Cluster Editing Parameterized Above Modification-Disjoint P?-Packings

Given a graph G = (V,E) and an integer k, the Cluster Editing problem asks whether we can transform G into a union of vertex-disjoint cliques by at most k modifications (edge deletions or insertions). In this paper, we study the following variant of Cluster Editing. We are given a graph G = (V,E), a packing ? of modification-disjoint induced P?s (no pair of P?s in H share an edge or non-edge) and an integer ?. The task is to decide whether G can be transformed into a union of vertex-disjoint cliques by at most ?+|H| modifications (edge deletions or insertions). We show that this problem is NP-hard even when ? = 0 (in which case the problem asks to turn G into a disjoint union of cliques by performing exactly one edge deletion or insertion per element of H) and when each vertex is in at most 23 P?s of the packing. This answers negatively a question of van Bevern, Froese, and Komusiewicz (CSR 2016, ToCS 2018), repeated by C. Komusiewicz at Shonan meeting no. 144 in March 2019. We then initiate the study to find the largest integer c such that the problem remains tractable when restricting to packings such that each vertex is in at most c packed P?s. Van Bevern et al. showed that the case c = 1 is fixed-parameter tractable with respect to ? and we show that the case c = 2 is solvable in |V|^{2? + O(1)} time

Cluster Editing parameterized above the size of a modification-disjoint P3P_3 packing is para-NP-hard

Given a graph $G=(V,E)$ and an integer $k$, the Cluster Editing problem asks whether we can transform $G$ into a union of vertex-disjoint cliques by at most $k$ modifications (edge deletions or insertions). In this paper, we study the following variant of Cluster Editing. We are given a graph $G=(V,E)$, a packing $\mathcal{H}$ of modification-disjoint induced $P_3$s (no pair of $P_3$s in $\cal H$ share an edge or non-edge) and an integer $\ell$. The task is to decide whether $G$ can be transformed into a union of vertex-disjoint cliques by at most $\ell+|\cal H|$ modifications (edge deletions or insertions). We show that this problem is NP-hard even when $\ell=0$ (in which case the problem asks to turn $G$ into a disjoint union of cliques by performing exactly one edge deletion or insertion per element of $\cal H$). This answers negatively a question of van Bevern, Froese, and Komusiewicz (CSR 2016, ToCS 2018), repeated by Komusiewicz at Shonan meeting no. 144 in March 2019.Comment: 18 pages, 5 figure

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes

International audienceFinding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches

New Graph Algorithms via Polyhedral Techniques

In this thesis we give new algorithms for two fundamental graph problems. We develop novel ways of using linear programming formulations, even exponential-sized ones, to extract structure from problem instances and to guide algorithms in making progress. Somewhat surprisingly, similar polyhedral techniques can be harnessed in the two seemingly disparate settings. In the first part of the thesis we address a benchmark problem in combinatorial optimization: the asymmetric traveling salesman problem (ATSP). It consists in finding the shortest tour that visits all vertices of a given directed graph with weights on edges. Due to its NP-hardness, the theoretical study of algorithms for ATSP has focused on approximation algorithms: ones that are provably both efficient and give solutions competitive with the optimum. Specifically, a rho-approximation algorithm for ATSP is one that runs in polynomial time and always outputs a tour that is at most rho times longer than the shortest tour. Finding such an approximation algorithm with rho bounded (i.e., a constant factor) had been a long-standing open problem. In this thesis, we give such an algorithm. Our approximation guarantee is analyzed with respect to the standard linear programming relaxation, and thus our result also confirms the conjectured constant integrality gap of that relaxation. Our techniques build upon the constant-factor approximation algorithm for the special case of node-weighted metrics due to Svensson. In particular, we give a generic reduction to structured instances that resemble but are more general than those arising from node-weighted metrics. This reduction takes advantage of a laminar family of vertex sets that arises from the linear programming relaxation. In the second part of the thesis we address the perfect matching problem. The first polynomial-time algorithm for it, given by Edmonds in 1965, is historically associated with the introduction of the class P and our notion that ``polynomial-time'' means ``efficient''. That algorithm is sequential and deterministic. We have also known since the 1980s that the matching problem has efficient parallel algorithms if the use of randomness is allowed. Formally, it is in the class RNC, i.e., it has randomized algorithms that use polynomially many processors and run in polylogarithmic time. However, we do not know if randomness is necessary - that is, whether the matching problem is in the class NC. In this thesis we show that the matching problem is in quasi-NC. That is, we give a deterministic parallel algorithm that runs in O(log^3 n) time on n^{O(log^2 n)} processors. The result is obtained by a derandomization of the Isolation Lemma for perfect matchings, which was introduced in the classic paper by Mulmuley, Vazirani and Vazirani to obtain an RNC algorithm. Our proof extends the framework of Fenner, Gurjar and Thierauf, who proved the analogous result in the special case of bipartite graphs. Compared to that setting, several new ingredients are needed due to the significantly more complex structure of perfect matchings in general graphs. In particular, our proof heavily relies on the laminar structure of the faces of the perfect matching polytope

多様なポストゲノムデータのためのアラインメントフリーなアルゴリズムの構造

学位の種別: 課程博士審査委員会委員 : （主査）東京大学教授 今井 浩, 東京大学教授 小林 直樹, 東京大学教授 五十嵐 健夫, 東京大学教授 杉山 将, 東京大学講師 笠原 雅弘University of Tokyo(東京大学

Engineering Adaptive Model-Driven User Interfaces for Enterprise Applications

Enterprise applications such as enterprise resource planning systems have numerous complex user interfaces (UIs). Usability problems plague these UIs because they are offered as a generic off-the-shelf solution to end-users with diverse needs in terms of their required features and layout preferences. Adaptive UIs can help in improving usability by tailoring the features and layout based on the context-of-use. The model-driven UI development approach offers the possibility of applying different types of adaptations on the various UI levels of abstraction. This approach forms the basis for many works researching the development of adaptive UIs. Yet, several gaps were identified in the state-of-the-art adaptive model-driven UI development systems. To fill these gaps, this thesis presents an approach that offers the following novel contributions: - The Cedar Architecture serves as a reference for developing adaptive model-driven enterprise application user interfaces. - Role-Based User Interface Simplification (RBUIS) is a mechanism for improving usability through adaptive behavior, by providing end-users with a minimal feature-set and an optimal layout based on the context-of-use. - Cedar Studio is an integrated development environment, which provides tool support for building adaptive model-driven enterprise application UIs using RBUIS based on the Cedar Architecture. The contributions were evaluated from the technical and human perspectives. Several metrics were established and applied to measure the technical characteristics of the proposed approach after integrating it into an open-source enterprise application. Additional insights about the approach were obtained through the opinions of industry experts and data from real-life projects. Usability studies showed the approach’s ability to significantly improve usability in terms of end-user efficiency, effectiveness and satisfaction

Programming Languages and Systems

This open access book constitutes the proceedings of the 29th European Symposium on Programming, ESOP 2020, which was planned to take place in Dublin, Ireland, in April 2020, as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2020. The actual ETAPS 2020 meeting was postponed due to the Corona pandemic. The papers deal with fundamental issues in the specification, design, analysis, and implementation of programming languages and systems

The HBP1 tumor suppressor is a negative epigenetic regulator of MYCN driven neuroblastoma through interaction with the PRC2 complex

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