Counting connected subgraphs with maximum-degree-aware sieving

Peer reviewe

Determinantal Sieving

We introduce determinantal sieving, a new, remarkably powerful tool in the toolbox of algebraic FPT algorithms. Given a polynomial $P(X)$ on a set of variables $X=\{x_1,\ldots,x_n\}$ and a linear matroid $M=(X,\mathcal{I})$ of rank $k$, both over a field $\mathbb{F}$ of characteristic 2, in $2^k$ evaluations we can sieve for those terms in the monomial expansion of $P$ which are multilinear and whose support is a basis for $M$. Alternatively, using $2^k$ evaluations of $P$ we can sieve for those monomials whose odd support spans $M$. Applying this framework, we improve on a range of algebraic FPT algorithms, such as: 1. Solving $q$-Matroid Intersection in time $O^*(2^{(q-2)k})$ and $q$-Matroid Parity in time $O^*(2^{qk})$, improving on $O^*(4^{qk})$ (Brand and Pratt, ICALP 2021) 2. $T$-Cycle, Colourful $(s,t)$-Path, Colourful $(S,T)$-Linkage in undirected graphs, and the more general Rank $k$ $(S,T)$-Linkage problem, all in $O^*(2^k)$ time, improving on $O^*(2^{k+|S|})$ respectively $O^*(2^{|S|+O(k^2 \log(k+|\mathbb{F}|))})$ (Fomin et al., SODA 2023) 3. Many instances of the Diverse X paradigm, finding a collection of $r$ solutions to a problem with a minimum mutual distance of $d$ in time $O^*(2^{r(r-1)d/2})$, improving solutions for $k$-Distinct Branchings from time $2^{O(k \log k)}$ to $O^*(2^k)$ (Bang-Jensen et al., ESA 2021), and for Diverse Perfect Matchings from $O^*(2^{2^{O(rd)}})$ to $O^*(2^{r^2d/2})$ (Fomin et al., STACS 2021) All matroids are assumed to be represented over a field of characteristic 2. Over general fields, we achieve similar results at the cost of using exponential space by working over the exterior algebra. For a class of arithmetic circuits we call strongly monotone, this is even achieved without any loss of running time. However, the odd support sieving result appears to be specific to working over characteristic 2

Deterministic Subgraph Detection in Broadcast CONGEST

We present simple deterministic algorithms for subgraph finding and enumeration in the broadcast CONGEST model of distributed computation: - For any constant k, detecting k-paths and trees on k nodes can be done in O(1) rounds. - For any constant k, detecting k-cycles and pseudotrees on k nodes can be done in O(n) rounds. - On d-degenerate graphs, cliques and 4-cycles can be enumerated in O(d + log n) rounds, and 5-cycles in O(d2 + log n) rounds. In many cases, these bounds are tight up to logarithmic factors. Moreover, we show that the algorithms for d-degenerate graphs can be improved to O(d/logn) and O(d2/logn), respect- ively, in the supported CONGEST model, which can be seen as an intermediate model between CONGEST and the congested clique

Deterministic subgraph detection in broadcast CONGEST

We present simple deterministic algorithms for subgraph finding and enumeration in the broadcast CONGEST model of distributed computation: For any constant k, detecting k-paths and trees on k nodes can be done in O(1) rounds. For any constant k, detecting k-cycles and pseudotrees on k nodes can be done in O(n) rounds. On d-degenerate graphs, cliques and 4-cycles can be enumerated in O(d+log n) rounds, and 5-cycles in O(d2 + log n) rounds. In many cases, these bounds are tight up to logarithmic factors. Moreover, we show that the algorithms for d-degenerate graphs can be improved to O(d/ log n) and O(d2/log n), respectively, in the supported CONGEST model, which can be seen as an intermediate model between CONGEST and the congested clique. © 2017 Janne H. Korhonen and Joel Rybicki.Peer reviewe

Paths and walks, forests and planes : arcadian algorithms and complexity

This dissertation is concerned with new results in the area of parameterized algorithms and complexity. We develop a new technique for hard graph problems that generalizes and unifies established methods such as Color-Coding, representative families, labelled walks and algebraic fingerprinting. At the heart of the approach lies an algebraic formulation of the problems, which is effected by means of a suitable exterior algebra. This allows us to estimate the number of simple paths of given length in directed graphs faster than before. Additionally, we give fast deterministic algorithms for finding paths of given length if the input graph contains only few of such paths. Moreover, we develop faster deterministic algorithms to find spanning trees with few leaves. We also consider the algebraic foundations of our new method. Additionally, we investigate the fine-grained complexity of determining the precise number of forests with a given number of edges in a given undirected graph. To wit, this happens in two ways. Firstly, we complete the complexity classification of the Tutte plane, assuming the exponential time hypothesis. Secondly, we prove that counting forests with a given number of edges is at least as hard as counting cliques of a given size.Diese Dissertation befasst sich mit neuen Ergebnissen auf dem Gebiet parametrisierter Algorithmen und Komplexitätstheorie. Wir entwickeln eine neue Technik für schwere Graphprobleme, die etablierte Methoden wie Color-Coding, representative families, labelled walks oder algebraic fingerprinting verallgemeinert und vereinheitlicht. Kern der Herangehensweise ist eine algebraische Formulierung der Probleme, die vermittels passender Graßmannalgebren geschieht. Das erlaubt uns, die Anzahl einfacher Pfade gegebener Länge in gerichteten Graphen schneller als bisher zu schätzen. Außerdem geben wir schnelle deterministische Verfahren an, Pfade gegebener Länge zu finden, falls der Eingabegraph nur wenige solche Pfade enthält. Übrigens entwickeln wir schnellere deterministische Algorithmen, um Spannbäume mit wenigen Blättern zu finden. Wir studieren außerdem die algebraischen Grundlagen unserer neuen Methode. Weiters untersuchen wir die fine-grained-Komplexität davon, die genaue Anzahl von Wäldern einer gegebenen Kantenzahl in einem gegebenen ungerichteten Graphen zu bestimmen. Und zwar erfolgt das auf zwei verschiedene Arten. Erstens vervollständigen wir die Komplexitätsklassifizierung der Tutte-Ebene unter Annahme der Expo- nentialzeithypothese. Zweitens beweisen wir, dass Wälder mit gegebener Kantenzahl zu zählen, wenigstens so schwer ist, wie Cliquen gegebener Größe zu zählen.Cluster of Excellence (Multimodal Computing and Interaction

Towards protein function annotations for matching remote homologs

Identifying functional similarities for proteins with low sequence identity and low structure similarity often suffers from high false positives and false negatives results. To improve the functional prediction ability based on the local protein structures, we proposed two different refinement and filtering approaches. We built a statistical model (known as Markov Random Field) to describe protein functional site structure. We also developed filters that consider the local environment around the active sites to remove the false positives. Our experimental results, as evaluated in five sets of enzyme families with less than 40% sequence identity, demonstrated that our methods can obtain more remote homologs that could not be detected by traditional sequence-based methods. At the same time, our method could reduce large amount of random matches. Our methods could improve up to 70% of the functional annotation ability (measured by their Area under the ROC curve) in extended motif method