IA Scholar Query: A Clause String DNA Algorithm for SAT.
https://scholar.archive.org/
Internet Archive Scholar query results feedeninfo@archive.orgThu, 22 Sep 2022 00:00:00 GMTfatcat-scholarhttps://scholar.archive.org/help1440Subsequences in Bounded Ranges: Matching and Analysis Problems
https://scholar.archive.org/work/kazqifkclbhplc4c5wne73iatu
In this paper, we consider a variant of the classical algorithmic problem of checking whether a given word v is a subsequence of another word w. More precisely, we consider the problem of deciding, given a number p (defining a range-bound) and two words v and w, whether there exists a factor w[i:i+p-1] (or, in other words, a range of length p) of w having v as subsequence (i. e., v occurs as a subsequence in the bounded range w[i:i+p-1]). We give matching upper and lower quadratic bounds for the time complexity of this problem. Further, we consider a series of algorithmic problems in this setting, in which, for given integers k, p and a word w, we analyse the set p-Subseq_k(w) of all words of length k which occur as subsequence of some factor of length p of w. Among these, we consider the k-universality problem, the k-equivalence problem, as well as problems related to absent subsequences. Surprisingly, unlike the case of the classical model of subsequences in words where such problems have efficient solutions in general, we show that most of these problems become intractable in the new setting when subsequences in bounded ranges are considered. Finally, we provide an example of how some of our results can be applied to subsequence matching problems for circular words.Maria Kosche, Tore Koß, Florin Manea, Viktoriya Pakwork_kazqifkclbhplc4c5wne73iatuThu, 22 Sep 2022 00:00:00 GMTA Parallel DNA Algorithm for Solving the Quota Traveling Salesman Problem Based on Biocomputing Model
https://scholar.archive.org/work/vg37fyolhffovek43d77ncfcpy
The quota traveling salesman problem (QTSP) is a variant of the traveling salesman problem (TSP), which is a classical optimization problem. In the QTSP, the salesman visits some of the n cities to meet a given sales quota Q while having minimized travel costs. In this paper, we develop a DNA algorithm based on Adleman-Lipton model to solve the quota traveling salesman problem. Its time complexity is O n 2 + Q , which is a significant improvement over previous algorithms with exponential complexity. A coding scheme of element information is pointed out, and a reasonable biological algorithm is raised by using limited conditions, whose feasibility is verified by simulation experiments. The innovation of this study is to propose a polynomial time complexity algorithm to solve the QTSP. This advantage will become more obvious as the problem scale increases compared with the algorithm of exponential computational complexity. The proposed DNA algorithm also has the significant advantages of having a large storage capacity and consuming less energy during the operation. With the maturity of DNA manipulation technology, DNA computing, as one of the parallel biological computing methods, has the potential to solve more complex NP-hard problems.Zhaocai Wang, Xian Wu, Tunhua Wu, Mario Versaciwork_vg37fyolhffovek43d77ncfcpyWed, 31 Aug 2022 00:00:00 GMTDissecting the Campylobacter jejuni flagellar motor using subtomogram averaging and rationally designed protein chimeras
https://scholar.archive.org/work/6b63bi2kyvhrjel4wsrz5tf6gi
Bacterial cells must traverse a variety of environments to survive and thrive. To achieve motility, they have evolved the bacterial flagella motor. This complex proteinacious nano-machine is composed of up to 25 different proteins, which assemble together in a range of stoichiometries across multiple membranes. They are able to harness the flux of ions across inner membrane bound stators, to kick a cytoplasmic C-ring, thus generating torque. Rotational torque is then transmitted through the periplasmic axle, which can be augmented by additional protein scaffolds, to the external hook and filament, propelling the cell forwards. Through developments of in situ Electron Cryo-Tomography (ECT), increased structural complexity in the motors of species such as Campylobacter jejuni have been explored to nanometer resolutions. This has revealed additional, intricate complexes which enable increased base and novel functions. Using the C. Jejuni motor as a model, I have applied and developed a number of methods to study its complexity, in hopes of understanding the structures of functional proteinacious nanomachines in their native context. By dissecting the in situ structure of the cytoplasmic C. jejuni C-ring, I have revealed the domain placements of FliG C terminal, FliM, FliN and FliY. Combining this with phylogenetic and operon analysis, I have also explored the evolved structural role of FliNY intercalation at the distal tip of the C-ring, revealing the greater role FliY plays in the structural anchoring of the ATPase complex to the C-ring in C. jejuni. Furthermore, I've characterised a previously unknown component of the periplasmic scaffold dubbed Mot1, which acts as a stabilising outer brace by anchoring the proximal and sub-basal disks. To overcome the resolution limitations of ECT, which prevent unambiguous identification of protein components in nano-machines, I've developed software which identifies protein chains to insert into macromolecules without disrupting tertiary or quaternary structure to act as electr [...]Louie Derek Henderson, Morgan Beeby, Martin Buck, Biotechnology And Biological Sciences Research Council (Great Britain)work_6b63bi2kyvhrjel4wsrz5tf6giThu, 30 Jun 2022 00:00:00 GMTProceedings of the 2022 Joint Workshop of the German Research Training Groups in Computer Science
https://scholar.archive.org/work/lvykkw5kcfhlvolc6paa2sxczu
Having spent two successive years running online to prevent the spread of the Corona virus, the traditional annual meeting of the German Research Training Groups (RTGs) funded by the Deutsche Forschungsgemeinschaft (DFG) in the field of computer science returns to Schloss Dagstuhl --– Leibniz Center for Informatics, one of the world's premier venues for computer science-related seminars. Returning to Dagstuhl and hosting this meeting as an in-person-only event was a deliberate decision to revive interaction modes that many of the funded researchers had yet to experience: fostering personal interchange of ideas and experiences in order to strengthen the connection within the German computer science community. This volume documents the abstracts of the research topics of funded researchers in the participating RTGs. The event was jointly organized by RTG 2475 (Cybercrime and Forensic Computing) and RTG 2428 (ConVeY --- Continuous Verification of Cyber-Physical Systems). It took place between Sunday, June 12 and Wednesday, June 15, 2022, as in-person only Dagstuhl Event 22243. The meeting featured the usual sequence of research presentations by funded researchers, networking meetings for PIs and RTG coordinators, as well as two invited talks, one by Professor Martina Seidl (JKU Linz, Austria) on "Competitions as Scientific Method" and another by Professor Jennifer Byrne (School of Medical Sciences, The University of Sydney, Australia) titled "An introduction to research paper mills". Because last year's event marked the 25th anniversary of the workshop series, it featured a live interview with Professor Otto Spaniol who had initiated the workshop series in 1996. We document the interview in this volume.Felix Freiling, Helmut Seidl, 2022 2022 Joint Workshop Of The German Research Training Groups In Computer Science June 12–June 15work_lvykkw5kcfhlvolc6paa2sxczuTue, 17 May 2022 00:00:00 GMTComplexity of Verification in Self-Assembly with Prebuilt Assemblies
https://scholar.archive.org/work/g5rcfian35cl3o3nz5qkibqo5a
We analyze the complexity of two fundamental verification problems within a generalization of the two-handed tile self-assembly model (2HAM) where initial system assemblies are not restricted to be singleton tiles, but may be larger pre-built assemblies. Within this model we consider the producibility problem, which asks if a given tile system builds, or produces, a given assembly, and the unique assembly verification (UAV) problem, which asks if a given system uniquely produces a given assembly. We show that producibility is NP-complete and UAV is coNP^{NP}-complete even when the initial assembly size and temperature threshold are both bounded by a constant. This is in stark contrast to results in the standard model with singleton input tiles where producibility is in P and UAV is in coNP for 𝒪(1) bounded temperature and coNP-complete when temperature is part of the input. We further provide preliminary results for producibility and UAV in the case of 1-dimensional linear assemblies with pre-built assemblies, and provide polynomial time solutions.David Caballero, Timothy Gomez, Robert Schweller, Tim Wylie, James Aspnes, Othon Michailwork_g5rcfian35cl3o3nz5qkibqo5aFri, 29 Apr 2022 00:00:00 GMTCulture^2
https://scholar.archive.org/work/uwh3yj6c6bge7gsl34qzymfc7a
How to do cultural studies in the twenty-first century? This essay collection is not a handbook, encyclopedia, or a »state of the field« compendium. Instead, it is a reflexive exercise in cultural studies, featuring fifteen accessible essays on a selection of critical key works published since 2000. The contributors aim to provide readers with a fresh and engaging look at recent criticism, exploring the interdisciplinary traffic of theories, methods, and ideas within the field of cultural and literary studies. This book shows how the work of Lauren Berlant, Rita Felski, Fred Moten, Anna Tsing, and others can inspire new thinking and theorizing for the twenty-first century.(:Unkn) Unknown, Universitätsbibliothek Der FU Berlin, Frank Kelleter, Alexander Starrework_uwh3yj6c6bge7gsl34qzymfc7aWed, 23 Mar 2022 00:00:00 GMT0027 | Collections of US
https://scholar.archive.org/work/lurzlmhse5egzjqpjm3liugkia
The kind of use the objective pronoun "us" to use the words in the framework of getting results. This style gives us many meaning and they are metaphor to every directions of words. The discussion of words are about two people which one of them is physically present but another person is virtually present in the terms of words. The kinds of words give the ways to live in the formations of words which record attendance of two people in the formation of virtuality and physically. Words go to make shock to make them to be back to the life but only in the terms of words and usages of words. This book come from the collections of books which follow same style but the difference is about the title of the contents. Words go to make shock to make them to be back to the life but only in the terms of words and usages of words. This book come from the collections of books which follow same style but the difference is about the title of the contents.Henry Garrettwork_lurzlmhse5egzjqpjm3liugkiaTue, 01 Mar 2022 00:00:00 GMTIntroduction
https://scholar.archive.org/work/26mhete3wvaxxcvhewvghyehpa
Contents Acknowledgements vii Foreword ix Part One 1.1 Welcome to the world of academic publishing 1.2 What exactly is open access anyway? A note on licensing 1.3 Why OA? Reason 1: It's the principle Reason 2: It makes economic sense Reason 3: It makes research more accessible -which benefits society Reason 4: Open access makes the research process faster and more efficient Reason 5: Open access improves the quality and trustability of research Reason 6: It's in the public interest Reason 7: It makes research more inclusive Reason 8: It allows for inclusiveness and connectivity Reason 9: It helps the Global South Reason 10: Academic research was always intended to be open 1.4 Academic publishing: a brief history History repeating Publishing becomes big business 1.5 The internet and OA: the early pioneers The European campaign A new era for academic publishing 1.6 The Wellcome Trust and Gates Foundation pave the way for OA 1.7 The Finch Report: taking OA to a political level 1.8 Brussels gets involved; the momentum picks up 1.9 Slow progress: the move towards OA stagnates Reason 1: Big business, big financial interests and demanding shareholders Hybrids: a halfway house Reason 2: Obsession with 'impact factor' Reason 3: Lip service to DORA Reason 4: Resistance to change; reluctance to take action 1.10 Time for a radical intervention Part Two 2.1 The open access envoy 2.2 Forming a plan 2.3 The impact on smaller publishers 2.4 Warning bells 2.5 Gaining allies 2.6 The European tour 2.7 Support arrives from the universities 2.8 Gaining support from the younger generation of researchers 2.9 Compromises, compromises 2.10 The Coalition is born for others it was the painful task of digging through documents from several years ago to provide sources, figures or background information. Thank you for your valuable insights and patience. All the publishers mentioned in the text were contacted with a request for an interview and given the right to respond to content. A special thanks to those who chose to respond. We would especially like to thank Frederick Fenter, Lia Noce, Agata Zaza and the rest of the team at Frontiers, without whom this book would not have been possible. Frontiers paid for Rachael's time spent writing the book, but had no influence over its content or editorial direction. Finally, this book was written with the intention of prompting debate as part of the continuing conversations happening around open access, and we welcome readers' comments and observations.Robert-Jan Smits, Rachael Pellswork_26mhete3wvaxxcvhewvghyehpaThu, 27 Jan 2022 00:00:00 GMTAmsellem_columbia_0054D_17252.pdf
https://scholar.archive.org/work/tcuxond7bzbbbjee7qyej4pwdm
Sound and Surveillance: The Making of the Neoliberal Ear Audrey Amsellem This dissertation is on sonic surveillance in the neoliberal context and its implication for privacy, agency, sovereignty, ownership and control. This research focuses on the social, political and ethical conceptions of privacy through musical consumption and sonic practices in the United States. I investigate non-creative recording practices in neoliberal life and identify the listening practices of surveillance capitalism to better understand how power circulates through sound. Through a multi-sited ethnography, I conduct three case studies on the recording and listening capacity of technological devices of everyday life in order to theorize what I term "the neoliberal ear"a twenty-first century mode of listening to the world embedded into surveillance capitalism. I analyze three sonic tools of surveillance capitalism: streaming service Spotify, Smart Home device Amazon Echo, and Smart City communication hub LinkNYC. These technologies, I argue, embody and promote neoliberal ideology, and the companies that produces them operate within a neoliberal mode of governance allowed by public policies. This dissertation is interdisciplinary in scope and operates at theoretical crossings of sound and power, technology and cultural practices, and disciplinary crossings of music, law and computer science. I draw from, and build connections between; sound studies, ethnomusicology, legal literature and scholarship on copyright and privacy, surveillance studies, science and technology studies, and discourses on AI and ethics, to form theories of sound and power in surveillance capitalism. i Table of Contents List of Charts, Graphs, Illustrations ........................................................................iv Acknowledgments.............................................................................................v Dedication....................................................................................................xiii I could never properly express the debt I have towards my family, friends, peers and mentors throughout the lengthy, beautiful and challenging process of writing this dissertation. My first thoughts go to Aaron Fox, who has taught me more than he will ever know. Of course, he has taught me to be a better thinker, writer, and academic. But mostly he has taught me how to be a better person, to lead with kindness, and to keep the sense of community at the center of my life. Everyone feels welcomed in Aaron's office, no person is too little or too dim. This is what I felt when I walked into his office sometime in 2014, then an undergrad with an interest in the politics of music circulation. When I brought up my project, his first response was: "Ok, but I'm not interested in advising people who will go on to work in the music business," "Oh, yeah I'm interested in investigating communist models of distributions," I replied. He nodded and we were instant friends. Since then, I've been in this office over and over again, for the better part of 7 years, where he has shared with extraordinary generosity, his advice, intellect and experience. rooftops across continents; as well as Sonja Wermager, Mary Stoumbos, Callum Blackmore,:unavwork_tcuxond7bzbbbjee7qyej4pwdmAstronomy and Literature | Canon and Stylometrics
https://scholar.archive.org/work/wv5jqcyafvhtjk4oi2ete2bxqm
This eighth issue of Interfaces contains two thematic clusters: the first cluster, entitled The Astronomical Imagination in Literature through the Ages, is edited by Dale Kedwards; the second cluster, entitled Medieval Authorship and Canonicity in the Digital Age, is edited by Jeroen De Gussem and Jeroen Deploige.Dale Kedwards, Tom McLeish, Mary Garrison, Divna Manolova, Victoria Flood, Matthew Francis, Jeroen Deploige, Jeroen De Gussem, Mary Dockray-Miller, Michael D.C. Drout, Sarah Kinkade, Jillian Valerio, Eveline Leclercq, Mike Kestemont, Gustavo Fernández Rivawork_wv5jqcyafvhtjk4oi2ete2bxqmFri, 31 Dec 2021 00:00:00 GMTA Christmas Chrestomathy
https://scholar.archive.org/work/xrctaaruuvbrxdisdrsumatkly
As the year draws to a close, the editors are delighted to present our second annual Christmas Chrestomathy, highlighting the essays that best represent our aims, ambitions, attitudes, and even our animadversions. As it turned out, 2021 was a milestone year for the journal with the launch of a new website, the switch to a rolling publication schedule, and the debut of a new section: The Rambler.The Editorswork_xrctaaruuvbrxdisdrsumatklyThu, 23 Dec 2021 00:00:00 GMTHow Compression and Approximation Affect Efficiency in String Distance Measures
https://scholar.archive.org/work/mtn3py5l3jektet6d4cfeammaq
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to quantify the gain in time complexity when the underlying data is highly compressible. We consider grammar compression, which unifies many practically relevant compression schemes. For two strings of total length N and total compressed size n, it is known that the edit distance and a longest common subsequence (LCS) can be computed exactly in time Õ(nN), as opposed to O(N^2) for the uncompressed setting. Many applications need to align multiple sequences simultaneously, and the fastest known exact algorithms for median edit distance and LCS of k strings run in O(N^k) time. This naturally raises the question of whether compression can help to reduce the running time significantly for k ≥ 3, perhaps to O(N^k/2n^k/2) or O(Nn^k-1). Unfortunately, we show lower bounds that rule out any improvement beyond Ω(N^k-1n) time for any of these problems assuming the Strong Exponential Time Hypothesis. At the same time, we show that approximation and compression together can be surprisingly effective. We develop an Õ(N^k/2n^k/2)-time FPTAS for the median edit distance of k sequences. In comparison, no O(N^k-Ω(1))-time PTAS is known for the median edit distance problem in the uncompressed setting. For two strings, we get an Õ(N^2/3n^4/3)-time FPTAS for both edit distance and LCS. In contrast, for uncompressed strings, there is not even a subquadratic algorithm for LCS that has less than a polynomial gap in the approximation factor. Building on the insight from our approximation algorithms, we also obtain results for many distance measures including the edit, Hamming, and shift distances.Arun Ganesh, Tomasz Kociumaka, Andrea Lincoln, Barna Sahawork_mtn3py5l3jektet6d4cfeammaqFri, 10 Dec 2021 00:00:00 GMTApproximating the Center Ranking Under Ulam
https://scholar.archive.org/work/lo2qbu5vmreubcsqaqiza5x3cq
We study the problem of approximating a center under the Ulam metric. The Ulam metric, defined over a set of permutations over [n], is the minimum number of move operations (deletion plus insertion) to transform one permutation into another. The Ulam metric is a simpler variant of the general edit distance metric. It provides a measure of dissimilarity over a set of rankings/permutations. In the center problem, given a set of permutations, we are asked to find a permutation (not necessarily from the input set) that minimizes the maximum distance to the input permutations. This problem is also referred to as maximum rank aggregation under Ulam. So far, we only know of a folklore 2-approximation algorithm for this NP-hard problem. Even for constantly many permutations, we do not know anything better than an exhaustive search over all n! permutations. In this paper, we achieve a (3/2 - 1/(3m))-approximation of the Ulam center in time n^O(m² ln m), for m input permutations over [n]. We therefore get a polynomial time bound while achieving better than a 3/2-approximation for constantly many permutations. This problem is of special interest even for constantly many permutations because under certain dissimilarity measures over rankings, even for four permutations, the problem is NP-hard. In proving our result, we establish a surprising connection between the approximate Ulam center problem and the closest string with wildcards problem (the center problem over the Hamming metric, allowing wildcards). We further study the closest string with wildcards problem and show that there cannot exist any (2-ε)-approximation algorithm (for any ε > 0) for it unless 𝖯 = NP. This inapproximability result is in sharp contrast with the same problem without wildcards, where we know of a PTAS.Diptarka Chakraborty, Kshitij Gajjar, Agastya Vibhuti Jha, Mikołaj Bojańczyk, Chandra Chekuriwork_lo2qbu5vmreubcsqaqiza5x3cqMon, 29 Nov 2021 00:00:00 GMTThe Complexity of Aggregates over Extractions by Regular Expressions
https://scholar.archive.org/work/ibzqt3aduzen3orhy64t6rk3gi
Regular expressions with capture variables, also known as regex-formulas, extract relations of spans (intervals identified by their start and end indices) from text. In turn, the class of regular document spanners is the closure of the regex formulas under the Relational Algebra. We investigate the computational complexity of querying text by aggregate functions, such as sum, average, and quantile, on top of regular document spanners. To this end, we formally define aggregate functions over regular document spanners and analyze the computational complexity of exact and approximate computation. More precisely, we show that in a restricted case, all studied aggregate functions can be computed in polynomial time. In general, however, even though exact computation is intractable, some aggregates can still be approximated with fully polynomial-time randomized approximation schemes (FPRAS).Johannes Doleschal, Benny Kimelfeld, Wim Martenswork_ibzqt3aduzen3orhy64t6rk3giThu, 28 Oct 2021 00:00:00 GMTIntroduction to Neural Network Verification
https://scholar.archive.org/work/m67g5mhpazcyzcapmjwmvofliy
Deep learning has transformed the way we think of software and what it can do. But deep neural networks are fragile and their behaviors are often surprising. In many settings, we need to provide formal guarantees on the safety, security, correctness, or robustness of neural networks. This book covers foundational ideas from formal verification and their adaptation to reasoning about neural networks and deep learning.Aws Albarghouthiwork_m67g5mhpazcyzcapmjwmvofliyMon, 04 Oct 2021 00:00:00 GMT