Jens Lagergren

According to our database, Jens Lagergren authored at least 65 papers between 1988 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Indirectly Parameterized Concrete Autoencoders.

Alfred Nilsson, Klas Wijk, Sai Bharath Chandra Gutha, Erik Englesson, Alexandra Hotti, Carlo Saccardi, Oskar Kviman, Jens Lagergren, Ricardo Vinuesa, Hossein Azizpour

CoRR, 2024

2023

Improved Variational Bayesian Phylogenetic Inference using Mixtures.

Oskar Kviman, Ricky Molén, Jens Lagergren

CoRR, 2023

Learning Stationary Markov Processes with Contrastive Adjustment.

Ludvig Bergenstråhle, Jens Lagergren, Joakim Lundeberg

CoRR, 2023

Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational Autoencoders.

Oskar Kviman, Ricky Molén, Alexandra Hotti, Semih Kurt, Víctor Elvira, Jens Lagergren

Proceedings of the International Conference on Machine Learning, 2023

2022

ToMExO: A probabilistic tree-structured model for cancer progression.

Mohammadreza Mohaghegh Neyshabouri, Jens Lagergren

PLoS Comput. Biol., December, 2022

Statistical Distance Based Deterministic Offspring Selection in SMC Methods.

Oskar Kviman, Hazal Koptagel, Harald Melin, Jens Lagergren

CoRR, 2022

Learning with MISELBO: The Mixture Cookbook.

Oskar Kviman, Ricky Molén, Alexandra Hotti, Semih Kurt, Víctor Elvira, Jens Lagergren

CoRR, 2022

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.

José Bonet, Mandi Chen, Marc Dabad, Simon Heath, Abel Gonzalez-Perez, Núria López-Bigas, Jens Lagergren

Bioinform., 2022

VaiPhy: a Variational Inference Based Algorithm for Phylogeny.

Hazal Koptagel, Oskar Kviman, Harald Melin, Negar Safinianaini, Jens Lagergren

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations.

Oskar Kviman, Harald Melin, Hazal Koptagel, Victor Elvira, Jens Lagergren

Proceedings of the International Conference on Artificial Intelligence and Statistics, 2022

2021

The Klarna Product Page Dataset: A Realistic Benchmark for Web Representation Learning.

Alexandra Hotti, Riccardo Sven Risuleo, Stefan Magureanu, Aref Moradi, Jens Lagergren

CoRR, 2021

2020

Inferring tumor progression in large datasets.

Mohammadreza Mohaghegh Neyshabouri, Seong-Hwan Jun, Jens Lagergren

PLoS Comput. Biol., 2020

Orthogonal Mixture of Hidden Markov Models.

Negar Safinianaini, Camila P. E. de Souza, Henrik Boström, Jens Lagergren

Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2020

2017

Fast and general tests of genetic interaction for genome-wide association studies.

Mattias Frånberg, Rona J. Strawbridge, Anders Hamsten, PROCARDIS consortium, Ulf de Faire, Jens Lagergren, Bengt Sennblad

PLoS Comput. Biol., 2017

2016

Computational Cancer Biology: An Evolutionary Perspective.

Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren

PLoS Comput. Biol., 2016

Viewpoint and Topic Modeling of Current Events.

Kerry Zhang, Jussi Karlgren, Cheng Zhang, Jens Lagergren

CoRR, 2016

Probabilistic inference of lateral gene transfer events.

Mehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Lars Arvestad, Jens Lagergren

BMC Bioinform., 2016

2014

Learning Bounded Tree-width Bayesian Networks using Integer Linear Programming.

Pekka Parviainen, Hossein Shahrabi Farahani, Jens Lagergren

Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, 2014

2013

GenPhyloData: realistic simulation of gene family evolution.

Joel Sjöstrand, Lars Arvestad, Jens Lagergren, Bengt Sennblad

BMC Bioinform., 2013

Genome-wide probabilistic reconciliation analysis across vertebrates.

Owais Mahmudi, Joel Sjöstrand, Bengt Sennblad, Jens Lagergren

BMC Bioinform., 2013

fastphylo: Fast tools for phylogenetics.

Mehmood Alam Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad

BMC Bioinform., 2013

2012

DLRS: gene tree evolution in light of a species tree.

Joel Sjöstrand, Bengt Sennblad, Lars Arvestad, Jens Lagergren

Bioinform., 2012

2011

Simultaneous Identification of Duplications and Lateral Gene Transfers.

Ali Tofigh, Michael T. Hallett, Jens Lagergren

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

A Global Structural EM Algorithm for a Model of Cancer Progression.

Ali Tofigh, Erik Sjölund, Mattias Höglund, Jens Lagergren

Proceedings of the Advances in Neural Information Processing Systems 24: 25th Annual Conference on Neural Information Processing Systems 2011. Proceedings of a meeting held 12-14 December 2011, 2011

2010

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.

Mats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S. Furey, Marie Öhman, Jens Lagergren

BMC Bioinform., 2010

2009

Fast neighbor joining.

Isaac Elias, Jens Lagergren

Theor. Comput. Sci., 2009

The gene evolution model and computing its associated probabilities.

Lars Arvestad, Jens Lagergren, Bengt Sennblad

J. ACM, 2009

2007

Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model.

Samuel A. Andersson, Jens Lagergren

J. Comput. Biol., 2007

primetv: a viewer for reconciled trees.

Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad

BMC Bioinform., 2007

Fast computation of distance estimators.

Isaac Elias, Jens Lagergren

BMC Bioinform., 2007

2006

Compatibility of unrooted phylogenetic trees is FPT.

David Bryant, Jens Lagergren

Theor. Comput. Sci., 2006

Genome-Wide Survey for Biologically Functional Pseudogenes.

Örjan Svensson, Lars Arvestad, Jens Lagergren

PLoS Comput. Biol., 2006

New Probabilistic Network Models and Algorithms for Oncogenesis.

Marcus Hjelm, Mattias Höglund, Jens Lagergren

J. Comput. Biol., 2006

Motif Yggdrasil: Sampling from a Tree Mixture Model.

Samuel A. Andersson, Jens Lagergren

Proceedings of the Research in Computational Molecular Biology, 2006

2004

Algorithms for RH Mapping: New Ideas and Improved Analysis.

Lars Ivansson, Jens Lagergren

SIAM J. Comput., 2004

MSCAN: identification of functional clusters of transcription factor binding sites.

Wynand Alkema, Öjvind Johansson, Jens Lagergren, Wyeth W. Wasserman

Nucleic Acids Res., 2004

Ancestral Maximum Likelihood of Evolutionary Trees Is Hard.

Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham

J. Bioinform. Comput. Biol., 2004

Simultaneous identification of duplications and lateral transfers.

Michael T. Hallett, Jens Lagergren, Ali Tofigh

Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution.

Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad

Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

2003

A Polynomial-Time Algorithm for Near-Perfect Phylogeny.

David Fernández-Baca, Jens Lagergren

SIAM J. Comput., 2003

Fitting points on the real line and its application to RH mapping.

Johan Håstad, Lars Ivansson, Jens Lagergren

J. Algorithms, 2003

Towards Identifying Lateral Gene Transfer Events.

Louigi Addario-Berry, Michael T. Hallett, Jens Lagergren

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.

Öjvind Johansson, Wynand Alkema, Wyeth W. Wasserman, Jens Lagergren

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002

Combining polynomial running time and fast convergence for the disk-covering method.

Jens Lagergren

J. Comput. Syst. Sci., 2002

2001

Efficient algorithms for lateral gene transfer problems.

Michael T. Hallett, Jens Lagergren

Proceedings of the Fifth Annual International Conference on Computational Biology, 2001

2000

New algorithms for the duplication-loss model.

Michael T. Hallett, Jens Lagergren

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

Hunting for Functionally Analogous Genes.

Michael T. Hallett, Jens Lagergren

Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 2000

1999

Guest Editors' Foreword.

Jens Lagergren, Peter Bro Miltersen

Nord. J. Comput., 1999

1998

Upper Bounds on the Size of Obstructions and Intertwines.

Jens Lagergren

J. Comb. Theory, Ser. B, 1998

Approximate Max <i>k</i>-Cut with Subgraph Guarantee.

Viggo Kann, Jens Lagergren, Alessandro Panconesi

Inf. Process. Lett., 1998

On the Approximability of the Steiner Tree Problem in Phylogeny.

David Fernández-Baca, Jens Lagergren

Discret. Appl. Math., 1998

1997

On the Hardness of Approximating Max k-Cut and its Dual.

Viggo Kann, Sanjeev Khanna, Jens Lagergren, Alessandro Panconesi

Chic. J. Theor. Comput. Sci., 1997

1996

Equivalent Definitions of Recognizability for Sets of Graphs of Bounded Tree-Width.

Bruno Courcelle, Jens Lagergren

Math. Struct. Comput. Sci., 1996

Efficient Parallel Algorithms for Graphs of Bounded Tree-Width.

Jens Lagergren

J. Algorithms, 1996

Approximability of Maximum Splitting of k-Sets and Some Other Apx-Complete Problems.

Viggo Kann, Jens Lagergren, Alessandro Panconesi

Inf. Process. Lett., 1996

Hypothesis Testing in Perfect Phylogeny for a Bounded Number of Characters.

Jens Lagergren

Proceedings of the STACS 96, 1996

1994

The Nonexistence of Reduction Rules Giving an Embedding into a K-tree.

Jens Lagergren

Discret. Appl. Math., 1994

The Size of an Interwine.

Jens Lagergren

Proceedings of the Automata, Languages and Programming, 21st International Colloquium, 1994

1993

Recognizable Sets of Graphs of Bounded Tree-Width.

Bruno Courcelle, Jens Lagergren

Proceedings of the Graph Transformations in Computer Science, International Workshop, 1993

1991

Easy Problems for Tree-Decomposable Graphs.

Stefan Arnborg, Jens Lagergren, Detlef Seese

J. Algorithms, 1991

Finding Minimal Forbidden Minors Using a Finite Congruence.

Jens Lagergren, Stefan Arnborg

Proceedings of the Automata, Languages and Programming, 18th International Colloquium, 1991

An upper bound on the size of an obstruction.

Jens Lagergren

Proceedings of the Graph Structure Theory, 1991

1990

Efficient Parallel Algorithms for Tree-Decomposition and Related Problems

Jens Lagergren

Proceedings of the 31st Annual Symposium on Foundations of Computer Science, 1990

1988

Problems Easy for Tree-Decomposable Graphs (Extended Abstract).

Stefan Arnborg, Jens Lagergren, Detlef Seese

Proceedings of the Automata, Languages and Programming, 15th International Colloquium, 1988