# Antti Honkela

- Professor, Department of Computer Science, University of Helsinki
- Coordinating Professor of Research Programme in Privacy-preserving and Secure AI, Finnish Center for Artificial Intelligence (FCAI)
- D.Sc. (Tech.), Docent in Statistical Machine Learning (Aalto University)

**Open postdoc and/or PhD positions in probabilistic modelling with differential privacy**

Antti Honkela is a Professor a Data Science (Machine Learning and AI) at the Department of Computer Science, University of Helsinki. Prior to his current appointment, he was an Assistant Professor of Statistics at the Department of Mathematics and Statistics and the Department of Public Health, University of Helsinki. He is the coordinating professor of Research Programme in Privacy-preserving and Secure AI at the Finnish Center for Artificial Intelligence (FCAI), a flagship of research excellence appointed by the Academy of Finland, and leader of the Privacy and infrastructures WP in European Lighthouse in Secure and Safe AI (ELSA), a European network of excellence in secure and safe AI. He serves in multiple advisory positions for the Finnish government in privacy of health data.

Prof. Honkela's research interests include privacy-preserving machine learning and differential privacy, Bayesian machine learning and probabilistic modelling, as well as their applications in computational biology and health.

Prof. Honkela is an action editor for the Transactions on Machine Learning and regularly serves as area chair for NeurIPS, ICML and AISTATS.

## News

- Started as a full professor in the beginning of 2023.
- New paper Strong pathogen competition in neonatal gut colonisation published in Nature Communications.
- European Lighthouse in Secure and Safe AI funded by Horizon Europe.
- New paper Differentially Private Bayesian Inference for Generalized Linear Models accepted to ICML 2021.
- New paper Tight Differential Privacy for Discrete-Valued Mechanisms and for the Subsampled Gaussian Mechanism Using FFT accepted to AISTATS 2021.
- Data Literacy for Responsible Decision-making project funded by the Strategic Research Council at the Academy of Finland.
- I am co-organising the Privacy-Preserving Machine Learning workshop at NeurIPS 2020.
- Two papers accepted to AISTATS 2020: Learning Rate Adaptation for Differentially Private Learning and Computing Tight Differential Privacy Guarantees Using FFT
- New paper Differentially Private Markov Chain Monte Carlo accepted as a spotlight at NeurIPS 2019.
- I am co-organising the Privacy in Machine Learning workshop at NeurIPS 2019.
- New paper Representation transfer for differentially private drug sensitivity prediction published at ISMB/ECCB 2019.
- I have started as an associate professor (tenure track) of data science at the Department of Computer Science at the University of Helsinki.
- I am co-organising the Machine Learning Open Source Software 2018: Sustainable communities workshop at NeurIPS 2018
- I am co-organising the Privacy in Machine Learning and Artificial Intelligence workshop at the Federated AI Meetings 2018 in Stockholm.
- New paper Differentially private Bayesian learning on distributed data accepted to NIPS 2017.
- I am co-organising the ICML 2017 Workshop on Privacy and Secure Machine Learning

## Research group

### Postdocs

Joonas Jälkö

Razane Tajeddine

### PhD students

Elio Nushi

Ossi Räisä

Marlon Tobaben

Aki Rehn

Gauri Pradhan

Talal Alrawajfeh

### Alumni

Onur Dikmen (Postdoc)

Mikko Heikkilä (PhD student)

Liisa Ilvonen (Postdoc)

Antti Koskela (Postdoc)

Tommi Mäklin (PhD student)

Ola Salman (Postdoc)

Hande Topa (PhD student)

## Selected projects

- ELSA - European Lighthouse on Secure and Safe AI
- DataLit - Data Literacy for Responsible Decision Making

## Contact information

Room D228 at the Department of Computer Science, Exactum,
Kumpula campus, University of Helsinki

Telephone: +358 2941 51253

Email: antti.honkela@helsinki.fi

Mobile: +358 50 311 2483

### Mailing address:

Department of Computer Science

University of Helsinki

P.O. Box 68 (Pietari Kalmin katu 5)

00014 University of Helsinki, Finland

## Software

- Differential privacy software on GitHub.
- My group's software releases on GitHub.
- BitSeq software for transcript-level expression and differential expression estimation from RNA-sequencing data is available as a standalone C++ package and in BitSeq Bioconductor package.
- The tigre package implementing the transcription factor target ranking method from our recent PNAS paper is available in Bioconductor. A Matlab implementation used to produce the results reported in the paper is also available.
- tigreBrowser is a web-based browser for displaying and ranking genomic modelling results. It allows easy viewing, sorting and filtering of visualisations of models from tigre or other tools.
- Older free software tools I have created are available on the pages of the Bayes and IVGA groups.

## Teaching

**University of Helsinki:**- Autumn 2022
- DATA11007 Statistics for Data Science
- DATA20019 Trustworthy Machine Learning
- Autumn 2021
- DATA20019 Trustworthy Machine Learning
- Autumn 2020
- MAST32001 Computational statistics I
- DATA20019 Trustworthy Machine Learning
- Autumn 2019
- MAST32001 Computational statistics I
- DATA20019 Trustworthy Machine Learning
- Autumn 2018
- MAST32001 Computational statistics I
- Spring 2018
- Statistical methods of medical research
- Autumn 2017
- MAST32001 Computational statistics I
- Spring 2017
- Statistical methods of medical research
- Autumn 2016
- 58316301 Seminar on Probabilistic Programming
- 582746 Modelling and Analysis in Bioinformatics
- Autumn 2015
- 582746 Modelling and Analysis in Bioinformatics
- Autumn 2014
- 58314301 Seminar in Probabilistic Models for Big Data
- Spring 2014
- 582637 Project in Probabilistic Models
- Spring 2013
- 582637 Project in Probabilistic Models
- Spring 2012
- 582637 Project in Probabilistic Models
- Spring 2011
- 582637 Project in Probabilistic Models

**Helsinki University of Technology:**- Spring 2009
- T-61.6070 Special Course in Bioinformatics I: Learning and Inference in Dynamic Models of Biological Networks
- Autumn 2008
- T-61.5110 Modelling of biological networks
- 2006-2007
- Scientific coordinator of the International Master's Programme in Machine Learning and Data Mining - Macadamia
- Spring 2007
- T-61.152 Informaatiotekniikan seminaari: tiedonhaku (Seminar in Computer and Information Science: Information retrieval)
- Autumn 2006
- T-61.6010 Special Course in Computer and Information Science I: Gaussian Processes for Machine Learning
- Spring 2006
- T-61.152 Informaatiotekniikan seminaari: ydinfunktiomenetelmät (Seminar in Computer and Information Science: Kernel methods)
- 2005-2006
- Coordinator for the lab of Computer and Information Science for the department of Computer Science and Engineering B.Sc. seminar (Kandidaattiseminaari)
- Autumn 2004
- T-61.182 Information Theory and Machine Learning
- Autumn 2001
- T-61.181 Independent Component Analysis

## Publications

Google ScholarPubmed

### Journal articles

A. Honkela, J. Peltonen, H. Topa, I. Charapitsa, F. Matarese, K. Grote,
H.G. Stunnenberg, G. Reid, N.D. Lawrence and M. Rattray.

Genome-wide modelling of transcription kinetics reveals patterns of RNA production delays.

PNAS (2015).

doi:10.1073/pnas.1420404112,
arXiv:1503.01081 [q-bio.GN].

J. Hensman, P. Papastamoulis, P. Glaus, A. Honkela, and M. Rattray.

Fast and accurate approximate inference of transcript expression from RNA-seq data.

Bioinformatics (2015).

doi:10.1093/bioinformatics/btv483, arXiv:1412.5995 [q-bio.QM].

(Earlier version as arXiv:1308.5953 [q-bio.GN])

K. Uziela and A. Honkela.

Probe region expression estimation for RNA-seq data for improved microarray comparability.

PLoS ONE 10(5):e0126545 (2015).

DOI:10.1371/journal.pone.0126545,
arXiv:1304.1698 [q-bio.GN]

H. Topa, Á Jónás, R. Kofler, C. Kosiol, and A. Honkela.

Gaussian process test for high-throughput sequencing time series: application to experimental evolution.

Bioinformatics 31(11):1762-1770 (2015).

doi:10.1093/bioinformatics/btv014,
arXiv:1403.4086 [q-bio.PE].

J. C. Costello, L. M. Heiser, E. Georgii, M. Gönen, M. P. Menden,
N. J. Wang, M. Bansal, M. Ammad-ud-din, P. Hintsanen, S. A. Khan,
J-P. Mpindi, O. Kallioniemi, A. Honkela, T. Aittokallio, K. Wennerberg,
NCI DREAM Community, J. J. Collins, D. Gallahan, D. Singer,
J. Saez-Rodriguez, S. Kaski, J. W. Gray, and G. Stolovitzky.

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

Nature Biotechnology 32:1202-1212 (2014).

doi:10.1038/nbt.2877

S. Seth, N. Välimäki, S. Kaski, and A. Honkela.

Exploration and retrieval of whole-metagenome sequencing samples.

Bioinformatics 30(17):2471-2479 (2014).

doi:10.1093/bioinformatics/btu340, arXiv:1308.6074 [q-bio.GN]

C. wa Maina, A. Honkela, F. Matarese, K. Grote, H. G. Stunnenberg,
G. Reid, N. D. Lawrence, and M. Rattray.

Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data.

PLoS Comput Biol 10(5):e1003598 (2014).

doi:10.1371/journal.pcbi.1003598, arXiv:1303.4926 [q-bio.QM]

M. Titsias^{*}, A. Honkela^{*}, N. D. Lawrence, and M. Rattray.

Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison.

BMC Systems Biology 6:53 (2012).

doi:10.1186/1752-0509-6-53

P. Glaus, A. Honkela^{*}, and M. Rattray^{*}.

Identifying differentially expressed transcripts from
RNA-seq data with biological variation.

Bioinformatics 28(13):1721-1728 (2012).

doi:10.1093/bioinformatics/bts260, arXiv:1109.0863 [q-bio.GN]

U. Remes, K. J. Palomäki, T. Raiko, A. Honkela, and M. Kurimo.

Missing-feature reconstruction with bounded nonlinear
state-space model.

IEEE Signal Processing Letters 18(10):563-566 (2011).

doi:10.1109/LSP.2011.2163508

A. Honkela, P. Gao, J. Ropponen, M. Rattray, N. D. Lawrence.

tigre:
Transcription factor Inference through Gaussian
process Reconstruction of Expression for Bioconductor.

Bioinformatics 27(7):1026-1027 (2011).

doi:10.1093/bioinformatics/btr057

A. Honkela^{*}, T. Raiko^{*}, M. Kuusela, M. Tornio, and J. Karhunen.

Approximate Riemannian conjugate
gradient learning for fixed-form variational Bayes.

Journal of Machine Learning Research 11(Nov):3235-3268 (2010).

(Also available: Pre-print pdf)

A. Honkela, C. Girardot, E. H. Gustafson, Y.-H. Liu, E. E. M. Furlong,
N. D. Lawrence and M. Rattray.

Model-based
method for transcription factor target identification with
limited data.

Proc. Natl. Acad. Sci. U S A 107(17):7793-7798 (2010).

doi:10.1073/pnas.0914285107

P. Gao, A. Honkela, M. Rattray, and N. D. Lawrence.

Gaussian
process modelling of latent chemical species: applications to
inferring transcription factor activities.

Bioinformatics 24(16):i70-i75 (2008).

Appeared in Proceedings of ECCB 2008.

doi:10.1093/bioinformatics/btn278

A. Honkela, J. Seppä, and E. Alhoniemi.

Agglomerative Independent
Variable Group Analysis.

Neurocomputing 71(7-9):1311-1320 (2008).

Appeared in Special Issue for the 15th European Symposium on Artificial
Neural Networks (ESANN 2007).

doi:10.1016/j.neucom.2007.11.024

A. Honkela, H. Valpola, A. Ilin, and J. Karhunen.

Blind Separation of Nonlinear
Mixtures by Variational Bayesian Learning.

Digital Signal Processing 17(5):914-934 (2007).

Appeared in Special Issue on Bayesian Source Separation.

doi:10.1016/j.dsp.2007.02.009

E. Alhoniemi, A. Honkela, K. Lagus, J. Seppä, P. Wagner, and
H. Valpola.

Compact Modeling of
Data Using Independent Variable Group Analysis.

IEEE Transactions on Neural Networks 18(6):1762-1776 (2007).

doi:10.1109/TNN.2007.900809

A. Honkela and H. Valpola.

Variational learning and bits-back coding: an
information-theoretic view to Bayesian learning.

IEEE Transactions on Neural Networks 15(4):800-810 (2004).

Appeared in Special Issue on Information Theoretic Learning.

doi:10.1109/TNN.2004.828762

A. Honkela, H. Valpola and J. Karhunen.

Accelerating Cyclic Update Algorithms for Parameter Estimation by
Pattern Searches.

Neural Processing Letters 17(2):191-203 (2003).

doi:10.1023/A:1023655202546

H. Valpola, E. Oja, A. Ilin, A. Honkela and J. Karhunen.

Nonlinear Blind Source Separation by Variational Bayesian Learning.

IEICE Transactions on Fundamentals of Electronics,
Communications and Computer Sciences E86-A(3):532-541 (2003).

Publisher electronic edition

### Book chapters

N. Lawrence, M. Rattray, A. Honkela, and M. Titsias.

Gaussian Process Inference for Differential Equation Models
of Transcriptional Regulation.

In M. P. H. Stumpf, D. J. Balding, and M. Girolami, eds.,
Handbook of Statistical Systems Biology, pp. 376-394,
John Wiley & Sons, Chichester, UK (2011).

doi:10.1002/9781119970606.ch19

H. Lappalainen and A. Honkela.

Bayesian Nonlinear Independent Component Analysis by Multi-Layer Perceptrons.

In M. Girolami, editor, Advances in
Independent Component Analysis, pp. 93 - 121, Springer (2000).

Also available as a PostScript version (420 kb).

### Conference papers

B. H. Menze, K. Van Leemput, A. Honkela, E. Konukoglu,
M. A. Weber, N. Ayache, and P. Golland.

A Generative Approach for
Image-Based Modeling of Tumor Growth.

In Proceedings of the 22nd International Conference
on Information Processing in Medical Imaging (IPMI 2011),
Kloster Irsee, Germany.

Vol. 6801 of Lecture Notes in Computer Science, pp. 735-747,
Springer-Verlag (2011).

doi:10.1007/978-3-642-22092-0_60

V. Peltola and A. Honkela.

Variational Inference and
Learning for Non-Linear State-Space Models with State-Dependent
Observation Noise.

In Proceedings of
the 2010 IEEE International Workshop on Machine Learning for
Signal Processing (MLSP 2010), Kittilä, Finland, pp. 190-195 (2010).

A. Honkela, M. Milo, M. Holley, M. Rattray, and N. D. Lawrence.

Ranking of Gene Regulators
through Differential Equations and Gaussian Processes.

In Proceedings of
the 2010 IEEE International Workshop on Machine Learning for
Signal Processing (MLSP 2010), Kittilä, Finland, pp. 154-159 (2010).

M. Kuusela, T. Raiko, A. Honkela, and J. Karhunen.

A
Gradient-Based Algorithm Competitive with Variational Bayesian EM
for Mixture of Gaussians.

In Proceedings of the
International Joint Conference on Neural Networks (IJCNN 2009),
Atlanta, Georgia, June 15-19 (2009).

A. Honkela, M. Tornio, T. Raiko, and J. Karhunen.

Natural Conjugate Gradient in
Variational Inference.

In Proceedings of the 14th International Conference on
Neural Information Processing (ICONIP 2007), Kitakyushu, Japan.

Vol. 4985 of Lecture Notes in Computer Science, pp. 305-314,
Springer-Verlag (2008).

doi:10.1007/978-3-540-69162-4_32

A. Honkela, J. Seppä, and E. Alhoniemi.

Agglomerative Independent Variable
Group Analysis.

In Proceedings of the 15th European Symposium on Artificial
Neural Networks (ESANN 2007), Bruges, Belgium, pp. 55-60 (2007).

M. Tornio, A. Honkela, and J. Karhunen.

Time Series Prediction
with Variational Bayesian Nonlinear State-Space Models.

In Proceedings of the European Symposium on Time Series Prediction
(ESTSP 2007), Espoo, Finland, pp. 11-19 (2007).

J. Nikkilä, A. Honkela, and S. Kaski.

Exploring the Independence of Gene
Regulatory Modules.

In J. Rousu, S. Kaski, and E. Ukkonen,
editors, Proc. Workshop on Probabilistic Modeling and Machine
Learning in Structural and Systems Biology, Tuusula, Finland,
pp. 131-136 (2006).

T. Raiko, M. Tornio, A. Honkela and J. Karhunen.

State Inference in Variational Bayesian Nonlinear State-Space Models.

In Proceedings of the Sixth
International Conference Independent Component Analysis and Blind
Signal Separation (ICA 2006), Charleston, South Carolina, USA.

Vol. 3889 of Lecture
Notes in Computer Science, pp. 222 - 229, Springer-Verlag (2006).

doi:10.1007/11679363_28

M. Harva, T. Raiko, A. Honkela, H. Valpola and J. Karhunen.

Bayes Blocks: An Implementation of the Variational Bayesian
Building Blocks Framework.

In Proceedings of the 21st Conference on Uncertainty in
Artificial Intelligence, Edinburgh, UK, pp. 259 - 266 (2005).

K. Lagus, E. Alhoniemi, J. Seppä, A. Honkela and P. Wagner.

Independent Variable Group Analysis in Learning Compact Representations
for Data.

In Proceedings of the International and Interdisciplinary
Conference on Adaptive Knowledge Representation and Reasoning (AKRR'05),
Helsinki, Finland, pp. 49 - 56 (2005).

A. Honkela, T. Östman, R. Vigário.

Empirical evidence of the linear nature of magnetoencephalograms.

In Proceedings of the 13th European Symposium on Artificial Neural
Networks (ESANN 2005), Bruges, Belgium, pp. 285 - 290 (2005).

A. Honkela and H. Valpola.

Unsupervised Variational Bayesian Learning
of Nonlinear Models.

In L. Saul, Y. Weiss, and L. Bottou, editors,
Advances in Neural Information Processing Systems 17, pp. 593 - 600,
The MIT Press (2005).

A. Ilin and A. Honkela.

Postnonlinear Independent Component Analysis
by Variational Bayesian Learning.

In Proceedings of the
Fifth International Conference Independent Component Analysis and
Blind Signal Separation (ICA 2004), Granada, Spain.

Vol. 3195 of
Lecture Notes in Computer Science, pp. 766 - 773, Springer-Verlag (2004).

Publisher electronic edition

A. Honkela, S. Harmeling, L. Lundqvist and H. Valpola.

Using Kernel
PCA for Initialisation of Variational Bayesian Nonlinear Blind Source
Separation Method.

In Proceedings of the Fifth
International Conference Independent Component Analysis and Blind
Signal Separation (ICA 2004), Granada, Spain.

Vol. 3195 of Lecture
Notes in Computer Science, pp. 790 - 797, Springer-Verlag (2004).

Publisher electronic edition

A. Honkela.

Approximating Nonlinear Transformations of Probability
Distributions for Nonlinear Independent Component Analysis.

In Proceedings of the 2004 IEEE International Joint Conference on
Neural Networks (IJCNN 2004), Budapest, Hungary, pp. 2169 - 2174 (2004).

V. Siivola and A. Honkela.

A State-Space Method for Language Modeling.

In Proceedings of the IEEE Workshop on Automatice Speech
Recognition and Understanding (ASRU 2003), St. Thomas,
U.S. Virgin Islands, pp. 548 - 553 (2003).

A. Honkela and H. Valpola.

On-line Variational Bayesian Learning.

In Proceedings of the Fourth International Symposium on
Independent Component Analysis and Blind Signal Separation
(ICA 2003), Nara, Japan, pp. 803 - 808 (2003).

A. Honkela.

Speeding Up Cyclic Update Schemes by Pattern Searches.

In Proceedings of the 9th International Conference on Neural Information Processing (ICONIP'02), Singapore, pp. 512 - 516 (2002).

H. Valpola, A. Honkela, and J. Karhunen.

An Ensemble Learning Approach to Nonlinear Dynamic Blind Source Separation Using State-Space Models.

In Proceedings of the International Joint Conference on Neural Networks (IJCNN'02), Honolulu, Hawaii, USA, pp. 460 - 465 (2002).

H. Valpola, A. Honkela, and J. Karhunen.

Nonlinear Static and Dynamic Blind Source Separation Using Ensemble Learning.

In Proceedings of the International Joint Conference on Neural Networks (IJCNN'01), Washington D.C., USA, pp. 2750 - 2755 (2001).

A. Honkela and J. Karhunen.

An Ensemble Learning Approach to Nonlinear Independent Component Analysis.

In Proceedings of the European Conference on
Circuit Theory and Design (ECCTD'01), Espoo, Finland,
pp. I-41 - 44 (2001).

H. Valpola, X. Giannakopoulos, A. Honkela, and J. Karhunen.

Nonlinear Independent Component Analysis
Using Ensemble Learning: Experiments and Discussion.

In Proceedings of the Second International Workshop on Independent Component Analysis and Blind Signal Separation, ICA 2000, Helsinki, Finland,
pp. 351 - 356 (2000).

H. Lappalainen, A. Honkela, X. Giannakopoulos, and J. Karhunen.

Nonlinear Source Separation Using Ensemble Learning and MLP Networks.

In Proceedings of the Symposium 2000 on Adaptive Systems for
Signal Processing, Communications, and Control (AS-SPCC), Lake Louise, Alberta,
Canada, pp. 187 - 192 (2000).

### Conference abstracts and presentations

A. Honkela, M. Tornio, and T. Raiko.

Variational Bayes for Continuous-Time
Nonlinear State-Space Models.

In NIPS*2006
Workshop on Dynamical Systems, Stochastic Processes and Bayesian
Inference, Whistler, B.C., Canada (2006).

A. Honkela, M. Harva, T. Raiko, H. Valpola, and J. Karhunen.

Bayes Blocks: A Python Toolbox for
Variational Bayesian Learning.

In NIPS*2006
Workshop on Machine Learning Open Source Software, Whistler, B.C.,
Canada (2006).

A. Honkela.

Distributed Bayes
Blocks for Variational Bayesian Learning.

In Conference on High
Performance Computing for Statistical Inference, Dublin, Ireland
(2006).

### Theses

A. Honkela.

Advances in
Variational Bayesian Nonlinear Blind Source Separation.

Doctoral thesis, Helsinki University of Technology,
Espoo, Finland (2005).

A. Honkela.

Nonlinear Switching State-Space Models.

Master's thesis, Helsinki University of Technology, Espoo, Finland (2001).

(Browsable HTML version also available.)

### Technical reports

H. Valpola and A. Honkela.

Hyperparameter Adaptation in Variational
Bayes for the Gamma Distribution.

Publications in Computer
and Information Science E6, Helsinki University of Technology, Espoo,
Finland, 2006.

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