An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries. - Mikko Koivisto; Markus Perola; T. Varilo; W. Hennah; J. Ekelund; Margus Lukk; L. Peltonen; Esko Ukkonen; Heikki Mannila (Pacific Symposium on Biocomputing, 2003)

Hidden Markov Modelling Techniques for Haplotype Analysis. - Mikko Koivisto; Teemu Kivioja; Heikki Mannila; Pasi Rastas; Esko Ukkonen (ALT, 2004)

Recombination Systems. - Mikko Koivisto; Pasi Rastas; Esko Ukkonen (Theory Is Forever, 2004)

Exact Bayesian Structure Discovery in Bayesian Networks. - Mikko Koivisto; Kismat Sood (J. Mach. Learn. Res., 2004)

Computational aspects of Bayesian partition models. - Mikko Koivisto; Kismat Sood (ICML, 2005)

A Hidden Markov Technique for Haplotype Reconstruction. - Pasi Rastas; Mikko Koivisto; Heikki Mannila; Esko Ukkonen (WABI, 2005)

Parent Assignment Is Hard for the MDL, AIC, and NML Costs. - Mikko Koivisto (COLT, 2006)

Bayesian Learning with Mixtures of Trees. - Jussi Kollin; Mikko Koivisto (ECML, 2006)

An O*(2^n ) Algorithm for Graph Coloring and Other Partitioning Problems via Inclusion–Exclusion. - Mikko Koivisto (FOCS, 2006)

Advances in Exact Bayesian Structure Discovery in Bayesian Networks. - Mikko Koivisto (UAI, 2006)

Optimal 2-constraint satisfaction via sum-product algorithms. - Mikko Koivisto (Inf. Process. Lett., 2006)

Fourier meets möbius: fast subset convolution. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (STOC, 2007)

08431 Open Problems - Moderately Exponential Time Algorithms. - Fedor V. Fomin; Kazuo Iwama; Dieter Kratsch; Petteri Kaski; Mikko Koivisto; Lukasz Kowalik; Yoshio Okamoto; Johan M. M. van Rooij; Ryan Williams 001 (Moderately Exponential Time Algorithms, 2008)

Computing the Tutte Polynomial in Vertex-Exponential Time. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (FOCS, 2008)

The Travelling Salesman Problem in Bounded Degree Graphs. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (ICALP (1), 2008)

Fast Bayesian Haplotype Inference Via Context Tree Weighting. - Pasi Rastas; Jussi Kollin; Mikko Koivisto (WABI, 2008)

The fast intersection transform with applications to counting paths - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (CoRR, 2008)

Counting Paths and Packings in Halves. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (ESA, 2009)

Partitioning into Sets of Bounded Cardinality. - Mikko Koivisto (IWPEC, 2009)

Exact Structure Discovery in Bayesian Networks with Less Space. - Pekka Parviainen; Mikko Koivisto (UAI, 2009)

On evaluation of permanents - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (CoRR, 2009)

Set Partitioning via Inclusion-Exclusion. - Andreas Björklund; Thore Husfeldt; Mikko Koivisto (SIAM J. Comput., 2009)

A Space-Time Tradeoff for Permutation Problems. - Mikko Koivisto; Pekka Parviainen (SODA, 2010)

Geodesic diameter of a polygonal domain in O(n^4 log n) time - Mikko Koivisto; Valentin Polishchuk (CoRR, 2010)

Evaluation of permanents in rings and semirings. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (Inf. Process. Lett., 2010)

Bayesian structure discovery in Bayesian networks with less space. - Pekka Parviainen; Mikko Koivisto (AISTATS, 2010)

Trimmed Moebius Inversion and Graphs of Bounded Degree. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (Theory Comput. Syst., 2010)

Ancestor Relations in the Presence of Unobserved Variables. - Pekka Parviainen; Mikko Koivisto (ECML/PKDD (2), 2011)

Partial Order MCMC for Structure Discovery in Bayesian Networks. - Teppo Niinimaki; Pekka Parviainen; Mikko Koivisto (UAI, 2011)

Covering and packing in linear space. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (Inf. Process. Lett., 2011)

Fast Monotone Summation over Disjoint Sets. - Petteri Kaski; Mikko Koivisto; Janne H. Korhonen (IPEC, 2012)

Homomorphic Hashing for Sparse Coefficient Extraction. - Petteri Kaski; Mikko Koivisto; Jesper Nederlof (IPEC, 2012)

Finding Efficient Circuits for Ensemble Computation. - Matti Järvisalo; Petteri Kaski; Mikko Koivisto; Janne H. Korhonen (SAT, 2012)

The traveling salesman problem in bounded degree graphs. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (ACM Trans. Algorithms, 2012)

Space-Time Tradeoffs for Subset Sum: An Improved Worst Case Algorithm. - Per Austrin; Petteri Kaski; Mikko Koivisto; Jussi Määttä (ICALP (1), 2013)

Annealed Importance Sampling for Structure Learning in Bayesian Networks. - Teppo Mikael Niinimäki; Mikko Koivisto (IJCAI, 2013)

Treedy: A Heuristic for Counting and Sampling Subsets. - Teppo Niinimaki; Mikko Koivisto (UAI, 2013)

Finding optimal Bayesian networks using precedence constraints. - Pekka Parviainen; Mikko Koivisto (J. Mach. Learn. Res., 2013)

Predicting the Hardness of Learning Bayesian Networks. - Brandon M. Malone; Kustaa Kangas; Matti Järvisalo; Mikko Koivisto; Petri Myllymäki (AAAI, 2014)

Learning Chordal Markov Networks by Dynamic Programming. - Kustaa Kangas; Mikko Koivisto; Teppo Mikael Niinimäki (NIPS, 2014)

Fast monotone summation over disjoint sets. - Petteri Kaski; Mikko Koivisto; Janne H. Korhonen; Igor S. Sergeev (Inf. Process. Lett., 2014)

Dealing with small data: On the generalization of context trees. - Ralf Eggeling; Mikko Koivisto; Ivo Grosse (ICML, 2015)

Subset Sum in the Absence of Concentration. - Per Austrin; Petteri Kaski; Mikko Koivisto; Jesper Nederlof (STACS, 2015)

Averaging of Decomposable Graphs by Dynamic Programming and Sampling. - Kustaa Kangas; Teppo Mikael Niinimäki; Mikko Koivisto (UAI, 2015)

On finding optimal polytrees. - Serge Gaspers; Mikko Koivisto; Mathieu Liedloff; Sebastian Ordyniak; Stefan Szeider (Theor. Comput. Sci., 2015)

Counting Linear Extensions of Sparse Posets. - Kustaa Kangas; Teemu Hankala; Teppo Mikael Niinimäki; Mikko Koivisto (IJCAI, 2016)

Dense Subset Sum May Be the Hardest. - Per Austrin; Petteri Kaski; Mikko Koivisto; Jesper Nederlof (STACS, 2016)

Pruning Rules for Learning Parsimonious Context Trees. - Ralf Eggeling; Mikko Koivisto (UAI, 2016)

Separating OR, SUM, and XOR circuits. - Magnus Find; Mika Göös; Matti Järvisalo; Petteri Kaski; Mikko Koivisto; Janne H. Korhonen (J. Comput. Syst. Sci., 2016)

Structure Discovery in Bayesian Networks by Sampling Partial Orders. - Teppo Niinimaki; Pekka Parviainen; Mikko Koivisto (J. Mach. Learn. Res., 2016)

Fast Zeta Transforms for Lattices with Few Irreducibles. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto; Jesper Nederlof; Pekka Parviainen (ACM Trans. Algorithms, 2016)

The Mixing of Markov Chains on Linear Extensions in Practice. - Topi Talvitie; Teppo Mikael Niinimäki; Mikko Koivisto (IJCAI, 2017)

AS-ASL: Algorithm Selection with Auto-sklearn. - Brandon M. Malone; Kustaa Kangas; Matti Järvisalo; Mikko Koivisto; Petri Myllymäki (OASC, 2017)

Narrow sieves for parameterized paths and packings. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (J. Comput. Syst. Sci., 2017)

Counting Linear Extensions in Practice: MCMC Versus Exponential Monte Carlo. - Topi Talvitie; Kustaa Kangas; Teppo Mikael Niinimäki; Mikko Koivisto (AAAI, 2018)

Intersection-Validation: A Method for Evaluating Structure Learning without Ground Truth. - Jussi Viinikka; Ralf Eggeling; Mikko Koivisto (AISTATS, 2018)

A Scalable Scheme for Counting Linear Extensions. - Topi Talvitie; Kustaa Kangas; Teppo Mikael Niinimäki; Mikko Koivisto (IJCAI, 2018)

Counting Connected Subgraphs with Maximum-Degree-Aware Sieving. - Andreas Björklund; Thore Husfeldt; Petteri Kaski; Mikko Koivisto (ISAAC, 2018)

Finding Optimal Bayesian Networks with Local Structure. - Topi Talvitie; Ralf Eggeling; Mikko Koivisto (PGM, 2018)

On the Number of Connected Sets in Bounded Degree Graphs. - Kustaa Kangas; Petteri Kaski; Janne H. Korhonen; Mikko Koivisto (Electron. J. Comb., 2018)

Empirical hardness of finding optimal Bayesian network structures: algorithm selection and runtime prediction. - Brandon M. Malone; Kustaa Kangas; Matti Järvisalo; Mikko Koivisto; Petri Myllymäki (Mach. Learn., 2018)

Sharper Upper Bounds for Unbalanced Uniquely Decodable Code Pairs. - Per Austrin; Petteri Kaski; Mikko Koivisto; Jesper Nederlof (IEEE Trans. Inf. Theory, 2018)

Counting and Sampling Markov Equivalent Directed Acyclic Graphs. - Topi Talvitie; Mikko Koivisto (AAAI, 2019)

On Structure Priors for Learning Bayesian Networks. - Ralf Eggeling; Jussi Viinikka; Aleksis Vuoksenmaa; Mikko Koivisto (AISTATS, 2019)

Exact Sampling of Directed Acyclic Graphs from Modular Distributions. - Topi Talvitie; Aleksis Vuoksenmaa; Mikko Koivisto (UAI, 2019)

Learning Bayesian networks with local structure, mixed variables, and exact algorithms. - Topi Talvitie; Ralf Eggeling; Mikko Koivisto (Int. J. Approx. Reason., 2019)

Algorithms for learning parsimonious context trees. - Ralf Eggeling; Ivo Grosse; Mikko Koivisto (Mach. Learn., 2019)

Error-Correcting and Verifiable Parallel Inference in Graphical Models. - Negin Karimi; Petteri Kaski; Mikko Koivisto (AAAI, 2020)

A Bayesian Approach for Estimating Causal Effects from Observational Data. - Johan Pensar; Topi Talvitie; Antti Hyttinen; Mikko Koivisto (AAAI, 2020)

Towards Scalable Bayesian Learning of Causal DAGs. - Jussi Viinikka; Antti Hyttinen; Johan Pensar; Mikko Koivisto (NeurIPS, 2020)

Fast Multi-Subset Transform and Weighted Sums over Acyclic Digraphs. - Mikko Koivisto; Antti Röyskö (SWAT, 2020)

Layering-MCMC for Structure Learning in Bayesian Networks. - Jussi Viinikka; Mikko Koivisto (UAI, 2020)

A Faster Tree-Decomposition Based Algorithm for Counting Linear Extensions. - Kustaa Kangas; Mikko Koivisto; Sami Salonen (Algorithmica, 2020)

NP-completeness results for partitioning a graph into total dominating sets. - Mikko Koivisto; Petteri Laakkonen; Juho Lauri (Theor. Comput. Sci., 2020)

Approximating the Permanent with Deep Rejection Sampling. - Juha Harviainen; Antti Röyskö; Mikko Koivisto (NeurIPS, 2021)

Trustworthy Monte Carlo. - Juha Harviainen; Mikko Koivisto; Petteri Kaski (NeurIPS, 2022)

A Faster Practical Approximation Scheme for the Permanent. - Juha Harviainen; Mikko Koivisto (AAAI, 2023)

Revisiting Bayesian network learning with small vertex cover. - Juha Harviainen; Mikko Koivisto (UAI, 2023)

On inference and learning with probabilistic generating circuits. - Juha Harviainen; Vaidyanathan Peruvemba Ramaswamy; Mikko Koivisto (UAI, 2023)

Estimating the Permanent by Nesting Importance Sampling. - Juha Harviainen; Mikko Koivisto (ICML, 2024)

Faster Perfect Sampling of Bayesian Network Structures. - Juha Harviainen; Mikko Koivisto (UAI, 2024)

Approximate Counting of Linear Extensions in Practice. - Topi Talvitie; Mikko Koivisto (J. Artif. Intell. Res., 2024)

Quantum Speedups for Bayesian Network Structure Learning. - Juha Harviainen; Kseniya Rychkova; Mikko Koivisto (UAI, 2025)