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In recent years, free energy perturbation (FEP) calculations have garnered increasing attention as tools to support drug discovery. The lead optimization mapper (Lomap) was proposed as an algorithm to calculate the relative free energy…

Biomolecules · Quantitative Biology 2023-04-11 Kairi Furui , Masahito Ohue

We introduce a family of reductions for removing proper and homogeneous pairs of cliques from a graph G. This family generalizes some routines presented in the literature, mostly in the context of claw-free graphs. These reductions can be…

Optimization and Control · Mathematics 2011-03-15 Yuri Faenza , Gianpaolo Oriolo , Claudia Snels

Symmetry breaking for graphs and other combinatorial objects is notoriously hard. On the one hand, complete symmetry breaks are exponential in size. On the other hand, current, state-of-the-art, partial symmetry breaks are often considered…

Logic in Computer Science · Computer Science 2026-04-01 Michael Codish , Mikoláš Janota

We derive bounds on the sample complexity of empirical risk minimization (ERM) in the context of minimizing non-convex risks that admit the strict saddle property. Recent progress in non-convex optimization has yielded efficient algorithms…

Machine Learning · Computer Science 2017-06-06 Alon Gonen , Shai Shalev-Shwartz

In a recent breakthrough, Kelley and Meka (FOCS 2023) obtained a strong upper bound on the density of sets of integers without nontrivial three-term arithmetic progressions. In this work, we extend their result, establishing similar bounds…

Combinatorics · Mathematics 2025-02-13 Yuval Filmus , Hamed Hatami , Kaave Hosseini , Esty Kelman

We study the parabolic free boundary problem of obstacle type $$ \lap u-\frac{\partial u}{\partial t}= f\chi_{{u\ne 0}}. $$ Under the condition that $f=Hv$ for some function $v$ with bounded second order spatial derivatives and bounded…

Analysis of PDEs · Mathematics 2012-10-11 John Andersson , Erik Lindgren , Henrik Shahgholian

Paul Erd\H{o}s suggested the following problem: Determine or estimate the number of maximal triangle-free graphs on $n$ vertices. Here we show that the number of maximal triangle-free graphs is at most $2^{n^2/8+o(n^2)}$, which matches the…

Combinatorics · Mathematics 2014-09-30 József Balogh , Šárka Petříčková

We give a proof of Szemeredi's regularity lemma in the special case of a graph with bounded VC dimension and show that it is possible to obtain "merely" doubly exponential bounds on the size of the partition in this case.

Combinatorics · Mathematics 2013-04-24 Henry Towsner

Fracture produces new mesh fragments that introduce additional degrees of freedom in the system dynamics. Existing finite element method (FEM) based solutions suffer from an explosion in computational cost as the system matrix size…

Graphics · Computer Science 2024-08-19 Avirup Mandal , Parag Chaudhuri , Subhasis Chaudhuri

Listing all triangles is a fundamental graph operation. Triangles can have important interpretations in real-world graphs, especially social and other interaction networks. Despite the lack of provably efficient (linear, or slightly…

Social and Information Networks · Computer Science 2014-07-07 Jonathan W. Berry , Luke A. Fostvedt , Daniel J. Nordman , Cynthia A. Phillips , C. Seshadhri , Alyson G. Wilson

In deriving their characterization of the perfect matchings polytope, Edmonds, Lov\'asz, and Pulleyblank introduced the so-called {\em Tight Cut Lemma} as the most challenging aspect of their work. The Tight Cut Lemma in fact claims {\em…

Combinatorics · Mathematics 2015-12-31 Nanao Kita

To enumerate 3-manifold triangulations with a given property, one typically begins with a set of potential face pairing graphs (also known as dual 1-skeletons), and then attempts to flesh each graph out into full triangulations using an…

Geometric Topology · Mathematics 2014-07-25 Benjamin A. Burton , William Pettersson

We present a new technique for efficiently removing almost all short cycles in a graph without unintentionally removing its triangles. Consequently, triangle finding problems do not become easy even in almost $k$-cycle free graphs, for any…

Data Structures and Algorithms · Computer Science 2022-10-18 Amir Abboud , Karl Bringmann , Seri Khoury , Or Zamir

The fundamental theorem of Tur\'{a}n from Extremal Graph Theory determines the exact bound on the number of edges $t_r(n)$ in an $n$-vertex graph that does not contain a clique of size $r+1$. We establish an interesting link between…

Data Structures and Algorithms · Computer Science 2023-07-17 Fedor V. Fomin , Petr A. Golovach , Danil Sagunov , Kirill Simonov

We consider the fundamental algorithmic problem of finding a cycle of minimum weight in a weighted graph. In particular, we show that the minimum weight cycle problem in an undirected n-node graph with edge weights in {1,...,M} or in a…

Data Structures and Algorithms · Computer Science 2011-04-15 Liam Roditty , Virginia Vassilevska Williams

The classical sharp threshold theorem of Friedgut and Kalai (1996) asserts that any symmetric monotone function $f:\{0,1\}^{n}\to\{0,1\}$ exhibits a sharp threshold phenomenon. This means that the expectation of $f$ with respect to the…

Combinatorics · Mathematics 2020-08-05 Noam Lifshitz

In the Block Graph Deletion problem, we are given a graph $G$ on $n$ vertices and a positive integer $k$, and the objective is to check whether it is possible to delete at most $k$ vertices from $G$ to make it a block graph, i.e., a graph…

Data Structures and Algorithms · Computer Science 2016-01-18 Eun Jung Kim , O-joung Kwon

We prove algorithmic weak and \Szemeredi{} regularity lemmas for several classes of sparse graphs in the literature, for which only weak regularity lemmas were previously known. These include core-dense graphs, low threshold rank graphs,…

Data Structures and Algorithms · Computer Science 2025-05-30 Greg Bodwin , Santosh Vempala

We develop a sparse graph regularity method that applies to graphs with few 4-cycles, including new counting and removal lemmas for 5-cycles in such graphs. Some applications include: * Every $n$-vertex graph with no 5-cycle can be made…

Combinatorics · Mathematics 2021-09-28 David Conlon , Jacob Fox , Benny Sudakov , Yufei Zhao

Ajtai, Koml\'os, and Szemer\'edi proved that for sufficiently large $t$ every triangle-free graph with $n$ vertices and average degree $t$ has an independent set of size at least $\frac{n}{100t}\log{t}$. We extend this by proving that the…

Combinatorics · Mathematics 2011-11-17 Jeff Cooper , Dhruv Mubayi
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