Janne H. Korhonen
Helsinki Institute for Information Technology
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Publication
Featured researches published by Janne H. Korhonen.
New Phytologist | 2009
Jordi Martínez-Vilalta; Hervé Cochard; Maurizia Mencuccini; Frank J. Sterck; Asier Herrero; Janne H. Korhonen; Pilar Llorens; Eero Nikinmaa; Angelo Nolè; Rafael Poyatos; Francesco Ripullone; Ute Sass-Klaassen; Roman Zweifel
* The variability of branch-level hydraulic properties was assessed across 12 Scots pine populations covering a wide range of environmental conditions, including some of the southernmost populations of the species. The aims were to relate this variability to differences in climate, and to study the potential tradeoffs between traits. * Traits measured included wood density, radial growth, xylem anatomy, sapwood- and leaf-specific hydraulic conductivity (K(S) and K(L)), vulnerability to embolism, leaf-to-sapwood area ratio (A(L) : A(S)), needle carbon isotope discrimination (Delta13C) and nitrogen content, and specific leaf area. * Between-population variability was high for most of the hydraulic traits studied, but it was directly associated with climate dryness (defined as a combination of atmospheric moisture demand and availability) only for A(L) : A(S), K(L) and Delta13C. Shoot radial growth and A(L) : A(S) declined with stand development, which is consistent with a strategy to avoid exceedingly low water potentials as tree size increases. In addition, we did not find evidence at the intraspecific level of some associations between hydraulic traits that have been commonly reported across species. * The adjustment of Scots pines hydraulic system to local climatic conditions occurred primarily through modifications of A(L) : A(S) and direct stomatal control, whereas intraspecific variation in vulnerability to embolism and leaf physiology appears to be limited.
Bioinformatics | 2009
Janne H. Korhonen; Petri Martinmäki; Cinzia Pizzi; Pasi Rastas; Esko Ukkonen
Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library. Availability: The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL). Contact: [email protected]
principles of distributed computing | 2015
Keren Censor-Hillel; Petteri Kaski; Janne H. Korhonen; Ami Paz; Jukka Suomela
In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an O(n1-2/ω) round matrix multiplication algorithm, where ω < 2.3728639 is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include: triangle and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) triangle counting algorithm of Dolev et al. [DISC 2012], a (1 + o(1))-approximation of all-pairs shortest paths in O(n0.158) rounds, improving upon the ~O (n1/2)-round (2 + o(1))-approximation algorithm of Nanongkai [STOC 2014], and computing the girth in O(n0.158) rounds, which is the first non-trivial solution in this model. In addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles.
mathematical foundations of computer science | 2013
Fedor V. Fomin; Petr A. Golovach; Janne H. Korhonen
We study the parameterized complexity of separating a small set of vertices from a graph by a small vertex-separator. That is, given a graph G and integers k, t, the task is to find a vertex set X with |X| ≤ k and |N(X)| ≤ t. We show that the problem is fixed-parameter tractable (FPT) when parameterized by t but W[1]-hard when parameterized by k, and a terminal variant of the problem, where X must contain a given vertex s, is W[1]-hard when parameterized either by k or by t alone, but is FPT when parameterized by k + t. We also show that if we consider edge cuts instead of vertex cuts, the terminal variant is NP-hard.
international symposium on stabilization safety and security of distributed systems | 2013
Danny Dolev; Janne H. Korhonen; Joel Rybicki; Jukka Suomela
Consider a complete communication network on n nodes, each of which is a state machine. In synchronous 2-counting, the nodes receive a common clock pulse and they have to agree on which pulses are “odd” and which are “even”. We require that the solution is self-stabilising (reaching the correct operation from any initial state) and it tolerates f Byzantine failures (nodes that send arbitrary misinformation). Prior algorithms are expensive to implement in hardware: they require a source of random bits or a large number of states. This work consists of two parts. In the first part, we use computational techniques (often known as synthesis) to construct very compact deterministic algorithms for the first non-trivial case of f = 1. While no algorithm exists for n < 4, we show that as few as 3 states per node are sufficient for all values n ≥ 4. Moreover, the problem cannot be solved with only 2 states per node for n = 4, but there is a 2-state solution for all values n ≥ 6. In the second part, we develop and compare two different approaches for synthesising synchronous counting algorithms. Both approaches are based on casting the synthesis problem as a propositional satisfiability (SAT) problem and employing modern SATsolvers. The difference lies in how to solve the SAT problem: either in a direct fashion, or incrementally within a counter-example guided abstraction refinement loop. Empirical results suggest that the former technique is more efficient if we want to synthesise time-optimal algorithms, while the latter technique discovers non-optimal algorithms more quickly. 1 ar X iv :1 30 4. 57 19 v2 [ cs .D C ] 5 J an 2 01 5
theory and applications of satisfiability testing | 2012
Matti Järvisalo; Petteri Kaski; Mikko Koivisto; Janne H. Korhonen
Given a Boolean function as input, a fundamental problem is to find a Boolean circuit with the least number of elementary gates (AND, OR, NOT) that computes the function. The problem generalises naturally to the setting of multiple Boolean functions: find the smallest Boolean circuit that computes all the functions simultaneously. We study an NP-complete variant of this problem titled Ensemble Computation and, especially, its relationship to the Boolean satisfiability (SAT) problem from both the theoretical and practical perspectives, under the two monotone circuit classes: OR-circuits and SUM-circuits. Our main result relates the existence of nontrivial algorithms for CNF-SAT with the problem of rewriting in subquadratic time a given OR-circuit to a SUM-circuit. Furthermore, by developing a SAT encoding for the ensemble computation problem and by employing state-of-the-art SAT solvers, we search for concrete instances that would witness a substantial separation between the size of optimal OR-circuits and optimal SUM-circuits. Our encoding allows for exhaustively checking all small witness candidates. Searching over larger witness candidates presents an interesting challenge for current SAT solver technology.
Journal of Artificial Intelligence Research | 2017
James Cussens; Matti Järvisalo; Janne H. Korhonen; Mark Bartlett
The challenging task of learning structures of probabilistic graphical models is an important problem within modern AI research. Recent years have witnessed several major algorithmic advances in structure learning for Bayesian networks---arguably the most central class of graphical models---especially in what is known as the score-based setting. A successful generic approach to optimal Bayesian network structure learning (BNSL), based on integer programming (IP), is implemented in the GOBNILP system. Despite the recent algorithmic advances, current understanding of foundational aspects underlying the IP based approach to BNSL is still somewhat lacking. Understanding fundamental aspects of cutting planes and the related separation problem( is important not only from a purely theoretical perspective, but also since it holds out the promise of further improving the efficiency of state-of-the-art approaches to solving BNSL exactly. In this paper, we make several theoretical contributions towards these goals: (i) we study the computational complexity of the separation problem, proving that the problem is NP-hard; (ii) we formalise and analyse the relationship between three key polytopes underlying the IP-based approach to BNSL; (iii) we study the facets of the three polytopes both from the theoretical and practical perspective, providing, via exhaustive computation, a complete enumeration of facets for low-dimensional family-variable polytopes; and, furthermore, (iv) we establish a tight connection of the BNSL problem to the acyclic subgraph problem.
symposium on the theory of computing | 2018
Alkida Balliu; Juho Hirvonen; Janne H. Korhonen; Tuomo Lempiäinen; Dennis Olivetti; Jukka Suomela
A number of recent papers – e.g. Brandt et al. (STOC 2016), Chang et al. (FOCS 2016), Ghaffari & Su (SODA 2017), Brandt et al. (PODC 2017), and Chang & Pettie (FOCS 2017) – have advanced our understanding of one of the most fundamental questions in theory of distributed computing: what are the possible time complexity classes of LCL problems in the LOCAL model? In essence, we have a graph problem Π in which a solution can be verified by checking all radius-O(1) neighbourhoods, and the question is what is the smallest T such that a solution can be computed so that each node chooses its own output based on its radius-T neighbourhood. Here T is the distributed time complexity of Π. The time complexity classes for deterministic algorithms in bounded-degree graphs that are known to exist by prior work are Θ(1), Θ(log* n), Θ(logn), Θ(n1/k), and Θ(n). It is also known that there are two gaps: one between ω(1) and o(loglog* n), and another between ω(log* n) and o(logn). It has been conjectured that many more gaps exist, and that the overall time hierarchy is relatively simple – indeed, this is known to be the case in restricted graph families such as cycles and grids. We show that the picture is much more diverse than previously expected. We present a general technique for engineering LCL problems with numerous different deterministic time complexities, including Θ(logα n) for any α ≥ 1, 2Θ(logα n) for any α ≤ 1, and Θ(nα) for any α < 1/2 in the high end of the complexity spectrum, and Θ(logα log* n) for any α ≥ 1, 2Θ(logα log* n) for any α ≤ 1, and Θ((log* n)α) for any α ≤ 1 in the low end of the complexity spectrum; here α is a positive rational number.
Evolutionary Applications | 2018
Toby Fountain; Arild Husby; Etsuko Nonaka; Michelle F DiLeo; Janne H. Korhonen; Pasi Rastas; Torsti Schulz; Marjo Saastamoinen; Ilkka Hanski
Dispersal is important for determining both species ecological processes, such as population viability, and its evolutionary processes, like gene flow and local adaptation. Yet obtaining accurate estimates in the wild through direct observation can be challenging or even impossible, particularly over large spatial and temporal scales. Genotyping many individuals from wild populations can provide detailed inferences about dispersal. We therefore utilized genomewide marker data to estimate dispersal in the classic metapopulation of the Glanville fritillary butterfly (Melitaea cinxia L.), in the Åland Islands in SW Finland. This is an ideal system to test the effectiveness of this approach due to the wealth of information already available covering dispersal across small spatial and temporal scales, but lack of information at larger spatial and temporal scales. We sampled three larvae per larval family group from 3732 groups over a six‐year period and genotyped for 272 SNPs across the genome. We used this empirical data set to reconstruct cases where full‐sibs were detected in different local populations to infer female effective dispersal distance, that is, dispersal events directly contributing to gene flow. On average this was one kilometre, closely matching previous dispersal estimates made using direct observation. To evaluate our power to detect full‐sib families, we performed forward simulations using an individual‐based model constructed and parameterized for the Glanville fritillary metapopulation. Using these simulations, 100% of predicted full‐sibs were correct and over 98% of all true full‐sib pairs were detected. We therefore demonstrate that even in a highly dynamic system with a relatively small number of markers, we can accurately reconstruct full‐sib families and for the first time make inferences on female effective dispersal. This highlights the utility of this approach in systems where it has previously been impossible to obtain accurate estimates of dispersal over both ecological and evolutionary scales.
Journal of Computer and System Sciences | 2016
Mika Göös; Matti Järvisalo; Petteri Kaski; Mikko Koivisto; Janne H. Korhonen
Given a boolean n × n matrix A we consider arithmetic circuits for computing the transformation x ↦ Ax over different semirings. Namely, we study three circuit models: monotone OR-circuits, monotone SUM-circuits (addition of non-negative integers), and non-monotone XOR-circuits (addition modulo 2). Our focus is on separating OR-circuits from the two other models in terms of circuit complexity: We show how to obtain matrices that admit OR-circuits of size O(n), but require SUM-circuits of size Ω(n3/2/log2n).We consider the task of rewriting a given OR-circuit as a XOR-circuit and prove that any subquadratic-time algorithm for this task violates the strong exponential time hypothesis.