On Conceptually Simple Algorithms for Variants of Online Bipartite Matching

We present a series of results regarding conceptually simple algorithms for bipartite matching in various online and related models. We first consider a deterministic adversarial model. The best approximation ratio possible for a one-pass deterministic online algorithm is $1/2$, which is achieved by any greedy algorithm. D\"urr et al. recently presented a $2$-pass algorithm called Category-Advice that achieves approximation ratio $3/5$. We extend their algorithm to multiple passes. We prove the exact approximation ratio for the $k$-pass Category-Advice algorithm for all $k \ge 1$, and show that the approximation ratio converges to the inverse of the golden ratio $2/(1+\sqrt{5}) \approx 0.618$ as $k$ goes to infinity. The convergence is extremely fast --- the $5$-pass Category-Advice algorithm is already within $0.01\%$ of the inverse of the golden ratio. We then consider a natural greedy algorithm in the online stochastic IID model---MinDegree. This algorithm is an online version of a well-known and extensively studied offline algorithm MinGreedy. We show that MinDegree cannot achieve an approximation ratio better than $1-1/e$, which is guaranteed by any consistent greedy algorithm in the known IID model. Finally, following the work in Besser and Poloczek, we depart from an adversarial or stochastic ordering and investigate a natural randomized algorithm (MinRanking) in the priority model. Although the priority model allows the algorithm to choose the input ordering in a general but well defined way, this natural algorithm cannot obtain the approximation of the Ranking algorithm in the ROM model

LIPIcs, Volume 244, ESA 2022, Complete Volume

LIPIcs, Volume 244, ESA 2022, Complete Volum

Proceedings of the Fifth European Workshop on Probabilistic Graphical Models

Peer reviewe

Circuit Design

Circuit Design = Science + Art! Designers need a skilled "gut feeling" about circuits and related analytical techniques, plus creativity, to solve all problems and to adhere to the specifications, the written and the unwritten ones. You must anticipate a large number of influences, like temperature effects, supply voltages changes, offset voltages, layout parasitics, and numerous kinds of technology variations to end up with a circuit that works. This is challenging for analog, custom-digital, mixed-signal or RF circuits, and often researching new design methods in relevant journals, conference proceedings and design tools unfortunately gives the impression that just a "wild bunch" of "advanced techniques" exist. On the other hand, state-of-the-art tools nowadays indeed offer a good cockpit to steer the design flow, which include clever statistical methods and optimization techniques.Actually, this almost presents a second breakthrough, like the introduction of circuit simulators 40 years ago! Users can now conveniently analyse all the problems (discover, quantify, verify), and even exploit them, for example for optimization purposes. Most designers are caught up on everyday problems, so we fit that "wild bunch" into a systematic approach for variation-aware design, a designer's field guide and more. That is where this book can help! Circuit Design: Anticipate, Analyze, Exploit Variations starts with best-practise manual methods and links them tightly to up-to-date automation algorithms. We provide many tractable examples and explain key techniques you have to know. We then enable you to select and setup suitable methods for each design task - knowing their prerequisites, advantages and, as too often overlooked, their limitations as well. The good thing with computers is that you yourself can often verify amazing things with little effort, and you can use software not only to your direct advantage in solving a specific problem, but also for becoming a better skilled, more experienced engineer. Unfortunately, EDA design environments are not good at all to learn about advanced numerics. So with this book we also provide two apps for learning about statistic and optimization directly with circuit-related examples, and in real-time so without the long simulation times. This helps to develop a healthy statistical gut feeling for circuit design. The book is written for engineers, students in engineering and CAD / methodology experts. Readers should have some background in standard design techniques like entering a design in a schematic capture and simulating it, and also know about major technology aspects

Circuit Design

Circuit Design = Science + Art! Designers need a skilled "gut feeling" about circuits and related analytical techniques, plus creativity, to solve all problems and to adhere to the specifications, the written and the unwritten ones. You must anticipate a large number of influences, like temperature effects, supply voltages changes, offset voltages, layout parasitics, and numerous kinds of technology variations to end up with a circuit that works. This is challenging for analog, custom-digital, mixed-signal or RF circuits, and often researching new design methods in relevant journals, conference proceedings and design tools unfortunately gives the impression that just a "wild bunch" of "advanced techniques" exist. On the other hand, state-of-the-art tools nowadays indeed offer a good cockpit to steer the design flow, which include clever statistical methods and optimization techniques.Actually, this almost presents a second breakthrough, like the introduction of circuit simulators 40 years ago! Users can now conveniently analyse all the problems (discover, quantify, verify), and even exploit them, for example for optimization purposes. Most designers are caught up on everyday problems, so we fit that "wild bunch" into a systematic approach for variation-aware design, a designer's field guide and more. That is where this book can help! Circuit Design: Anticipate, Analyze, Exploit Variations starts with best-practise manual methods and links them tightly to up-to-date automation algorithms. We provide many tractable examples and explain key techniques you have to know. We then enable you to select and setup suitable methods for each design task - knowing their prerequisites, advantages and, as too often overlooked, their limitations as well. The good thing with computers is that you yourself can often verify amazing things with little effort, and you can use software not only to your direct advantage in solving a specific problem, but also for becoming a better skilled, more experienced engineer. Unfortunately, EDA design environments are not good at all to learn about advanced numerics. So with this book we also provide two apps for learning about statistic and optimization directly with circuit-related examples, and in real-time so without the long simulation times. This helps to develop a healthy statistical gut feeling for circuit design. The book is written for engineers, students in engineering and CAD / methodology experts. Readers should have some background in standard design techniques like entering a design in a schematic capture and simulating it, and also know about major technology aspects

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Computational analysis of transcriptional and post-transcriptional regulation of gene expression

The regulation of gene expression is fundamental to all life on Earth. Dynamic but precise control is vital to cell survival and function, and takes place at various tightly interwoven levels. In this thesis, we review and study the crosstalk between different types of regulators, including epigenetic regulators, transcription factors (TFs), RNA-binding proteins (RBPs) and microRNAs (miRNAs). First, we focus on the interplay between miRNAs and other types of regulators, in particular TFs and epigenetic regulators, both of which are strongly enriched among the predicted targets of miRNAs. Indeed, the direct interplay of miRNAs with other regulators that have genome-wide impact is one possible explanation for the reported importance of miRNAs to fundamental biological processes, including cell fate. We introduce a computational strategy that we apply in order to infer the transcription regulatory circuitries that act downstream of embryonic miRNAs. More precisely, we analyze genome-wide expression changes with an extended motif activity response analysis (MARA) model in order to identify transcriptional regulators that are direct targets of embryonic miRNAs and change in activity upon expression of the miRNAs. We experimentally validate our most promising predictions and integrate the extended MARA model into an automated system in order to make it available to other researchers. We demonstrate its application by modeling diverse high-throughput datasets, including paired liver biopsies of patients with chronic hepatitis C virus infections. Finally, we study alternative cleavage and polyadenylation, a process that impacts gene expression in various ways, including modulating the presence of cis-regulatory elements, such as miRNA and RBP binding sites, which tend to be located at the 3' ends of transcripts. We demonstrate that global shortening of untranslated transcript regions, which is associated with proliferative states, has a very limited effect on mRNA stability and protein output. By analyzing a large array of high-throughput 3' end sequencing data, we create comprehensive catalogs of 3' end processing sites for both human and mouse. Moreover, we identify novel cis-regulatory motifs that are involved in cleavage and polyadenylation, and point out a regulator, HNRNPC, that binds to one of the motifs, thereby globally impacting the usage of cleavage and polyadenylation sites