoulussa 1999-2000

Methods for Exploratory Cluster Analysis

Samuel Kaski, J. Nikkilä, T. Kohonen 2000 SSGRR 2000, International Conference on Advances in Infrastructure for Electronic Business, Science, and Education on the Internet, L'Aquila, Italy, July 31-August 6, 2000

Metrics That Learn Relevance

Samuel Kaski, J. Sinkkonen 2000

Self Organization of a Massive Document Collection

Teuvo Kohonen, S. Kaski, K. Lagus, Jarkko Salojärvi, Jukka Honkela, Vesa Paatero, Antti Saarela 2000 IEEE Transactions on Neural Networks

Automatic Content-based Sequential Ordering of Newspaper Articles for Electronic Books

Ville Ollikainen, Christer Bäckström, Samuel Kaski 2000 International Conference on Engineering Applications of Neural Networks (EANN 2000), Kingston, UK, July 17-19, 2000

Clustering by Similarity in an Auxiliary Space

Janne Sinkkonen, Samuel Kaski 2000 Second International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2000), Hong Kong, December 13-15, 2000

Semisupervised Clustering Based on Conditional Distributions in an Auxiliary Space

Janne Sinkkonen, S. Kaski 2000

Coloring that Reveals Cluster Structures in Multidimensional Data

Jarkko Venna, S. Kaski 2000 STeP'00, Finnish Artificial Intelligence Conference, 'AI of Tomorrow': Symposium on Theory, Espoo, Finland, August 28-31, 2000

Coloring that Reveals High-Dimensional Structures in Data

S. Kaski, J. Venna, T. Kohonen 1999 6th International Conference on Neural Information Processing (ICONIP'99), Perth, Australia, November 16-20, 1999

Fast Winner Search for SOM-Based Monitoring and Retrieval of High-Dimensional Data

S. Kaski 1999 Ninth International Conference on Artificial Neural Networks (ICANN'99), Edinburgh, U.K., September 7-10, 1999

Metrics Induced by Maximizing Mutual Information

S. Kaski, J. Sinkkonen 1999

Self-Organization of a Massive Text Document Collection

T. Kohonen, S. Kaski, K. Lagus, J. Salojärvi, J. Honkela, V. Paatero, A. Saarela 1999 Kohonen Maps

Keyword Selection Method for Characterizing Text Document Maps

K. Lagus, S. Kaski 1999

WEBSOM for Textual Data Mining

K. Lagus, T. Honkela, S. Kaski, T. Kohonen 1999 Artificial Intelligence Review

Kohonen Maps

E. Oja, S. Kaski 1999

Self-Organizing Maps of Large Document Collections

T. Honkela, K. Lagus, S. Kaski 1998 Visual Explorations in Finance with Self-Organizing Maps

Self-Organizing Maps of Very Large Document Collections: Justification for the WEBSOM Method

T. Honkela, S. Kaski, T. Kohonen, K. Lagus 1998 Classification, Data Analysis, and Data Highways

3043 Works that Have Been Based on the Self-Organizing Map (SOM) Method Developed by Kohonen

Jari Kangas, S. Kaski 1998

Bibliography of Self-Organizing Map (SOM) Papers: 1981-1997

S. Kaski, J. Kangas, T. Kohonen 1998 Neural Computing Surveys

Dimensionality Reduction by Random Mapping: Fast Similarity Computation for Clustering

S. Kaski 1998 International Joint Conference on Neural Networks (IJCNN'98), Anchorage, Alaska, May 4-9, 1998

Methods for Interpreting a Self-Organized Map in Data Analysis

S. Kaski, J. Nikkilä, T. Kohonen 1998 6th European Symposium on Artificial Neural Networks (ESANN'98), Bruges, Belgium

Statistical Aspects of the WEBSOM System in Organizing Document Collections

S. Kaski, K. Lagus, T. Honkela, T. Kohonen 1998 29th Symposium on the Interface, Houston, Texas, May 14-17, 1997

Tips for Processing and Color-Coding of Self-Organizing Maps

S. Kaski, T. Kohonen 1998 Visual Explorations in Finance with Self-Organizing Maps

WEBSOM - Self-Organizing Maps of Document Collections

S. Kaski, T. Honkela, K. Lagus, T. Kohonen 1998 Neurocomputing

WEBSOM - Self-Organizing Maps of Document Collections

T. Honkela, S. Kaski, K. Lagus, T. Kohonen 1997 Workshop on Self-Organizing Maps (WSOM'97), Espoo, Finland, June 4-6, 1997

Computationally Efficient Approximation of a Probabilistic Model for Document Representation in the WEBSOM Full-Text Analysis Method

S. Kaski 1997 Neural Processing Letters

Automatic Coloring of Data According to Its Cluster Structure

Teuvo Kohonen, S. Kaski, J. Venna 1997

Self-Organized Formation of Various Invariant-Feature Filters in the Adaptive-Subspace SOM

T. Kohonen, S. Kaski, H. Lappalainen 1997 Neural Computation

The Adaptive-Subspace Self-Organizing Map (ASSOM)

T. Kohonen, S. Kaski, H. Lappalainen, J. Salojärvi 1997 Workshop on Self-Organizing Maps (WSOM'97), Espoo, Finland, June 4-6, 1997

Topographic Components Model with Adaptive Latencies

J. Sinkkonen, S. Kaski 1997 NeuroImage

Topographic Components Model with Adaptive Latencies

J. Sinkkonen, S. Kaski 1997

Exploration of Full-Text Databases with Self-Organizing Maps

T. Honkela, S. Kaski, K. Lagus, T. Kohonen 1996 IEEE International Conference on Neural Networks (ICNN'96), Washington, D.C., USA, June 2-6, 1996

Newsgroup Exploration with WEBSOM Method and Browsing Interface

T. Honkela, S. Kaski, K. Lagus, T. Kohonen 1996

Self-Organizing Maps of Document Collections

T. Honkela, S. Kaski, K. Lagus, T. Kohonen 1996 Polysteekki, English ed.

Compression of Vector Quantization Code Sequences Based on Code Frequencies and Spatial Redundancies

J. Kangas, S. Kaski 1996

Comparing Self-Organizing Maps

S. Kaski, K. Lagus 1996

Computationally Efficient Approximation of a Probabilistic Model for Document Representation in the WEBSOM Full-Text Analysis Method

S. Kaski 1996

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