Professorship Kaski Samuel

Research output

Research output per year 2011 2016 2017 2018 2019 2020 2021 2022 2023 2024

• 196 Article
• 170 Conference article in proceedings
• 15 Paper
• 10 Chapter
• 46 More
  • 7 Doctoral Thesis
  • 6 Conference article
  • 5 Abstract
  • 5 Review Article
  • 4 Software
  • 3 Book
  • 3 Meeting Abstract
  • 3 Other contribution
  • 2 Anthology
  • 2 Poster
  • 2 Letter
  • 2 Patent
  • 1 Foreword / postscript
  • 1 Special issue

Research output per year

Research output per year

Search results

• 2016

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

  Remes, S., Mononen, T. & Kaski, S., 14 May 2016, Proceedings of the 5th Workshop on Machine Learning and Interpretation in Neuroimaging (MLINI) at NIPS 2015. Rish, I., Wehbe, L., Langs, G., Grosse-Wentrup, M., Murphy, B. & Cecchi, G. (eds.). https://arxiv.org/abs/1605.04435, 8 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Professional

  Open Access

  • Models 100%
  • Classification 100%
  • Analysis Model 66%
  • Magnetoencephalography 66%
  • Motivation 33%

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

  Sieberts, S. K., Zhu, F., García-García, J., Stahl, E., Pratap, A., Pandey, G., Pappas, D., Aguilar, D., Anton, B., Bonet, J., Eksi, R., Fornés, O., Guney, E., Li, H., Marín, M. A., Panwar, B., Planas-Iglesias, J., Poglayen, D., Cui, J. & Falcao, A. O. & 73 others, Suver, C., Hoff, B., Balagurusamy, V. S. K., Dillenberger, D., Neto, E. C., Norman, T., Aittokallio, T., Ammad-Ud-Din, M., Azencott, C. A., Bellón, V., Boeva, V., Bunte, K., Chheda, H., Cheng, L., Corander, J., Dumontier, M., Goldenberg, A., Gopalacharyulu, P., Hajiloo, M., Hidru, D., Jaiswal, A., Kaski, S., Khalfaoui, B., Khan, S. A., Kramer, E. R., Marttinen, P., Mezlini, A. M., Molparia, B., Pirinen, M., Saarela, J., Samwald, M., Stoven, V., Tang, H., Tang, J., Torkamani, A., Vert, J. P., Wang, B., Wang, T., Wennerberg, K., Wineinger, N. E., Xiao, G., Xie, Y., Yeung, R., Zhan, X., Zhao, C., Greenberg, J., Kremer, J., Michaud, K., Barton, A., Coenen, M., Mariette, X., Miceli, C., Shadick, N., Weinblatt, M., De Vries, N., Tak, P. P., Gerlag, D., Huizinga, T. W. J., Kurreeman, F., Allaart, C. F., Louis Bridges, S., Criswell, L., Moreland, L., Klareskog, L., Saevarsdottir, S., Padyukov, L., Gregersen, P. K., Friend, S., Plenge, R., Stolovitzky, G., Oliva, B., Guan, Y. & Mangravite, L. M., 23 Aug 2016, In: Nature Communications. 7, p. 1-9 12460.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Treatment Response 100%
  • Rheumatoid Arthritis 100%
  • Assessment 100%
  • Treatment 100%
  • Tumor Necrosis Factor 100%
  69 Citations (Scopus)

  222 Downloads (Pure)

• DeepMeSH: Deep semantic representation for improving large-scale MeSH indexing

  Peng, S., You, R., Wang, H., Zhai, C., Mamitsuka, H. & Zhu, S., 15 Jun 2016, In: Bioinformatics. 32, 12, p. i70-i79 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Semantic Representation 100%
  • Subject Heading 100%
  • Semantics 12%
  • Context Dependent 12%
  • Text Mining 12%
  102 Citations (Scopus)

  300 Downloads (Pure)

• Diffusion of a Brownian ellipsoid in a force field

  Aurell, E., Bo, S., Dias, M., Eichhorn, R. & Marino, R., 1 May 2016, In: EPL. 114, 3, 30005.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Behavior 100%
  • Diffusion 100%
  • Particle 100%
  • Ellipsoid 100%
  • Field Theory (Physics) 100%
  11 Citations (Scopus)

• DrugE-Rank: Improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank

  Yuan, Q., Gao, J., Wu, D., Zhang, S., Mamitsuka, H. & Zhu, S., 15 Jun 2016, In: Bioinformatics. 32, 12, p. i18-i27 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Drug 100%
  • Cross-Validation 9%
  • Drug Discovery 9%
  109 Citations (Scopus)

  155 Downloads (Pure)

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

  Ammad-ud-din, M., Khan, S. A., Malani, D., Murumägi, A., Kallioniemi, O., Aittokallio, T. & Kaski, S., 3 Sept 2016, In: Bioinformatics. 32, 17, p. i455-i463 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Matrix 100%
  • Prediction 100%
  • Factorization 100%
  • Matrix Factorization 100%
  • Drug 100%
  79 Citations (Scopus)

  88 Downloads (Pure)

• ELFI: Engine for Likelihood-Free Inference

  Kangasrääsiö, A., Lintusaari, J., Skyten, K., Järvenpää, M., Vuollekoski, H., Gutmann, M., Vehtari, A., Corander, J. & Kaski, S., 9 Dec 2016. 4 p.

  Research output: Contribution to conference › Paper › Scientific

  • User 100%
  • Inference Engines 100%
  • Design 50%
  • Models 50%
  • Gaussian Process 50%

• Entropy production of a Brownian ellipsoid in the overdamped limit

  Marino, R., Eichhorn, R. & Aurell, E., 19 Jan 2016, In: Physical Review E. 93, 1, p. 1-15 012132.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Entropy 100%
  • Entropy Production 100%
  • Particle 83%
  • Shape 33%
  • Thermodynamics 33%
  14 Citations (Scopus)

  196 Downloads (Pure)

• Extracting relevance and affect information from physiological text annotation

  Barral, O., Kosunen, I., Ruotsalo, T., Spapé, M. M., Eugster, M. J. A., Ravaja, N., Kaski, S. & Jacucci, G., 1 Dec 2016, In: User Modeling and User-Adapted Interaction. 26, 5, p. 493-520 28 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  • User 100%
  • Text Annotation 100%
  • Annotation 33%
  • User Information 33%
  • Design 16%
  22 Citations (Scopus)

• Fundamentals and Recent Developments in Approximate Bayesian Computation

  Lintusaari, J., Gutmann, M., Dutta, R., Kaski, S. & Corander, J., 2016, In: SYSTEMATIC BIOLOGY. 66, 1, p. e66-e82

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Approximate Bayesian Computation 100%
  • Inference 33%
  • Approximates 33%
  • Bayesian Inference 16%
  • Minimal Set 16%
  153 Citations (Scopus)

  224 Downloads (Pure)

• Generating data to improve protein stability prediction

  Heinonen, M. (Inventor), Jokinen, E. (Inventor), Kaski, S. (Inventor), Rousu, J. (Inventor) & Lähdesmäki, H. (Inventor), 2016, Patent No. Provisional US 62/361511

  Research output: Patent

• Interactive intent modeling from multiple feedback domains

  Daee, P., Pyykkö, J., Glowacka, D. & Kaski, S., 7 Mar 2016, International Conference on Intelligent User Interfaces, Proceedings IUI. ACM, Vol. 07-10-March-2016. p. 71-75 5 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • Domains 100%
  • User 100%
  • Modeling 100%
  • Intents 100%
  • Models 20%
  14 Citations (Scopus)

• Interactive modeling of concept drift and errors in relevance feedback

  Kangasrääsiö, A., Chen, Y., Głowacka, D. & Kaski, S., 13 Jul 2016, UMAP 2016 - Proceedings of the 2016 Conference on User Modeling Adaptation and Personalization. ACM, p. 185-193 9 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • User 100%
  • Modeling 100%
  • Concept Drift 100%
  • Relevance Feedback 100%
  • Models 40%
  7 Citations (Scopus)

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

  Sundin, I., Micallef, L., Marttinen, P., Ammad-Ud-Din, M., Peltola, T., Soare, M., Jacucci, G. & Kaski, S., 2016, p. 1-5.

  Research output: Contribution to conference › Paper › Scientific

  • Models 100%
  • User 100%
  • Modeling 100%
  • Intents 100%
  • Interactive User 100%

• Ladder Variational Autoencoders

  Kaae Sønderby, C., Raiko, T., Maaløe, L., Kaae Sønderby, S. & Winther, O., 2016, Advances in Neural Information Processing Systems. Neural Information Processing Systems Foundation, p. 3745-3753 9 p. (Advances in neural information processing systems; vol. 29).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • Model 100%
  • Ladder 100%
  • Autoencoder 100%
  • Models 62%
  • Inference 37%

• Modelling-based experiment retrieval: A case study with gene expression clustering

  Blomstedt, P., Dutta, R., Seth, S., Brazma, A. & Kaski, S., 1 May 2016, In: Bioinformatics. 32, 9, p. 1388-1394 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Models 100%
  • Case Study 100%
  • Contexts 20%
  • Control 20%
  • Good Performance 20%
  9 Citations (Scopus)

• Modern tools for old content-in search of named entities in a Finnish OCRed historical newspaper collection 1771-1910

  Kettunen, K., Mäkelä, E., Kuokkala, J., Ruokolainen, T. & Niemi, J., 2016, Lernen, Wissen, Daten, Analysen 2016: Proceedings of the Conference "Lernen, Wissen, Daten, Analysen", Potsdam, Germany, September 12-14, 2016. Krestel, R., Mottin, D. & Müller, E. (eds.). CEUR, p. 124-135 12 p. (CEUR Workshop Proceedings; vol. 1670).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  Open Access

  File

  • Named Entity Recognition 100%
  • Evaluation 75%
  • Computing 25%
  • Standards 25%
  • Classification 25%
  72 Downloads (Pure)

• Multiple output regression with latent noise

  Gillberg, L., Marttinen, P., Pirinen, M., Kangas, A. J., Soininen, P., Ali, M., Havulinna, A. S., Järvelin, M. R., Ala-Korpela, M. & Kaski, S., 1 Jun 2016, In: Journal of Machine Learning Research. 17, p. 1-35 35 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Regression Output 100%
  • Models 100%
  • Regression 100%
  • Reduced-Rank Regression Model 80%
  • Modeling 40%
  10 Citations (Scopus)

  110 Downloads (Pure)

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

  Eugster, M., Ruotsalo, T., Spape, M., Barral, O., Ravaja, N., Jacucci, G. & Kaski, S., 9 Nov 2016, In: Scientific Reports. 6, p. 1-10 38580 .

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • User 100%
  • Relevant Information 100%
  • Wikipedia 100%
  • Information Interface 100%
  • Internet 50%
  40 Citations (Scopus)

  235 Downloads (Pure)

• New Resistance Distances with Global Information on Large Graphs

  Nguyen, C. H. & Mamitsuka, H., May 2016, Proceedings of the 19th International Conference on Artificial Intelligence and Statistics. Gretton, A. & Robert, C. C. (eds.). MIT Press, p. 639-647 (JMLR: Workshop and Conference Proceedings; vol. 51).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  Open Access

  File

  • Global Information 100%
  • Random Walk 33%
  • Distance Function 33%
  • Cluster Structure 33%
  • Energy Function 33%
  463 Downloads (Pure)

• On one-step replica symmetry breaking in the Edwards-Anderson spin glass model

  Del Ferraro, G., Wang, C., Zhou, H.-J. & Aurell, E., Jul 2016, In: Journal of Statistical Mechanics: Theory and Experiment. 2016, 7, 32 p., 073305.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Free Energy 100%
  • Symmetry Breaking 100%
  • Approximation 75%
  • Classes 50%
  • Graph 50%
  1 Citation (Scopus)

• On the identifiability of transmission dynamic models for infectious diseases

  Lintusaari, J., Gutmann, M., Kaski, S. & Corander, J., 1 Mar 2016, In: Genetics. 202, 3, p. 911-918 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Models 100%
  • Transmission Dynamic 100%
  • Identifiability 100%
  • Infectious Disease 100%
  • Infection 100%
  19 Citations (Scopus)

• Peacock bundles: Bundle coloring for graphs with globality-locality trade-off

  Peltonen, J. & Lin, Z., 2016, Graph Drawing and Network Visualization - 24th International Symposium, GD 2016, Revised Selected Papers. Springer, Vol. 9801 LNCS. p. 52-64 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9801 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • Coloring 100%
  • Bundling 100%
  • User 20%
  • Optimization 20%
  • Algorithms 20%
  1 Citation (Scopus)

• Personalization of Search Results using Interactive Intent Modeling

  Kangasrääsiö, A., Głowacka, D. & Kaski, S., 24 Jun 2016, ICML 2016 Workshop on Computational Frameworks for Personalization. 6 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  File

  • Modeling 100%
  • Intents 100%
  • Models 50%
  • User 50%
  • User Interfaces 25%
  290 Downloads (Pure)

• Preliminary studies on personalized preference prediction from gaze in comparing visualizations

  Rezazadegan Tavakoli, H., Poostchimohammadabadi, H., Peltonen, J., Laaksonen, J. & Kaski, S., 2016, Advances in Visual Computing: 12th International Symposium, ISVC 2016, Las Vegas, NV, USA, December 12-14, 2016, Proceedings, Part II. Springer, p. 576-585 (Lecture Notes in Computer Science; vol. 10073).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • User 100%
  • Visualization 100%
  • User Preference 50%
  • Gaussian Process 25%
  • Human Computer Interaction 25%
  2 Citations (Scopus)

• Probabilistic Expert Knowledge Elicitation of Feature Relevances in Sparse Linear Regression

  Daee, P., Peltola, T., Soare, M. & Kaski, S., 2016, 4 p. CEUR.

  Research output: Other contribution › Scientific › peer-review

  Open Access

  File
  58 Downloads (Pure)

• Probabilistic model to treat flexibility in molecular contacts

  Hakulinen, R. & Puranen, S., 2016, In: MOLECULAR PHYSICS. 114, 21, p. 3201-3220 20 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Probability Theory 100%
  • Flexibility 100%
  • Strength 40%
  • Density 40%
  • Torque 40%
  2 Citations (Scopus)

• Scalable gradient-based tuning of continuous regularization hyperparameters

  Luketina, J., Berglund, M., Greff, K. & Raiko, T., 2016, 33rd International Conference on Machine Learning, ICML 2016. International Machine Learning Society , Vol. 6. p. 4333-4341 9 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • Models 100%
  • Regularization 100%
  • Optimization 50%
  • Validation 50%
  • Parameter Model 50%
  29 Citations (Scopus)

• Set Visualization Challenges for Big Data

  Micallef, L., 2016, Proceedings of the International Workshop on Set Visualization and Reasoning (SetVR 2016). RWTH Aachen University, p. 1-3 (CEUR Workshop Proceedings ; vol. 1655).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific

  Open Access

  File

  • Visualization 100%
  • Big Data 100%
  • Real World 50%
  105 Downloads (Pure)

• Sparse group factor analysis for biclustering of multiple data sources

  Bunte, K., Leppäaho, E., Saarinen, I. & Kaski, S., 15 Aug 2016, In: Bioinformatics. 32, 16, p. 2457-2463 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Factor Analysis 100%
  • Data Source 100%
  • Multiple Data Source 100%
  • Drug Sensitivity 50%
  • Introspection 25%
  23 Citations (Scopus)

• Statistical mechanics analysis of thresholding 1-bit compressed sensing

  Xu, Y. & Kabashima, Y., 22 Aug 2016, In: Journal of Statistical Mechanics: Theory and Experiment. 2016, 8, p. 1-16 083405.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Compressed Sensing 100%
  • Heuristics 66%
  • Threshold Value 66%
  • Statistical Property 33%
  • Computational Cost 33%
  2 Citations (Scopus)

• Structure discovery in Bayesian networks by sampling partial orders

  Niinimäki, T., Parviainen, P. & Koivisto, M., 1 Apr 2016, In: Journal of Machine Learning Research. 17

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Bayesian Network 100%
  • Partial Order 100%
  • Bayesian 100%
  • Order 100%
  • Number 33%
  31 Citations (Scopus)

  75 Downloads (Pure)

• The bulk and the tail of minimal absent words in genome sequences

  Aurell, E., Innocenti, N. & Zhou, H. J., 4 Apr 2016, In: Physical Biology. 13, 2, p. 1-10 026004.

  Research output: Contribution to journal › Article › Scientific › peer-review

  • Volume 100%
  • Organisms 33%
  • Length 33%
  • Escherichia coli 33%
  • Yeast 33%
  2 Citations (Scopus)

• The Maximum Entropy Fallacy Redux?

  Aurell, E., 1 May 2016, In: PLoS computational biology. 12, 5, p. 1-7 e1004777.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  17 Citations (Scopus)

  167 Downloads (Pure)

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

  Virtanen, S., Afrabandpey, H. & Kaski, S., 18 May 2016, ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. IEEE, Vol. 2016-May. p. 2464-2468 5 p. 7472120

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • User 100%
  • Visualization 100%
  • Factorization 100%
  • Primary Data 75%
  • Models 25%
• 2014

  PicSOM Experiments in TRECVID 2014

  Ishikawa, S., Koskela, M., Sjöberg, M., Anwer, R. M., Laaksonen, J. & Oja, E., 2014, TRECVID workshop, TRECVID, Orlando, USA, November 10-12 2014.

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Professional
• 2011

  A generative approach for image-based modeling of tumor growth

  Menze, B. H., Van Leemput, K., Honkela, A., Konukoglu, E., Weber, M. A., Ayache, N. & Golland, P., 2011, INFORMATION PROCESSING IN MEDICAL IMAGING. Springer, p. 735-747 13 p. (Lecture Notes in Computer Science; vol. 6801).

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

  • Models 100%
  • Modeling 100%
  • Generative Approach 100%
  • Standards 20%
  • Approximation (Algorithm) 20%
  48 Citations (Scopus)