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1

An Introduction to Variational Methods for Graphical Models

Michael I. Jordan, Zoubin Ghahramani, Tommi S. Jaakkola, Lawrence K. Saul

Journal:

Machine Learning

Year:

1999

Language:

english

File:

PDF, 547 KB

english, 1999

2

Convergence Results for Single-Step On-Policy Reinforcement-Learning Algorithms

Satinder Singh, Tommi Jaakkola, Michael L. Littman, Csaba Szepesvári

Journal:

Machine Learning

Year:

2000

Language:

english

File:

PDF, 117 KB

english, 2000

3

Bayesian parameter estimation via variational methods

Tommi S. Jaakkola, Michael I. Jordan

Journal:

Statistics and Computing

Year:

2000

Language:

english

File:

PDF, 191 KB

english, 2000

4

Binary surface-relief gratings for array illumination in digital optics

Vasara, Antti, Taghizadeh, Mohammad R., Turunen, Jari, Westerholm, Jan, Noponen, Eero, Ichikawa, Hiroyuki, Miller, J. Michael, Jaakkola, Tommi, Kuisma, Sirpa

Journal:

Year:

1992

Language:

english

File:

PDF, 2.69 MB

english, 1992

5

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

Sherwood, Richard I, Hashimoto, Tatsunori, O'Donnell, Charles W, Lewis, Sophia, Barkal, Amira A, van Hoff, John Peter, Karun, Vivek, Jaakkola, Tommi, Gifford, David K

Journal:

Nature Biotechnology

Year:

2014

Language:

english

File:

PDF, 1.00 MB

english, 2014

6

Prediction of Organic Reaction Outcomes Using Machine Learning

Coley, Connor W., Barzilay, Regina, Jaakkola, Tommi S., Green, William H., Jensen, Klavs F.

Journal:

ACS Central Science

Year:

2017

Language:

english

File:

PDF, 1.71 MB

english, 2017

7

Physical Network Models

Yeang, Chen-Hsiang, Ideker, Trey, Jaakkola, Tommi

Journal:

Journal of Computational Biology

Year:

2004

Language:

english

File:

PDF, 507 KB

english, 2004

8

[Society of Petroleum Engineers SPE Annual Technical Conference and Exhibition - Amsterdam, The Netherlands (2014-10-27)] SPE Annual Technical Conference and Exhibition - Integration of Principal-Component-Analysis and Streamline Information for the History Matching of Channelized Reservoirs

Chen, Chaohui, Gao, Guohua, Honorio, Jean, Gelderblom, Paul, Jimenez, Eduardo, Jaakkola, Tommi

Language:

english

File:

PDF, 4.04 MB

english

9

Convolutional embedding of attributed molecular graphs for physical property prediction

Coley, Connor W., Barzilay, Regina, Green, William H., Jaakkola, Tommi S., Jensen, Klavs F.

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 1.14 MB

english, 2017

10

Word Embeddings as Metric Recovery in Semantic Spaces

Hashimoto, Tatsunori B., Alvarez-Melis, David, Jaakkola, Tommi S.

Journal:

Transactions of the Association for Computational Linguistics

Year:

2016

Language:

english

File:

PDF, 1.64 MB

english, 2016

11

Analyzing Learned Molecular Representations for Property Prediction

Yang, Kevin, Swanson, Kyle, Jin, Wengong, Coley, Connor W., Eiden, Philipp, Gao, Hua, Guzman-Perez, Angel, Hopper, Tim, Kelley, Brian, Mathea, Miriam, Palmer, Andrew, Settels, Volker, Jaakkola, Tommi

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 4.80 MB

english, 2019

12

BODIL: a molecular modeling environment for structure-function analysis and drug design

Jukka V. Lehtonen, Dan-Johan Still, Ville-v. Rantanen, Jan Ekholm, Dag Björklund, Zuhair Iftikhar, Mikko Huhtala, Susanna Repo, Antti Jussila, Jussi Jaakkola, Olli Pentikäinen, Tommi Nyrönen, Tiina Sa

Journal:

Journal of Computer-Aided Molecular Design

Year:

2004

Language:

english

File:

PDF, 529 KB

english, 2004

13

Tractable Bayesian learning of tree belief networks

Marina Meilă, Tommi Jaakkola

Journal:

Statistics and Computing

Year:

2006

Language:

english

File:

PDF, 362 KB

english, 2006

14

Erratum: High-resolution computational models of genome binding events

Qi, Yuan, Rolfe, Alex, MacIsaac, Kenzie D, Gerber, Georg K, Pokholok, Dmitry, Zeitlinger, Julia, Danford, Timothy, Dowell, Robin D, Fraenkel, Ernest, Jaakkola, Tommi S

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 122 KB

english, 2006

15

High-resolution computational models of genome binding events

Qi, Yuan, Rolfe, Alex, MacIsaac, Kenzie D, Gerber, Georg K, Pokholok, Dmitry, Zeitlinger, Julia, Danford, Timothy, Dowell, Robin D, Fraenkel, Ernest, Jaakkola, Tommi S

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 1.99 MB

english, 2006

16

Computational discovery of gene modules and regulatory networks

Bar-Joseph, Ziv, Gerber, Georg K, Lee, Tong Ihn, Rinaldi, Nicola J, Yoo, Jane Y, Robert, François, Gordon, D Benjamin, Fraenkel, Ernest, Jaakkola, Tommi S, Young, Richard A

Journal:

Nature Biotechnology

Year:

2003

Language:

english

File:

PDF, 1.13 MB

english, 2003

17

Tree consistency and bounds on the performance of the max-product algorithm and its generalizations

Martin Wainwright, Tommi Jaakkola, Alan Willsky

Journal:

Statistics and Computing

Year:

2004

Language:

english

File:

PDF, 446 KB

english, 2004

18

In Vivo Detection of Vascular Adhesion Protein-1 in Experimental Inflammation

Kimmo Jaakkola, Tuomo Nikula, Riikka Holopainen, Tommi Vähäsilta, Marja-Terttu Matikainen, Marja-Leena Laukkanen, Risto Huupponen, Lauri Halkola, Lauri Nieminen, Jukka Hiltunen, Sakari Parviainen, Mic

Journal:

The American Journal of Pathology

Year:

2000

Language:

english

File:

PDF, 1.29 MB

english, 2000

19

Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle

Itamar Simon, John Barnett, Nancy Hannett, Christopher T Harbison, Nicola J Rinaldi, Thomas L Volkert, John J Wyrick, Julia Zeitlinger, David K Gifford, Tommi S Jaakkola, Richard A Young

Journal:

Year:

2001

Language:

english

File:

PDF, 419 KB

english, 2001

20

Special Issue on the Fifth European Workshop on Probabilistic Graphical Models (PGM-2010)

Teemu Roos, Petri Myllymäki, Tommi Jaakkola

Journal:

International Journal of Approximate Reasoning

Year:

2012

Language:

english

File:

PDF, 114 KB

english, 2012

21

The relation of oxidized LDL autoantibodies and long-term hormone replacement therapy to ultrasonographically assessed atherosclerotic plaque quantity and severity in postmenopausal women

Tommi A. Koivu, Prasun Dastidar, Hannu Jokela, Seppo T. Nikkari, Olli Jaakkola, Timo Koivula, Reijo Punnonen, Terho Lehtimäki

Journal:

Atherosclerosis

Year:

2001

Language:

english

File:

PDF, 210 KB

english, 2001

22

[IEEE 2008 IEEE Ultrasonics Symposium (IUS) - Beijing, China (2008.11.2-2008.11.5)] 2008 IEEE Ultrasonics Symposium - Piezoelectrically transduced single-crystal-silicon plate resonators

Jaakkola, Antti, Rosenberg, Piia, Asmala, Samuli, Nurmela, Arto, Pensala, Tuomas, Riekkinen, Tommi, Dekker, James, Mattila, Tomi, Alastalo, Ari, Holmgren, Olli, Kokkonen, Kimmo

Year:

2008

Language:

english

File:

PDF, 1.22 MB

english, 2008

23

[ACM Press the sixth annual international conference - Washington, DC, USA (2002.04.18-2002.04.21)] Proceedings of the sixth annual international conference on Computational biology - RECOMB '02 - A new approach to analyzing gene expression time series data

Bar-Joseph, Ziv, Gerber, Georg, Gifford, David K., Jaakkola, Tommi S., Simon, Itamar

Year:

2002

Language:

english

File:

PDF, 1.61 MB

english, 2002

24

Modeling the Combinatorial Functions of Multiple Transcription Factors

Yeang, Chen-Hsiang, Jaakkola, Tommi

Journal:

Journal of Computational Biology

Year:

2006

Language:

english

File:

PDF, 393 KB

english, 2006

25

[ACM Press the 19th ACM international conference - Toronto, ON, Canada (2010.10.26-2010.10.30)] Proceedings of the 19th ACM international conference on Information and knowledge management - CIKM '10 - Collaborative future event recommendation

Minkov, Einat, Charrow, Ben, Ledlie, Jonathan, Teller, Seth, Jaakkola, Tommi

Year:

2010

Language:

english

File:

PDF, 598 KB

english, 2010

26

[IEEE 2008 IEEE Ultrasonics Symposium (IUS) - Beijing, China (2008.11.2-2008.11.5)] 2008 IEEE Ultrasonics Symposium - Piezoelectrically actuated micromechanical BAW resonators

Rosenberg, Piia, Jaakkola, Antti, Dekker, James, Nurmela, Arto, Pensala, Tuomas, Asmala, Samuli, Riekkinen, Tommi, Mattila, Tomi, Alastalo, Ari

Year:

2008

Language:

english

File:

PDF, 513 KB

english, 2008

27

Continuous Representations of Time-Series Gene Expression Data

Bar-Joseph, Ziv, Gerber, Georg K., Gifford, David K., Jaakkola, Tommi S., Simon, Itamar

Journal:

Journal of Computational Biology

Year:

2003

Language:

english

File:

PDF, 297 KB

english, 2003

28

A Discriminative Framework for Detecting Remote Protein Homologies

Jaakkola, Tommi, Diekhans, Mark, Haussler, David

Journal:

Journal of Computational Biology

Year:

2000

Language:

english

File:

PDF, 274 KB

english, 2000

29

On the Convergence of Stochastic Iterative Dynamic Programming Algorithms

Jaakkola, Tommi, Jordan, Michael I., Singh, Satinder P.

Journal:

Neural Computation

Year:

1994

Language:

english

File:

PDF, 816 KB

english, 1994

30

TIME SERIES ANALYSIS OF GENE EXPRESSION AND LOCATION DATA

YEANG, CHEN-HSIANG, JAAKKOLA, TOMMI

Journal:

International Journal of Artificial Intelligence Tools

Year:

2005

Language:

english

File:

PDF, 626 KB

english, 2005

31

Automated Discovery of Functional Generality of Human Gene Expression Programs

Gerber, Georg K., Dowell, Robin D., Jaakkola, Tommi S., Gifford, David K.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 1.18 MB

english, 2007

32

[ACM Press the 28th annual international ACM SIGIR conference - Salvador, Brazil (2005.08.15-2005.08.19)] Proceedings of the 28th annual international ACM SIGIR conference on Research and development in information retrieval - SIGIR '05 - Using term informativeness for named entity detection

Rennie, Jason D. M., Jaakkola, Tommi

Year:

2005

Language:

english

File:

PDF, 167 KB

english, 2005

33

SPIE Proceedings [SPIE BiOS 2001 The International Symposium on Biomedical Optics - San Jose, CA (Saturday 20 January 2001)] Microarrays: Optical Technologies and Informatics - Maximum-likelihood estimation of optimal scaling factors for expression array normalization

Hartemink, Alexander J., Gifford, David K., Jaakkola, Tommi S., Young, Richard A., Bittner, Michael L., Chen, Yidong, Dorsel, Andreas N., Dougherty, Edward R.

Year:

2001

Language:

english

File:

PDF, 1.47 MB

english, 2001

34

[Society of Petroleum Engineers SPE Annual Technical Conference and Exhibition - Houston, Texas, USA (2015-09-28)] SPE Annual Technical Conference and Exhibition - Integration of PCA with a Novel Machine Learning Method for Reparameterization and Assisted History Matching Geologically Complex Reservoirs

Honorio, Jean, Chen, Chaohui, Gao, Guohua, Du, Kuifu, Jaakkola, Tommi

Language:

english

File:

PDF, 4.61 MB

english

35

A synergistic DNA logic predicts genome-wide chromatin accessibility

Hashimoto, Tatsunori B, Sherwood, Richard, Kang, Daniel D, Rajagopal, Nisha, Barkal, Amira A, Zeng, Haoyang, Emons, Bart JM, Srinivasan, Sharanya, Jaakkola, Tommi, Gifford, David

Journal:

Genome Research

Year:

2016

Language:

english

File:

PDF, 2.61 MB

english, 2016

36

Modeling Persistent Trends in Distributions

Mueller, Jonas, Jaakkola, Tommi, Gifford, David

Journal:

Journal of the American Statistical Association

Year:

2017

Language:

english

File:

PDF, 5.34 MB

english, 2017

37

High Dimensional Inference with Random Maximum A-Posteriori Perturbations

Hazan, Tamir, Orabona, Francesco, Sarwate, Anand D., Maji, Subhransu, Jaakkola, Tommi S.

Journal:

IEEE Transactions on Information Theory

Year:

2019

Language:

english

File:

PDF, 1.32 MB

english, 2019

38

Burden of non-motor symptoms in unclear parkinsonism and tremor: A study with [123I]FP-CIT SPECT

Jaakkola, Elina, Joutsa, Juho, Mäkinen, Elina, Noponen, Tommi, Pitkonen, Miia, Levo, Reeta, Mertsalmi, Tuomas, Scheperjans, Filip, Kaasinen, Valtteri

Journal:

Journal of the Neurological Sciences

Year:

2019

Language:

english

File:

PDF, 473 KB

english, 2019

39

Bidirectional Inference Networks:A Class of Deep Bayesian Networks for Health Profiling

Wang, Hao, Mao, Chengzhi, He, Hao, Zhao, Mingmin, Jaakkola, Tommi S., Katabi, Dina

Journal:

Proceedings of the AAAI Conference on Artificial Intelligence

Year:

2019

Language:

english

File:

PDF, 1.02 MB

english, 2019

40

Correction to Analyzing Learned Molecular Representations for Property Prediction

Yang, Kevin, Swanson, Kyle, Jin, Wengong, Coley, Connor, Eiden, Philipp, Gao, Hua, Guzman-Perez, Angel, Hopper, Timothy, Kelley, Brian, Mathea, Miriam, Palmer, Andrew, Settels, Volker, Jaakkola, Tommi

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 748 KB

2019