Jens Lagergren

Publication Activity (10 Years)

Years Active: 1988-2024
Publications (10 Years): 23

Top Topics

Importance Sampling

Variational Inference

Top Venues

PLoS Comput. Biol.

Publications

Alfred Nilsson, Klas Wijk, Sai Bharath Chandra Gutha, Erik Englesson, Alexandra Hotti, Carlo Saccardi, Oskar Kviman, Jens Lagergren, Ricardo Vinuesa, Hossein Azizpour
Indirectly Parameterized Concrete Autoencoders. CoRR (2024)
Alexandra Maria Hotti, Lennart Alexander Van der Goten, Jens Lagergren
Benefits of Non-Linear Scale Parameterizations in Black Box Variational Inference through Smoothness Results and Gradient Variance Bounds. AISTATS (2024)
Alexandra Hotti, Oskar Kviman, Ricky Molén, Víctor Elvira, Jens Lagergren
Efficient Mixture Learning in Black-Box Variational Inference. CoRR (2024)
Oskar Kviman, Nicola Branchini, Víctor Elvira, Jens Lagergren
Variational Resampling. AISTATS (2024)
Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren
VICTree - A Variational Inference Method for Clonal Tree Reconstruction. RECOMB (2024)
Oskar Kviman, Ricky Molén, Alexandra Hotti, Semih Kurt, Víctor Elvira, Jens Lagergren
Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational Autoencoders. ICML (2023)
Oskar Kviman, Ricky Molén, Jens Lagergren
Improved Variational Bayesian Phylogenetic Inference using Mixtures. CoRR (2023)
Ludvig Bergenstråhle, Jens Lagergren, Joakim Lundeberg
Learning Stationary Markov Processes with Contrastive Adjustment. CoRR (2023)
Oskar Kviman, Harald Melin, Hazal Koptagel, Víctor Elvira, Jens Lagergren
Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations. CoRR (2022)
Oskar Kviman, Harald Melin, Hazal Koptagel, Victor Elvira, Jens Lagergren
Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations. AISTATS (2022)
Mohammadreza Mohaghegh Neyshabouri, Jens Lagergren
ToMExO: A probabilistic tree-structured model for cancer progression. PLoS Comput. Biol. 18 (12) (2022)
Oskar Kviman, Hazal Koptagel, Harald Melin, Jens Lagergren
Statistical Distance Based Deterministic Offspring Selection in SMC Methods. CoRR (2022)
Oskar Kviman, Ricky Molén, Alexandra Hotti, Semih Kurt, Víctor Elvira, Jens Lagergren
Learning with MISELBO: The Mixture Cookbook. CoRR (2022)
Hazal Koptagel, Oskar Kviman, Harald Melin, Negar Safinianaini, Jens Lagergren
VaiPhy: a Variational Inference Based Algorithm for Phylogeny. NeurIPS (2022)
Hazal Koptagel, Oskar Kviman, Harald Melin, Negar Safinianaini, Jens Lagergren
VaiPhy: a Variational Inference Based Algorithm for Phylogeny. CoRR (2022)
José Bonet, Mandi Chen, Marc Dabad, Simon Heath, Abel Gonzalez-Perez, Núria López-Bigas, Jens Lagergren
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. Bioinform. 38 (5) (2022)
Alexandra Hotti, Riccardo Sven Risuleo, Stefan Magureanu, Aref Moradi, Jens Lagergren
The Klarna Product Page Dataset: A Realistic Benchmark for Web Representation Learning. CoRR (2021)
Mohammadreza Mohaghegh Neyshabouri, Seong-Hwan Jun, Jens Lagergren
Inferring tumor progression in large datasets. PLoS Comput. Biol. 16 (10) (2020)
Negar Safinianaini, Camila P. E. de Souza, Henrik Boström, Jens Lagergren
Orthogonal Mixture of Hidden Markov Models. ECML/PKDD (1) (2020)
Mattias Frånberg, Rona J. Strawbridge, Anders Hamsten, PROCARDIS consortium, Ulf de Faire, Jens Lagergren, Bengt Sennblad
Fast and general tests of genetic interaction for genome-wide association studies. PLoS Comput. Biol. 13 (6) (2017)
Kerry Zhang, Jussi Karlgren, Cheng Zhang, Jens Lagergren
Viewpoint and Topic Modeling of Current Events. CoRR (2016)
Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren
Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput. Biol. 12 (2) (2016)
Mehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Lars Arvestad, Jens Lagergren
Probabilistic inference of lateral gene transfer events. BMC Bioinform. 17 (S-14) (2016)
Pekka Parviainen, Hossein Shahrabi Farahani, Jens Lagergren
Learning Bounded Tree-width Bayesian Networks using Integer Linear Programming. AISTATS (2014)
Joel Sjöstrand, Lars Arvestad, Jens Lagergren, Bengt Sennblad
GenPhyloData: realistic simulation of gene family evolution. BMC Bioinform. 14 (2013)
Mehmood Alam Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
fastphylo: Fast tools for phylogenetics. BMC Bioinform. 14 (2013)
Owais Mahmudi, Joel Sjöstrand, Bengt Sennblad, Jens Lagergren
Genome-wide probabilistic reconciliation analysis across vertebrates. BMC Bioinform. 14 (S-15) (2013)
Joel Sjöstrand, Bengt Sennblad, Lars Arvestad, Jens Lagergren
DLRS: gene tree evolution in light of a species tree. Bioinform. 28 (22) (2012)
Ali Tofigh, Michael T. Hallett, Jens Lagergren
Simultaneous Identification of Duplications and Lateral Gene Transfers. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (2) (2011)
Ali Tofigh, Erik Sjölund, Mattias Höglund, Jens Lagergren
A Global Structural EM Algorithm for a Model of Cancer Progression. NIPS (2011)
Mats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S. Furey, Marie Öhman, Jens Lagergren
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. BMC Bioinform. 11 (2010)
Isaac Elias, Jens Lagergren
Fast neighbor joining. Theor. Comput. Sci. 410 (21-23) (2009)
Lars Arvestad, Jens Lagergren, Bengt Sennblad
The gene evolution model and computing its associated probabilities. J. ACM 56 (2) (2009)
Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad
primetv: a viewer for reconciled trees. BMC Bioinform. 8 (2007)
Isaac Elias, Jens Lagergren
Fast computation of distance estimators. BMC Bioinform. 8 (2007)
Samuel A. Andersson, Jens Lagergren
Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model. J. Comput. Biol. 14 (5) (2007)
Samuel A. Andersson, Jens Lagergren
Motif Yggdrasil: Sampling from a Tree Mixture Model. RECOMB (2006)
David Bryant, Jens Lagergren
Compatibility of unrooted phylogenetic trees is FPT. Theor. Comput. Sci. 351 (3) (2006)
Örjan Svensson, Lars Arvestad, Jens Lagergren
Genome-Wide Survey for Biologically Functional Pseudogenes. PLoS Comput. Biol. 2 (5) (2006)
Marcus Hjelm, Mattias Höglund, Jens Lagergren
New Probabilistic Network Models and Algorithms for Oncogenesis. J. Comput. Biol. 13 (4) (2006)
Isaac Elias, Jens Lagergren
Fast Neighbor Joining. ICALP (2005)
Michael T. Hallett, Jens Lagergren, Ali Tofigh
Simultaneous identification of duplications and lateral transfers. RECOMB (2004)
Wynand Alkema, Öjvind Johansson, Jens Lagergren, Wyeth W. Wasserman
MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham
Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. J. Bioinform. Comput. Biol. 2 (2) (2004)
Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. RECOMB (2004)
Lars Ivansson, Jens Lagergren
Algorithms for RH Mapping: New Ideas and Improved Analysis. SIAM J. Comput. 34 (1) (2004)
Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham
Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. WABI (2003)
Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad
Bayesian gene/species tree reconciliation and orthology analysis using MCMC. ISMB (Supplement of Bioinformatics) (2003)
Öjvind Johansson, Wynand Alkema, Wyeth W. Wasserman, Jens Lagergren
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. ISMB (Supplement of Bioinformatics) (2003)
Louigi Addario-Berry, Michael T. Hallett, Jens Lagergren
Towards Identifying Lateral Gene Transfer Events. Pacific Symposium on Biocomputing (2003)
Johan Håstad, Lars Ivansson, Jens Lagergren
Fitting points on the real line and its application to RH mapping. J. Algorithms 49 (1) (2003)
David Fernández-Baca, Jens Lagergren
A Polynomial-Time Algorithm for Near-Perfect Phylogeny. SIAM J. Comput. 32 (5) (2003)
Jens Lagergren
Combining polynomial running time and fast convergence for the disk-covering method. J. Comput. Syst. Sci. 65 (3) (2002)
Michael T. Hallett, Jens Lagergren
Efficient algorithms for lateral gene transfer problems. RECOMB (2001)
Michael T. Hallett, Jens Lagergren
Hunting for Functionally Analogous Genes. FSTTCS (2000)
Michael T. Hallett, Jens Lagergren
New algorithms for the duplication-loss model. RECOMB (2000)
Jens Lagergren, Peter Bro Miltersen
Guest Editors' Foreword. Nord. J. Comput. 6 (2) (1999)
Jens Lagergren
Upper Bounds on the Size of Obstructions and Intertwines. J. Comb. Theory, Ser. B 73 (1) (1998)
Johan Håstad, Lars Ivansson, Jens Lagergren
Fitting Points on the Real Line and Its Application to RH Mapping. ESA (1998)
David Fernández-Baca, Jens Lagergren
On the Approximability of the Steiner Tree Problem in Phylogeny. Discret. Appl. Math. 88 (1-3) (1998)
Viggo Kann, Jens Lagergren, Alessandro Panconesi
-Cut with Subgraph Guarantee. Inf. Process. Lett. 65 (3) (1998)
Viggo Kann, Sanjeev Khanna, Jens Lagergren, Alessandro Panconesi
On the Hardness of Approximating Max k-Cut and its Dual. Chic. J. Theor. Comput. Sci. 1997 (1997)
Viggo Kann, Sanjeev Khanna, Jens Lagergren, Alessandro Panconesi
On the Hardness of Approximating Max k-Cut and Its Dual. ISTCS (1996)
Jens Lagergren
Hypothesis Testing in Perfect Phylogeny for a Bounded Number of Characters. STACS (1996)
Viggo Kann, Jens Lagergren, Alessandro Panconesi
Approximability of Maximum Splitting of k-Sets and Some Other Apx-Complete Problems. Inf. Process. Lett. 58 (3) (1996)
David Fernández-Baca, Jens Lagergren
A Polynomial-Time Algorithm for Near-Perfect Phylogeny. ICALP (1996)
David Fernández-Baca, Jens Lagergren
On the Approximability of the Steiner Tree Problem in Phylogeny. ISAAC (1996)
Jens Lagergren
Efficient Parallel Algorithms for Graphs of Bounded Tree-Width. J. Algorithms 20 (1) (1996)
Bruno Courcelle, Jens Lagergren
Equivalent Definitions of Recognizability for Sets of Graphs of Bounded Tree-Width. Math. Struct. Comput. Sci. 6 (2) (1996)
Jens Lagergren
The Size of an Interwine. ICALP (1994)
Jens Lagergren
The Nonexistence of Reduction Rules Giving an Embedding into a K-tree. Discret. Appl. Math. 54 (2-3) (1994)
Bruno Courcelle, Jens Lagergren
Recognizable Sets of Graphs of Bounded Tree-Width. Dagstuhl Seminar on Graph Transformations in Computer Science (1993)
Stefan Arnborg, Jens Lagergren, Detlef Seese
Easy Problems for Tree-Decomposable Graphs. J. Algorithms 12 (2) (1991)
Jens Lagergren, Stefan Arnborg
Finding Minimal Forbidden Minors Using a Finite Congruence. ICALP (1991)
Jens Lagergren
An upper bound on the size of an obstruction. Graph Structure Theory (1991)
Jens Lagergren
Efficient Parallel Algorithms for Tree-Decomposition and Related Problems FOCS (1990)
Stefan Arnborg, Jens Lagergren, Detlef Seese
Problems Easy for Tree-Decomposable Graphs (Extended Abstract). ICALP (1988)