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List of works by Tommi S. Jaakkola

A Game Theoretic Approach to Class-wise Selective Rationalization ⬇️

scientific article published in January 2019

A graph-convolutional neural network model for the prediction of chemical reactivity.

scientific article published on 26 November 2018

A synergistic DNA logic predicts genome-wide chromatin accessibility

scientific article

Active Information Retrieval ⬇️

Approximate inference using planar graph decomposition ⬇️

scientific article published in January 2007

Approximating Posterior Distributions in Belief Networks Using Mixtures ⬇️

Automated discovery of functional generality of human gene expression programs

scientific article

Autonomous, multiproperty-driven molecular discovery: From predictions to measurements and back

scientific article published on 21 December 2023

Bayesian network approach to cell signaling pathway modeling

scientific article

Bias-Corrected Bootstrap and Model Uncertainty ⬇️

scientific article published in January 2004

Clusters and Coarse Partitions in LP Relaxations ⬇️

Combining location and expression data for principled discovery of genetic regulatory network models

scientific article

Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes

scientific article published on 21 August 2003

Computational discovery of gene modules and regulatory networks

scientific article published on 12 October 2003

Continuous representations of time-series gene expression data

scientific article

Controlling privacy in recommender systems ⬇️

scientific article published in January 2014

Convergence Rate Analysis of MAP Coordinate Minimization Algorithms ⬇️

scientific article published in January 2012

Convergence of Stochastic Iterative Dynamic Programming Algorithms ⬇️

scientific article published in January 1994

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction

scientific article

Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis

scientific article published on 03 April 2020

Direct Optimization through arg max for Discrete Variational Auto-Encoder ⬇️

scientific article published in January 2019

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

scientific article published on 19 January 2014

Distributed Information Regularization on Graphs ⬇️

scientific article published in January 2005

Exact MAP Estimates by (Hyper)tree Agreement ⬇️

scientific article published in January 2003

Exploiting Generative Models in Discriminative Classifiers ⬇️

Fast Learning by Bounding Likelihoods in Sigmoid Type Belief Networks ⬇️

scientific article published in January 1996

Fixing Max-Product: Convergent Message Passing Algorithms for MAP LP-Relaxations ⬇️

scholarly article by Amir Globerson & Tommi S. Jaakkola published 2008 in Advances in Neural Information Processing Systems 20

From random walks to distances on unweighted graphs ⬇️

scientific article published in January 2015

Game Theoretic Algorithms for Protein-DNA binding ⬇️

scientific article published in January 2007

Generalization Error Bounds for Collaborative Prediction with Low-Rank Matrices ⬇️

Generative Models for Graph-Based Protein Design ⬇️

scientific article published in January 2019

Information Regularization with Partially Labeled Data ⬇️

scientific article published in January 2003

K-ary clustering with optimal leaf ordering for gene expression data

scientific article

Kernel Expansions with Unlabeled Examples ⬇️

Learning Efficient Random Maximum A-Posteriori Predictors with Non-Decomposable Loss Functions ⬇️

Learning Tree Structured Potential Games ⬇️

scientific article published in January 2016

Lineage-based identification of cellular states and expression programs ⬇️

scientific article published on June 15, 2012

Linear Dependent Dimensionality Reduction ⬇️

scientific article published in January 2004

Local Aggregative Games ⬇️

scientific article published in January 2017

Maximum Entropy Discrimination ⬇️

scientific article published in January 2000

Maximum-Margin Matrix Factorization ⬇️

Modeling Persistent Trends in Distributions

scientific article published on 12 June 2018

Modeling the combinatorial functions of multiple transcription factors.

scientific article published in March 2006

More data means less inference: A pseudo-max approach to structured learning ⬇️

article by David Sontag et al published 2010 in Advances in Neural Information Processing Systems 23

New Outer Bounds on the Marginal Polytope ⬇️

scientific article published in January 2008

On Sampling from the Gibbs Distribution with Random Maximum A-Posteriori Perturbations ⬇️

On the Dirichlet Prior and Bayesian Regularization ⬇️

scientific article published in January 2003

Online Learning of Non-stationary Sequences ⬇️

scientific article published in January 2004

Parameter Expanded Variational Bayesian Methods ⬇️

scientific article published in January 2007

Partially labeled classification with Markov random walks ⬇️

Physical network models

scientific article published in January 2004

Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network ⬇️

scientific article published in January 2017

Prediction of Organic Reaction Outcomes Using Machine Learning

scientific article published on 18 April 2017

Principal Differences Analysis: Interpretable Characterization of Differences between Distributions ⬇️

Recursive Algorithms for Approximating Probabilities in Graphical Models ⬇️

scientific article published in January 1997

Reinforcement Learning Algorithm for Partially Observable Markov Decision Problems ⬇️

scientific article published in January 1995

Reinforcement Learning with Soft State Aggregation ⬇️

scientific article published in January 1995

Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo

scientific article published in July 2006

Sequentially Fitting ``Inclusive'' Trees for Inference in Noisy-OR Networks ⬇️

Solving graph compression via optimal transport ⬇️

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

scholarly article by Teemu Roos et al published December 2012 in International Journal of Approximate Reasoning

Style Transfer from Non-Parallel Text by Cross-Alignment ⬇️

scientific article published in January 2017

Tight Certificates of Adversarial Robustness for Randomly Smoothed Classifiers ⬇️

Towards Robust Interpretability with Self-Explaining Neural Networks ⬇️

Tree-based reparameterization for approximate inference on loopy graphs ⬇️

Validation and refinement of gene-regulatory pathways on a network of physical interactions

scientific article

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