Jens Lagergren

88 papers A* 10A 6B 7C 2Misc 1Journal 53Unranked 8

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Multi-Marginal Flow Matching with Adversarially Learnt Interpolants. CoRR Oskar Kviman, Kirill Tamogashev, Nicola Branchini, Víctor Elvira, Jens Lagergren, Nikolay Malkin
2024	A	`conf`	Benefits of Non-Linear Scale Parameterizations in Black Box Variational Inference through Smoothness Results and Gradient Variance Bounds. AISTATS Alexandra Maria Hotti, Lennart Alexander Van der Goten, Jens Lagergren
2024	J	`jnl`	CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference. Comput. Biol. Chem. Negar Safinianaini, Camila P. E. de Souza, Andrew Roth, Hazal Koptagel, Hosein Toosi, Jens Lagergren
2024	J	`jnl`	CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics. Bioinform. Semih Kurt, Mandi Chen, Hosein Toosi, Xinsong Chen, Camilla Engblom, Jeff E. Mold, Johan Hartman, Jens Lagergren
2024	A*	`conf`	Efficient Mixture Learning in Black-Box Variational Inference. ICML Alexandra Hotti, Oskar Kviman, Ricky Molén, Víctor Elvira, Jens Lagergren
2024	J	`jnl`	Efficient Mixture Learning in Black-Box Variational Inference. CoRR Alexandra Hotti, Oskar Kviman, Ricky Molén, Víctor Elvira, Jens Lagergren
2024	J	`jnl`	Improved Variational Bayesian Phylogenetic Inference using Mixtures. Trans. Mach. Learn. Res. Ricky Molén, Oskar Kviman, Jens Lagergren
2024	A*	`conf`	Indirectly Parameterized Concrete Autoencoders. ICML Alfred Nilsson, Klas Wijk, Sai Bharath Chandra Gutha, Erik Englesson, Alexandra Hotti, Carlo Saccardi, Oskar Kviman, Jens Lagergren, Ricardo Vinuesa, Hossein Azizpour
2024	J	`jnl`	Indirectly Parameterized Concrete Autoencoders. CoRR Alfred Nilsson, Klas Wijk, Sai Bharath Chandra Gutha, Erik Englesson, Alexandra Hotti, Carlo Saccardi, Oskar Kviman, Jens Lagergren, Ricardo Vinuesa, Hossein Azizpour
2024	J	`jnl`	Scuphr: A probabilistic framework for cell lineage tree reconstruction. PLoS Comput. Biol. Hazal Koptagel, Seong-Hwan Jun, Joanna Hård, Jens Lagergren
2024	J	`jnl`	Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix. Bioinform. Semih Kurt, Alexandre Bouchard-Côté, Jens Lagergren
2024	J	`jnl`	The Klarna Product Page Dataset: Web Element Nomination with Graph Neural Networks and Large Language Models. Trans. Mach. Learn. Res. Alexandra Hotti, Riccardo Sven Risuleo, Stefan Magureanu, Aref Moradi, Jens Lagergren
2024	B	`conf`	VICTree - A Variational Inference Method for Clonal Tree Reconstruction. RECOMB Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren
2024	A	`conf`	Variational Resampling. AISTATS Oskar Kviman, Nicola Branchini, Víctor Elvira, Jens Lagergren
2023	A*	`conf`	Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational Autoencoders. ICML Oskar Kviman, Ricky Molén, Alexandra Hotti, Semih Kurt, Víctor Elvira, Jens Lagergren
2023	J	`jnl`	Improved Variational Bayesian Phylogenetic Inference using Mixtures. CoRR Oskar Kviman, Ricky Molén, Jens Lagergren
2023	J	`jnl`	Learning Stationary Markov Processes with Contrastive Adjustment. CoRR Ludvig Bergenstråhle, Jens Lagergren, Joakim Lundeberg
2022	J	`jnl`	DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. Bioinform. José Bonet, Mandi Chen, Marc Dabad, Simon Heath, Abel González-Pérez, Núria López-Bigas, Jens Lagergren
2022	J	`jnl`	Learning with MISELBO: The Mixture Cookbook. CoRR Oskar Kviman, Ricky Molén, Alexandra Hotti, Semih Kurt, Víctor Elvira, Jens Lagergren
2022	A	`conf`	Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations. AISTATS Oskar Kviman, Harald Melin, Hazal Koptagel, Victor Elvira, Jens Lagergren
2022	J	`jnl`	Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations. CoRR Oskar Kviman, Harald Melin, Hazal Koptagel, Víctor Elvira, Jens Lagergren
2022	J	`jnl`	Statistical Distance Based Deterministic Offspring Selection in SMC Methods. CoRR Oskar Kviman, Hazal Koptagel, Harald Melin, Jens Lagergren
2022	J	`jnl`	ToMExO: A probabilistic tree-structured model for cancer progression. PLoS Comput. Biol. Mohammadreza Mohaghegh Neyshabouri, Jens Lagergren
2022	A*	`conf`	VaiPhy: a Variational Inference Based Algorithm for Phylogeny. NeurIPS Hazal Koptagel, Oskar Kviman, Harald Melin, Negar Safinianaini, Jens Lagergren
2022	J	`jnl`	VaiPhy: a Variational Inference Based Algorithm for Phylogeny. CoRR Hazal Koptagel, Oskar Kviman, Harald Melin, Negar Safinianaini, Jens Lagergren
2021	J	`jnl`	The Klarna Product Page Dataset: A Realistic Benchmark for Web Representation Learning. CoRR Alexandra Hotti, Riccardo Sven Risuleo, Stefan Magureanu, Aref Moradi, Jens Lagergren
2020	J	`jnl`	Inferring tumor progression in large datasets. PLoS Comput. Biol. Mohammadreza Mohaghegh Neyshabouri, Seong-Hwan Jun, Jens Lagergren
2020	—	`conf`	Orthogonal Mixture of Hidden Markov Models. ECML/PKDD (1) Negar Safinianaini, Camila P. E. de Souza, Henrik Boström, Jens Lagergren
2017	J	`jnl`	Fast and general tests of genetic interaction for genome-wide association studies. PLoS Comput. Biol. Mattias Frånberg, Rona J. Strawbridge, Anders Hamsten, PROCARDIS Consortium, Ulf de Faire, Jens Lagergren, Bengt Sennblad
2016	J	`jnl`	Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput. Biol. Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren
2016	J	`jnl`	Probabilistic inference of lateral gene transfer events. BMC Bioinform. Mehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Lars Arvestad, Jens Lagergren
2016	J	`jnl`	Viewpoint and Topic Modeling of Current Events. CoRR Kerry Zhang, Jussi Karlgren, Cheng Zhang, Jens Lagergren
2014	A	`conf`	Learning Bounded Tree-width Bayesian Networks using Integer Linear Programming. AISTATS Pekka Parviainen, Hossein Shahrabi Farahani, Jens Lagergren
2013	J	`jnl`	GenPhyloData: realistic simulation of gene family evolution. BMC Bioinform. Joel Sjöstrand, Lars Arvestad, Jens Lagergren, Bengt Sennblad
2013	J	`jnl`	Genome-wide probabilistic reconciliation analysis across vertebrates. BMC Bioinform. Owais Mahmudi, Joel Sjöstrand, Bengt Sennblad, Jens Lagergren
2013	J	`jnl`	fastphylo: Fast tools for phylogenetics. BMC Bioinform. Mehmood Alam Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
2012	J	`jnl`	DLRS: gene tree evolution in light of a species tree. Bioinform. Joel Sjöstrand, Bengt Sennblad, Lars Arvestad, Jens Lagergren
2011	—	`conf`	A Global Structural EM Algorithm for a Model of Cancer Progression. NIPS Ali Tofigh, Erik Sjölund, Mattias Höglund, Jens Lagergren
2011	J	`jnl`	Simultaneous Identification of Duplications and Lateral Gene Transfers. IEEE ACM Trans. Comput. Biol. Bioinform. Ali Tofigh, Michael T. Hallett, Jens Lagergren
2010	J	`jnl`	A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. BMC Bioinform. Mats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S. Furey, Marie Öhman, Jens Lagergren
2009	J	`jnl`	Fast neighbor joining. Theor. Comput. Sci. Isaac Elias, Jens Lagergren
2009	J	`jnl`	The gene evolution model and computing its associated probabilities. J. ACM Lars Arvestad, Jens Lagergren, Bengt Sennblad
2008	C	`ed.`	Algorithms in Bioinformatics, 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings WABI Keith A. Crandall, Jens Lagergren
2007	J	`jnl`	Fast computation of distance estimators. BMC Bioinform. Isaac Elias, Jens Lagergren
2007	J	`jnl`	Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model. J. Comput. Biol. Samuel A. Andersson, Jens Lagergren
2007	J	`jnl`	primetv: a viewer for reconciled trees. BMC Bioinform. Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad
2006	J	`jnl`	Compatibility of unrooted phylogenetic trees is FPT. Theor. Comput. Sci. David Bryant, Jens Lagergren
2006	J	`jnl`	Genome-Wide Survey for Biologically Functional Pseudogenes. PLoS Comput. Biol. Örjan Svensson, Lars Arvestad, Jens Lagergren
2006	B	`conf`	Motif Yggdrasil: Sampling from a Tree Mixture Model. RECOMB Samuel A. Andersson, Jens Lagergren
2006	J	`jnl`	New Probabilistic Network Models and Algorithms for Oncogenesis. J. Comput. Biol. Marcus Hjelm, Mattias Höglund, Jens Lagergren
2005	—	`ed.`	Comparative Genomics, RECOMB 2004 International Workshop, RCG 2004, Bertinoro, Italy, October 16-19, 2004, Revised Selected Papers Comparative Genomics Jens Lagergren
2005	A*	`conf`	Fast Neighbor Joining. ICALP Isaac Elias, Jens Lagergren
2004	J	`jnl`	Algorithms for RH Mapping: New Ideas and Improved Analysis. SIAM J. Comput. Lars Ivansson, Jens Lagergren
2004	J	`jnl`	Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. J. Bioinform. Comput. Biol. Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham
2004	B	`conf`	Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. RECOMB Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad
2004	J	`jnl`	MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res. Wynand Alkema, Öjvind Johansson, Jens Lagergren, Wyeth W. Wasserman
2004	B	`conf`	Simultaneous identification of duplications and lateral transfers. RECOMB Michael T. Hallett, Jens Lagergren, Ali Tofigh
2003	J	`jnl`	A Polynomial-Time Algorithm for Near-Perfect Phylogeny. SIAM J. Comput. David Fernández-Baca, Jens Lagergren
2003	C	`conf`	Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. WABI Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham
2003	—	`conf`	Bayesian gene/species tree reconciliation and orthology analysis using MCMC. ISMB (Supplement of Bioinformatics) Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad
2003	J	`jnl`	Fitting points on the real line and its application to RH mapping. J. Algorithms Johan Håstad, Lars Ivansson, Jens Lagergren
2003	—	`conf`	Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. ISMB (Supplement of Bioinformatics) Öjvind Johansson, Wynand Alkema, Wyeth W. Wasserman, Jens Lagergren
2003	Misc	`conf`	Towards Identifying Lateral Gene Transfer Events. Pacific Symposium on Biocomputing Louigi Addario-Berry, Michael T. Hallett, Jens Lagergren
2002	J	`jnl`	Combining polynomial running time and fast convergence for the disk-covering method. J. Comput. Syst. Sci. Jens Lagergren
2001	B	`conf`	Efficient algorithms for lateral gene transfer problems. RECOMB Michael T. Hallett, Jens Lagergren
2000	—	`conf`	Hunting for Functionally Analogous Genes. FSTTCS Michael T. Hallett, Jens Lagergren
2000	B	`conf`	New algorithms for the duplication-loss model. RECOMB Michael T. Hallett, Jens Lagergren
1999	J	`jnl`	Guest Editors' Foreword. Nord. J. Comput. Jens Lagergren, Peter Bro Miltersen
1998	J	`jnl`	Approximate Max Inf. Process. Lett. Viggo Kann, Jens Lagergren, Alessandro Panconesi
1998	A	`conf`	Fitting Points on the Real Line and Its Application to RH Mapping. ESA Johan Håstad, Lars Ivansson, Jens Lagergren
1998	J	`jnl`	On the Approximability of the Steiner Tree Problem in Phylogeny. Discret. Appl. Math. David Fernández-Baca, Jens Lagergren
1998	J	`jnl`	Upper Bounds on the Size of Obstructions and Intertwines. J. Comb. Theory B Jens Lagergren
1997	J	`jnl`	On the Hardness of Approximating Max k-Cut and its Dual. Chic. J. Theor. Comput. Sci. Viggo Kann, Sanjeev Khanna, Jens Lagergren, Alessandro Panconesi
1996	A*	`conf`	A Polynomial-Time Algorithm for Near-Perfect Phylogeny. ICALP David Fernández-Baca, Jens Lagergren
1996	J	`jnl`	Approximability of Maximum Splitting of k-Sets and Some Other Apx-Complete Problems. Inf. Process. Lett. Viggo Kann, Jens Lagergren, Alessandro Panconesi
1996	J	`jnl`	Efficient Parallel Algorithms for Graphs of Bounded Tree-Width. J. Algorithms Jens Lagergren
1996	J	`jnl`	Equivalent Definitions of Recognizability for Sets of Graphs of Bounded Tree-Width. Math. Struct. Comput. Sci. Bruno Courcelle, Jens Lagergren
1996	A	`conf`	Hypothesis Testing in Perfect Phylogeny for a Bounded Number of Characters. STACS Jens Lagergren
1996	B	`conf`	On the Approximability of the Steiner Tree Problem in Phylogeny. ISAAC David Fernández-Baca, Jens Lagergren
1996	—	`conf`	On the Hardness of Approximating Max k-Cut and Its Dual. ISTCS Viggo Kann, Sanjeev Khanna, Jens Lagergren, Alessandro Panconesi
1994	J	`jnl`	The Nonexistence of Reduction Rules Giving an Embedding into a K-tree. Discret. Appl. Math. Jens Lagergren
1994	A*	`conf`	The Size of an Interwine. ICALP Jens Lagergren
1993	—	`conf`	Recognizable Sets of Graphs of Bounded Tree-Width. Dagstuhl Seminar on Graph Transformations in Computer Science Bruno Courcelle, Jens Lagergren
1991	—	`conf`	An upper bound on the size of an obstruction. Graph Structure Theory Jens Lagergren
1991	J	`jnl`	Easy Problems for Tree-Decomposable Graphs. J. Algorithms Stefan Arnborg, Jens Lagergren, Detlef Seese
1991	A*	`conf`	Finding Minimal Forbidden Minors Using a Finite Congruence. ICALP Jens Lagergren, Stefan Arnborg
1990	A*	`conf`	Efficient Parallel Algorithms for Tree-Decomposition and Related Problems FOCS Jens Lagergren
1988	A*	`conf`	Problems Easy for Tree-Decomposable Graphs (Extended Abstract). ICALP Stefan Arnborg, Jens Lagergren, Detlef Seese