Publications

Amazon SageMaker Automatic Model Tuning: Scalable Black-box Optimization

Published in arXiv, 2020

Recommended citation: Valerio Perrone, Huibin Shen, Aida Zolic, Iaroslav Shcherbatyi, Amr Ahmed, Tanya Bansal, Michele Donini, Fela Winkelmolen, Rodolphe Jenatton, Jean Baptiste Faddoul, Barbara Pogorzelska, Miroslav Miladinovic, Krishnaram Kenthapadi, Matthias Seeger, Cédric Archambeau. (2020). "Amazon SageMaker Automatic Model Tuning: Scalable Black-box Optimization" arXiv preprint arXiv:2012.08489 https://arxiv.org/pdf/2012.08489

A Quantile-based Approach for Hyperparameter Transfer Learning

Published in Proceedings of the 37th International Conference on Machine Learning, 2020

Link: [pdf]

Recommended citation: David Salinas, Huibin Shen, Valerio Perrone. (2020). "A Quantile-based Approach for Hyperparameter Transfer Learning" Proceedings of the 37th International Conference on Machine Learning (ICML 2020) http://proceedings.mlr.press/v119/salinas20a.html

A quantile-based approach to hyperparameter transfer learning

Published in Advances in Neural Information Processing Systems Workshop on Meta-Learning, 2019

Link: [pdf]

Recommended citation: David Salinas, Huibin Shen, Valerio Perrone. (2019). "A quantile-based approach to hyperparameter transfer learning" Advances in Neural Information Processing Systems Workshop on Meta-Learning http://metalearning.ml/2019/papers/metalearn2019-salinas.pdf

Learning search spaces for Bayesian optimization: Another view of hyperparameter transfer learning

Published in Advances in Neural Information Processing Systems 32 (NeurIPS 2019), 2019

Links: [pdf] [bib]

Recommended citation: Valerio Perrone, Huibin Shen, Matthias W. Seeger, Cedric Archambeau, Rodolphe Jenatton. (2019). "Learning search spaces for Bayesian optimization: Another view of hyperparameter transfer learning" Advances in Neural Information Processing Systems 32 (NeurIPS 2019) https://papers.nips.cc/paper/2019/hash/6ea3f1874b188558fafbab78e8c3a968-Abstract.html

Machine Learning for Small Molecule Identification

Published in Aalto University publication series DOCTORAL DISSERTATIONS, 25/2017, 2017

Link: [pdf]

Recommended citation: Huibin Shen (2017). "Machine Learning for Small Molecule Identification" Aalto University publication series DOCTORAL DISSERTATIONS, 25/2017 https://aaltodoc.aalto.fi/handle/123456789/24783

Soft kernel target alignment for two-stage multiple kernel learning

Published in International Conference on Discovery Science, 2016

Link

Recommended citation: Huibin Shen, Sandor Szedmak, Céline Brouard, Juho Rousu. (2016). "Soft kernel target alignment for two-stage multiple kernel learning" International Conference on Discovery Science https://link.springer.com/chapter/10.1007/978-3-319-46307-0_27

Fast metabolite identification with input output kernel regression

Published in Bioinformatics, 2016

Link: [pdf]

Recommended citation: Céline Brouard, Huibin Shen, Kai Dührkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu. (2017). "Fast metabolite identification with input output kernel regression" Bioinformatics https://academic.oup.com/bioinformatics/article/32/12/i28/2288626?login=true

Searching molecular structure databases with tandem mass spectra using CSI: FingerID

Published in Proceedings of the National Academy of Sciences, 2015

Link: [pdf]

Recommended citation: Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, Sebastian Böcker. (2017). "Searching molecular structure databases with tandem mass spectra using CSI: FingerID" Proceedings of the National Academy of Sciences https://www.pnas.org/content/112/41/12580.short

Metabolite identification through multiple kernel learning on fragmentation trees

Published in Bioinformatics, 2014

Link: [pdf]

Recommended citation: Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu. (2014). "Metabolite identification through multiple kernel learning on fragmentation trees" Bioinformatics https://academic.oup.com/bioinformatics/article/30/12/i157/386855?login=true

Metabolite identification through machine learning—Tackling CASMI challenge using fingerID

Published in Metabolites, 2013

Link: [pdf]

Recommended citation: Huibin Shen, Nicola Zamboni, Markus Heinonen, Juho Rousu. (2013). "Metabolite identification through machine learning—Tackling CASMI challenge using fingerID" Metabolites https://www.mdpi.com/2218-1989/3/2/484

Metabolite identification and molecular fingerprint prediction through machine learning

Published in Bioinformatics, 2012

Link: [pdf]

Recommended citation: Markus Heinonen, Huibin Shen, Nicola Zamboni, Juho Rousu. (2013). "Metabolite identification and molecular fingerprint prediction through machine learning" Bioinformatics https://academic.oup.com/bioinformatics/article/28/18/2333/252360?login=true