Jens Lagergren - researchr alias

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Viewing Publication 1 - 73 from 73

2024

Benefits of Non-Linear Scale Parameterizations in Black Box Variational Inference through Smoothness Results and Gradient Variance BoundsAlexandra Maria Hotti, Lennart Alexander Van der Goten, Jens Lagergren. aistats 2024: 3538-3546 [doi]

The Klarna Product Page Dataset: Web Element Nomination with Graph Neural Networks and Large Language ModelsAlexandra Hotti, Riccardo Sven Risuleo, Stefan Magureanu, Aref Moradi, Jens Lagergren. tmlr, 2024, 2024. [doi]

Efficient Mixture Learning in Black-Box Variational InferenceAlexandra Hotti, Oskar Kviman, Ricky Molén, Víctor Elvira, Jens Lagergren. icml 2024: [doi]

Scuphr: A probabilistic framework for cell lineage tree reconstructionHazal Koptagel, Seong-Hwan Jun, Joanna Hård, Jens Lagergren. ploscb, 20(5):1012094, 2024. [doi]

Variational ResamplingOskar Kviman, Nicola Branchini, Víctor Elvira, Jens Lagergren. aistats 2024: 3286-3294 [doi]

VICTree - A Variational Inference Method for Clonal Tree ReconstructionHarald Melin, Vittorio Zampinetti, Andrew McPherson 0003, Jens Lagergren. recomb 2024: 429-433 [doi]

Improved Variational Bayesian Phylogenetic Inference using MixturesRicky Molén, Oskar Kviman, Jens Lagergren. tmlr, 2024, 2024. [doi]

Indirectly Parameterized Concrete AutoencodersAlfred Nilsson, Klas Wijk, Sai Bharath Chandra Gutha, Erik Englesson, Alexandra Hotti, Carlo Saccardi, Oskar Kviman, Jens Lagergren, Ricardo Vinuesa, Hossein Azizpour. icml 2024: [doi]

CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inferenceNegar Safinianaini, Camila P. E. de Souza, Andrew Roth, Hazal Koptagel, Hosein Toosi, Jens Lagergren. CANDC, 113:108257, 2024. [doi]

2023

Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational AutoencodersOskar Kviman, Ricky Molén, Alexandra Hotti, Semih Kurt, Víctor Elvira, Jens Lagergren. icml 2023: 18008-18022 [doi]

2022

2020

Inferring tumor progression in large datasetsMohammadreza Mohaghegh Neyshabouri, Seong-Hwan Jun, Jens Lagergren. ploscb, 16(10), 2020. [doi]

Orthogonal Mixture of Hidden Markov ModelsNegar Safinianaini, Camila P. E. de Souza, Henrik Boström, Jens Lagergren. pkdd 2021: 509-525 [doi]

2017

Fast and general tests of genetic interaction for genome-wide association studiesMattias Frånberg, Rona J. Strawbridge, Anders Hamsten, PROCARDIS consortium, Ulf de Faire, Jens Lagergren, Bengt Sennblad. ploscb, 13(6), 2017. [doi]

2016

Computational Cancer Biology: An Evolutionary PerspectiveNiko Beerenwinkel, Chris D. Greenman, Jens Lagergren. ploscb, 12(2), 2016. [doi]

Probabilistic inference of lateral gene transfer eventsMehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Lars Arvestad, Jens Lagergren. bmcbi, 17(S-14):263-270, 2016. [doi]

2014

Learning Bounded Tree-width Bayesian Networks using Integer Linear ProgrammingPekka Parviainen, Hossein Shahrabi Farahani, Jens Lagergren. aistats 2014: 751-759 [doi]

2013

2012

DLRS: gene tree evolution in light of a species treeJoel Sjöstrand, Bengt Sennblad, Lars Arvestad, Jens Lagergren. bioinformatics, 28(22):2994-2995, 2012. [doi]

2011

A Global Structural EM Algorithm for a Model of Cancer ProgressionAli Tofigh, Erik Sjlund, Mattias Höglund, Jens Lagergren. nips 2011: 163-171 [doi]

Simultaneous Identification of Duplications and Lateral Gene TransfersAli Tofigh, Michael T. Hallett, Jens Lagergren. tcbb, 8(2):517-535, 2011. [doi]

2010

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteinsMats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S. Furey, Marie Öhman, Jens Lagergren. bmcbi, 11:6, 2010. [doi]

2009

The gene evolution model and computing its associated probabilitiesLars Arvestad, Jens Lagergren, Bengt Sennblad. JACM, 56(2), 2009. [doi]

Fast neighbor joiningIsaac Elias, Jens Lagergren. TCS, 410(21-23):1993-2000, 2009. [doi]

2007

Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture ModelSamuel A. Andersson, Jens Lagergren. jcb, 14(5):682-697, 2007. [doi]

Fast computation of distance estimatorsIsaac Elias, Jens Lagergren. bmcbi, 8, 2007. [doi]

primetv: a viewer for reconciled treesBengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad. bmcbi, 8, 2007. [doi]

2006

2005

Fast Neighbor JoiningIsaac Elias, Jens Lagergren. icalp 2005: 1263-1274 [doi]

2004

Ancestral Maximum Likelihood of Evolutionary Trees Is HardLouigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham. jbcb, 2(2):257-272, 2004. [doi]

MSCAN: identification of functional clusters of transcription factor binding sitesWynand Alkema, Öjvind Johansson, Jens Lagergren, Wyeth W. Wasserman. nar, 32(Web-Server-Issue):195-198, 2004.

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolutionLars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad. recomb 2004: 326-335 [doi]

Simultaneous identification of duplications and lateral transfersMichael T. Hallett, Jens Lagergren, Ali Tofigh. recomb 2004: 347-356 [doi]

Algorithms for RH Mapping: New Ideas and Improved AnalysisLars Ivansson, Jens Lagergren. SICOMP, 34(1):89-108, 2004. [doi]

2003

Towards Identifying Lateral Gene Transfer EventsLouigi Addario-Berry, Michael T. Hallett, Jens Lagergren. psb 2003: 279-290 [doi]

Ancestral Maximum Likelihood of Evolutionary Trees Is HardLouigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham. wabi 2003: 202-215 [doi]

Bayesian gene/species tree reconciliation and orthology analysis using MCMCLars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad. ismb 2003: 7-15 [doi]

A Polynomial-Time Algorithm for Near-Perfect PhylogenyDavid Fernández-Baca, Jens Lagergren. SICOMP, 32(5):1115-1127, 2003. [doi]

Fitting points on the real line and its application to RH mappingJohan Håstad, Lars Ivansson, Jens Lagergren. jal, 49(1):42-62, 2003. [doi]

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithmÖjvind Johansson, Wynand Alkema, Wyeth W. Wasserman, Jens Lagergren. ismb 2003: 169-176 [doi]

2002

Combining polynomial running time and fast convergence for the disk-covering methodJens Lagergren. jcss, 65(3):481-493, 2002. [doi]

2001

Efficient algorithms for lateral gene transfer problemsMichael T. Hallett, Jens Lagergren. recomb 2001: 149-156 [doi]

2000

New algorithms for the duplication-loss modelMichael T. Hallett, Jens Lagergren. recomb 2000: 138-146 [doi]

Hunting for Functionally Analogous GenesMichael T. Hallett, Jens Lagergren. fsttcs 2000: 465-476 [doi]

1999

Guest Editors ForewordJens Lagergren, Peter Bro Miltersen. njc, 6(2):135-136, 1999.

1998

1997

On the Hardness of Approximating Max k-Cut and its DualViggo Kann, Sanjeev Khanna, Jens Lagergren, Alessandro Panconesi. cjtcs, 1997, 1997. [doi]

1996

Equivalent Definitions of Recognizability for Sets of Graphs of Bounded Tree-WidthBruno Courcelle, Jens Lagergren. mscs, 6(2):141-165, 1996.

A Polynomial-Time Algorithm for Near-Perfect PhylogenyDavid Fernández-Baca, Jens Lagergren. icalp 1996: 670-680

On the Approximability of the Steiner Tree Problem in PhylogenyDavid Fernández-Baca, Jens Lagergren. isaac 1996: 65-74

Approximability of Maximum Splitting of k-Sets and Some Other Apx-Complete ProblemsViggo Kann, Jens Lagergren, Alessandro Panconesi. ipl, 58(3):105-110, 1996. [doi]

On the Hardness of Approximating Max k-Cut and Its DualViggo Kann, Sanjeev Khanna, Jens Lagergren, Alessandro Panconesi. istcs 1996: 61-67

Hypothesis Testing in Perfect Phylogeny for a Bounded Number of CharactersJens Lagergren. STACS 1996: 605-616

Efficient Parallel Algorithms for Graphs of Bounded Tree-WidthJens Lagergren. jal, 20(1):20-44, 1996.

1994

The Size of an InterwineJens Lagergren. icalp 1994: 520-531

The Nonexistence of Reduction Rules Giving an Embedding into a K-treeJens Lagergren. DAM, 54(2-3):219-223, 1994. [doi]

1993

Recognizable Sets of Graphs of Bounded Tree-WidthBruno Courcelle, Jens Lagergren. Dagstuhl 1994: 138-152

1991

Easy Problems for Tree-Decomposable GraphsStefan Arnborg, Jens Lagergren, Detlef Seese. jal, 12(2):308-340, 1991.

An upper bound on the size of an obstructionJens Lagergren. gst 1993: 601-622

Finding Minimal Forbidden Minors Using a Finite CongruenceJens Lagergren, Stefan Arnborg. icalp 1991: 532-543

1990

Efficient Parallel Algorithms for Tree-Decomposition and Related ProblemsJens Lagergren. focs 1990: 173-182

1988

Problems Easy for Tree-Decomposable Graphs (Extended Abstract)Stefan Arnborg, Jens Lagergren, Detlef Seese. icalp 1988: 38-51

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