IA Scholar Query: Satisfiability Coding Lemma.
https://scholar.archive.org/
Internet Archive Scholar query results feedeninfo@archive.orgFri, 30 Sep 2022 00:00:00 GMTfatcat-scholarhttps://scholar.archive.org/help1440Runtime Complexity Bounds Using Squeezers
https://scholar.archive.org/work/rl374t3unrghnc7chpb4a65oie
Determining upper bounds on the time complexity of a program is a fundamental problem with a variety of applications, such as performance debugging, resource certification, and compile-time optimizations. Automated techniques for cost analysis excel at bounding the resource complexity of programs that use integer values and linear arithmetic. Unfortunately, they fall short when the complexity depends more intricately on the evolution of data during execution. In such cases, state-of-the-art analyzers have shown to produce loose bounds, or even no bound at all. We propose a novel technique that generalizes the common notion of recurrence relations based on ranking functions. Existing methods usually unfold one loop iteration and examine the resulting arithmetic relations between variables. These relations assist in establishing a recurrence that bounds the number of loop iterations. We propose a different approach, where we derive recurrences by comparing whole traces with whole traces of a lower rank, avoiding the need to analyze the complexity of intermediate states. We offer a set of global properties, defined with respect to whole traces, that facilitate such a comparison and show that these properties can be checked efficiently using a handful of local conditions. To this end, we adapt state squeezers , an induction mechanism previously used for verifying safety properties. We demonstrate that this technique encompasses the reasoning power of bounded unfolding, and more. We present some seemingly innocuous, yet intricate, examples that previous tools based on cost relations and control flow analysis fail to solve, and that our squeezer-powered approach succeeds.Oren Ish-Shalom, Shachar Itzhaky, Noam Rinetzky, Sharon Shohamwork_rl374t3unrghnc7chpb4a65oieFri, 30 Sep 2022 00:00:00 GMTNested Session Types
https://scholar.archive.org/work/cdzjx4x355eyjn7slpugmdj6di
Session types statically describe communication protocols between concurrent message-passing processes. Unfortunately, parametric polymorphism even in its restricted prenex form is not fully understood in the context of session types. In this article, we present the metatheory of session types extended with prenex polymorphism and, as a result, nested recursive datatypes. Remarkably, we prove that type equality is decidable by exhibiting a reduction to trace equivalence of deterministic first-order grammars. Recognizing the high theoretical complexity of the latter, we also propose a novel type equality algorithm and prove its soundness. We observe that the algorithm is surprisingly efficient and, despite its incompleteness, sufficient for all our examples. We have implemented our ideas by extending the Rast programming language with nested session types. We conclude with several examples illustrating the expressivity of our enhanced type system.Ankush Das, Henry Deyoung, Andreia Mordido, Frank Pfenningwork_cdzjx4x355eyjn7slpugmdj6diFri, 30 Sep 2022 00:00:00 GMTBayesian Topological Learning for Classifying the Structure of Biological Networks
https://scholar.archive.org/work/brh6p3sv2zh63argco6fa7krja
Actin cytoskeleton networks generate local topological signatures due to the natural variations in the number, size, and shape of holes of the networks. Persistent homology is a method that explores these topological properties of data and summarizes them as persistence diagrams. In this work, we analyze and classify simulated actin filament networks by transforming them into persistence diagrams whose variability is quantified via a Bayesian framework on the space of persistence diagrams. The proposed generalized Bayesian framework adopts an independent and identically distributed cluster point process characterization of persistence diagrams and relies on a substitution likelihood argument. This framework provides the flexibility to estimate the posterior cardinality distribution of points in a persistence diagram and their posterior spatial distribution simultaneously. We present a closed form of the posteriors under the assumption of a Gaussian mixture and binomial for prior intensity and cardinality respectively. Using this posterior calculation, finally, we implement a Bayes factor algorithm to classify simulated actin filament networks and benchmark it against several state-of-the-art classification methods.Vasileios Maroulas, Cassie Putman Micucci, Farzana Nasrinwork_brh6p3sv2zh63argco6fa7krjaThu, 01 Sep 2022 00:00:00 GMTIdentifying patient-specific root causes of disease
https://scholar.archive.org/work/swnc3t2uabchhoiyvt4gguz62e
Complex diseases are caused by a multitude of factors that may differ between patients. As a result, hypothesis tests comparing all patients to all healthy controls can detect many significant variables with inconsequential effect sizes. A few highly predictive root causes may nevertheless generate disease within each patient. In this paper, we define patient-specific root causes as variables subject to exogenous "shocks" which go on to perturb an otherwise healthy system and induce disease. In other words, the variables are associated with the exogenous errors of a structural equation model (SEM), and these errors predict a downstream diagnostic label. We quantify predictivity using sample-specific Shapley values. This derivation allows us to develop a fast algorithm called Root Causal Inference for identifying patient-specific root causes by extracting the error terms of a linear SEM and then computing the Shapley value associated with each error. Experiments highlight considerable improvements in accuracy because the method uncovers root causes that may have large effect sizes at the individual level but clinically insignificant effect sizes at the group level. An R implementation is available at github.com/ericstrobl/RCI.Eric V. Strobl, Thomas A. Laskowork_swnc3t2uabchhoiyvt4gguz62eSun, 07 Aug 2022 00:00:00 GMTArcheGEO
https://scholar.archive.org/work/rtq6rs3b2vbhff36qvpzuyexxi
Transciptomic data stored in the Gene Expression Omnibus (GEO) serves thousands of queries per day, but a lack of standardized machine-readable metadata causes many searches to return irrelevant hits, which impede convenient access to useful data in the GEO repository. Here, we describe ArcheGEO, a novel end-to-end framework that improves results from the GEO Browser by automatically determining the relevance of these results. Unlike existing tools, ArcheGEO reports on the irrelevant results and provides reasoning for their exclusion. Such reasoning can be leveraged to improve annotations of metadata.Huey-Eng Chua, Lisa Tucker-Kellogg, Sourav S Bhowmickwork_rtq6rs3b2vbhff36qvpzuyexxiSun, 07 Aug 2022 00:00:00 GMTCompletion and Embedding Problems for Combinatorial Designs
https://scholar.archive.org/work/cvk2kik2b5artcfkh2dp3g3gei
Combinatorial design theory studies arrangements and combinations of discrete objects according to different rules. Applications of designs are not only limited to analysis of experiments, but also useful in network analysis, cryptography and communication protocols, error correcting codes, mathematical biology, algorithm design, tournament scheduling, lotteries, etc. The topic of when a partial combinatorial design can be completed or embedded has attracted a great deal of interest over the years. In this thesis, we investigate four topics related to the completion or embedding of partial H-designs. We make progress on partial Steiner triple systems, partial block designs and partial star designs.AJANI RUWANDHIKA CHULANGI DE VAS GUNASEKARAwork_cvk2kik2b5artcfkh2dp3g3geiSat, 06 Aug 2022 00:00:00 GMTThe solution path of the Li-Stephens haplotype copying model
https://scholar.archive.org/work/4tcbz4bzmbhm3ah4p7dv22jb3u
The Li-Stephens (LS) haplotype copying model forms the basis of a number of important statistical inference procedures in genetics. LS is a probabilistic generative model which supposes that a sampled chromosome is an imperfect mosaic of other chromosomes found in a population. In the frequentist setting which is the focus of this paper, the output of LS is a "copying path" through chromosome space. The behavior of LS depends crucially on two user-specified parameters, θ and ρ, which are respectively interpreted as the rates of mutation and recombination. However, because LS is not based on a realistic model of ancestry, the precise connection between these parameters and the biological phenomena they represent is unclear. Here, we offer an alternative perspective, which considers θ and ρ as tuning parameters, and seeks to understand their impact on the LS output. We derive an algorithm which, for a given dataset, efficiently partitions the (θ,ρ) plane into regions where the output of the algorithm is constant, thereby enumerating all possible solutions to the LS model at one go. We extend this approach to the "diploid LS" model commonly used for phasing. We demonstrate the usefulness of our method by studying the effects changing of θ and ρ when using LS for common bioinformatic tasks. Our findings indicate that using the conventional (i.e., population-scaled) values for θ and ρ produces near optimal results for imputation, but may systematically inflate switch error in the case of phasing diploid genotypes.Yifan Jin, Jonathan Terhorstwork_4tcbz4bzmbhm3ah4p7dv22jb3uFri, 05 Aug 2022 00:00:00 GMTPhysical Layer Waveform Design for High Mobility Wireless Channels
https://scholar.archive.org/work/mhiamyviafawrpu6lv5hi4xrwa
With the advent of high-speed trains, unmanned aerial vehicles, and drones, reliable communications in high mobility wireless channels have become necessary for next-generation wireless networks. Orthogonal frequency division multiplexing (OFDM) has been the standard physical-layer modulation scheme deployed in 4G and 5G mobile systems but suffers from severe performance degradation in high-mobility environments. Hence, robust modulation techniques in both slow and fast time-varying channels are needed to solve the 'reliable communications' problem in such channels. This thesis investigates new physical layer techniques for high-mobility wireless channels, focusing on a recently proposed waveform known as orthogonal time frequency space (OTFS) modulation.THARAJ THAJwork_mhiamyviafawrpu6lv5hi4xrwaFri, 05 Aug 2022 00:00:00 GMTStrictification of Weakly Stable Type-Theoretic Structures Using Generic Contexts
https://scholar.archive.org/work/isjbnzszujbxhlprsdmenwdj4m
We present a new strictification method for type-theoretic structures that are only weakly stable under substitution. Given weakly stable structures over some model of type theory, we construct equivalent strictly stable structures by evaluating the weakly stable structures at generic contexts. These generic contexts are specified using the categorical notion of familial representability. This generalizes the local universes method of Lumsdaine and Warren. We show that generic contexts can also be constructed in any category with families which is freely generated by collections of types and terms, without any definitional equality. This relies on the fact that they support first-order unification. These free models can only be equipped with weak type-theoretic structures, whose computation rules are given by typal equalities. Our main result is that any model of type theory with weakly stable weak type-theoretic structures admits an equivalent model with strictly stable weak type-theoretic structures.Rafaël Bocquet, Henning Basold, Jesper Cockx, Silvia Ghilezanwork_isjbnzszujbxhlprsdmenwdj4mThu, 04 Aug 2022 00:00:00 GMTLIPIcs, Volume 238, DNA 28, Complete Volume
https://scholar.archive.org/work/627o3xn4vbbgpdox5dwolgcuny
LIPIcs, Volume 238, DNA 28, Complete VolumeThomas E. Ouldridge, Shelley F. J. Wickhamwork_627o3xn4vbbgpdox5dwolgcunyThu, 04 Aug 2022 00:00:00 GMTFairTraDEX: A Decentralised Exchange Preventing Value Extraction
https://scholar.archive.org/work/ut2lkxyyrvgdbbko4qcowpxppe
We present FairTraDEX, a decentralized exchange (DEX) protocol based on frequent batch auctions (FBAs), which provides formal game-theoretic guarantees against extractable value. FBAs when run by a trusted third-party provide unique game-theoretic optimal strategies which ensure players are shown prices equal to the liquidity provider's fair price, excluding explicit, pre-determined fees. FairTraDEX replicates the key features of an FBA that provide these game-theoretic guarantees using a combination of set-membership in zero-knowledge protocols and an escrow-enforced commit-reveal protocol. We extend the results of FBAs to handle monopolistic and/or malicious liquidity providers. We provide real-world examples that demonstrate that the costs of executing orders in existing academic and industry-standard protocols become prohibitive as order size increases due to basic value extraction techniques, popularized as maximal extractable value. We further demonstrate that FairTraDEX protects against these execution costs, guaranteeing a fixed fee model independent of order size, the first guarantee of it's kind for a DEX protocol. We also provide detailed Solidity and pseudo-code implementations of FairTraDEX, making FairTraDEX a novel and practical contribution.Conor McMenamin and Vanesa Daza and Matthias Fitzi and Padraic O'Donoghuework_ut2lkxyyrvgdbbko4qcowpxppeThu, 04 Aug 2022 00:00:00 GMTOn synthesizing Skolem functions for first order logic formulae
https://scholar.archive.org/work/qmqrsxhjy5e23itimqto4mj7lm
Skolem functions play a central role in the study of first order logic, both from theoretical and practical perspectives. While every Skolemized formula in first-order logic makes use of Skolem constants and/or functions, not all such Skolem constants and/or functions admit effectively computable interpretations. Indeed, the question of whether there exists an effectively computable interpretation of a Skolem function, and if so, how to automatically synthesize it, is fundamental to their use in several applications, such as planning, strategy synthesis, program synthesis etc. In this paper, we investigate the computability of Skolem functions and their automated synthesis in the full generality of first order logic. We first show a strong negative result, that even under mild assumptions on the vocabulary, it is impossible to obtain computable interpretations of Skolem functions. We then show a positive result, providing a precise characterization of first-order theories that admit effective interpretations of Skolem functions, and also present algorithms to automatically synthesize such interpretations. We discuss applications of our characterization as well as complexity bounds for Skolem functions (interpreted as Turing machines).S. Akshay, Supratik Chakrabortywork_qmqrsxhjy5e23itimqto4mj7lmThu, 04 Aug 2022 00:00:00 GMTA new complete algorithm for Irreducible Diophantine Pythagorean Triangles (IDPTs)
https://scholar.archive.org/work/yac3ghgpc5cm3klq7os4alvqtm
It is well known that a triangle with side lengths 3, 4 and 5 is right-angled. Euclid was the first to give a formula for generating other right-angled triangles with integer side lengths. In this text, I present a novel algorithm to generate all possible right-angled triangles with integer side lengths, in which the three side lengths have no common divisor. The algorithm is based on the difference in length between the hypothenuse and the largest of the two other sides. I also prove the completeness of this algorithm: it generates all possible such triangles and nothing but such triangles.Jan Pieter Zwartwork_yac3ghgpc5cm3klq7os4alvqtmThu, 04 Aug 2022 00:00:00 GMTIdeal operators and higher indescribability
https://scholar.archive.org/work/f3xfy5ewazelzhbvncvqvsbxuq
We investigate properties of the ineffability and the Ramsey operator, and a common generalization of those that was introduced by the second author, with respect to higher indescribability, as introduced by the first author. This extends earlier investigations on the ineffability operator by James Baumgartner, and on the Ramsey operator by Qi Feng, by Philip Welch et al. and by the first author.Brent Cody, Peter Holywork_f3xfy5ewazelzhbvncvqvsbxuqThu, 04 Aug 2022 00:00:00 GMTTighter Bound Estimation for Efficient Biquadratic Optimization Over Unit Spheres
https://scholar.archive.org/work/norccf55erf25dxnrxxsxzjhma
Bi-quadratic programming over unit spheres is a fundamental problem in quantum mechanics introduced by pioneer work of Einstein, Schr\"odinger, and others. It has been shown to be NP-hard; so it must be solve by efficient heuristic algorithms such as the block improvement method (BIM). This paper focuses on the maximization of bi-quadratic forms, which leads to a rank-one approximation problem that is equivalent to computing the M-spectral radius and its corresponding eigenvectors. Specifically, we provide a tight upper bound of the M-spectral radius for nonnegative fourth-order partially symmetric (PS) tensors, which can be considered as an approximation of the M-spectral radius. Furthermore, we showed that the proposed upper bound can be obtained more efficiently, if the nonnegative fourth-order PS-tensors is a member of certain monoid semigroups. Furthermore, as an extension of the proposed upper bound, we derive the exact solutions of the M-spectral radius and its corresponding M-eigenvectors for certain classes of fourth-order PS-tensors. Lastly, as an application of the proposed bound, we obtain a practically testable sufficient condition for nonsingular elasticity M-tensors with strong ellipticity condition. We conduct several numerical experiments to demonstrate the utility of the proposed results. The results show that: (a) our proposed method can attain a tight upper bound of the M-spectral radius with little computational burden, and (b) such tight and efficient upper bounds greatly enhance the convergence speed of the BIM-algorithm, allowing it to be applicable for large-scale problems in applications.Shigui Li, Linzhang Lu, Xing Qiu, Zhen Chen, Delu Zengwork_norccf55erf25dxnrxxsxzjhmaThu, 04 Aug 2022 00:00:00 GMTDegrees of Freedom of a K-User Interference Channel in the Presence of an Instantaneous Relay
https://scholar.archive.org/work/qhtom6m5fzer5gvbcqdsyrxsiu
In this paper, we study the degrees of freedom (DoF) of a frequency-selective K-user interference channel in the presence of an instantaneous relay (IR) with multiple receiving and transmitting antennas. We investigate two scenarios based on the IR antennas' cooperation ability. First, we assume that the IR receiving and transmitting antennas can coordinate with each other and that the transmitted signal of each transmitting antenna can depend on the received signals of all receiving antennas, and we derive lower and upper bounds for the sum DoF of this model. In an interference alignment scheme, we divide receivers into two groups called clean and dirty receivers. We design our scheme such that a part of the messages of clean receivers can be de-multiplexed at the IR. Thus, the IR can use these message streams for an interference cancellation at the clean receivers. Next, we consider an IR, the antennas of which do not have coordination with each other and where the transmitted signal of each transmitting antenna depends only on the received signal of its corresponding receiving antenna. We also derive lower and upper bounds for the sum DoF for this model of IR. We show that the achievable sum DoF decreases considerably compared with the coordinated case. In both of these models, our schemes achieve the maximum K sum DoF if the number of transmitting and receiving antennas is more than a finite threshold.Ali H. Abdollahi Bafghi, Mahtab Mirmohseni, Masoumeh Nasiri-Kenariwork_qhtom6m5fzer5gvbcqdsyrxsiuThu, 04 Aug 2022 00:00:00 GMTA Joint Model Considering Measurement Errors for Optimally Identifying Tumor Mutation Burden Threshold
https://scholar.archive.org/work/okawp6o4jnhl5kfb2vt7hocp2u
Tumor mutation burden (TMB) is a recognized stratification biomarker for immunotherapy. Nevertheless, the general TMB-high threshold is unstandardized due to severe clinical controversies, with the underlying cause being inconsistency between multiple assessment criteria and imprecision of the TMB value. The existing methods for determining TMB thresholds all consider only a single dimension of clinical benefit and ignore the interference of the TMB error. Our research aims to determine the TMB threshold optimally based on multifaceted clinical efficacies accounting for measurement errors. We report a multi-endpoint joint model as a generalized method for inferring the TMB thresholds, facilitating consistent statistical inference using an iterative numerical estimation procedure considering mis-specified covariates. The model optimizes the division by combining objective response rate and time-to-event outcomes, which may be interrelated due to some shared traits. We augment previous works by enabling subject-specific random effects to govern the communication among distinct endpoints. Our simulations show that the proposed model has advantages over the standard model in terms of precision and stability in parameter estimation and threshold determination. To validate the feasibility of the proposed thresholds, we pool a cohort of 73 patients with non-small-cell lung cancer and 64 patients with nasopharyngeal carcinoma who underwent anti-PD-(L)1 treatment, as well as validation cohorts of 943 patients. Analyses revealed that our approach could grant clinicians a holistic efficacy assessment, culminating in a robust determination of the TMB screening threshold for superior patients. Our methodology has the potential to yield innovative insights into therapeutic selection and support precision immuno-oncology.Yixuan Wang, Xin Lai, Jiayin Wang, Ying Xu, Xuanping Zhang, Xiaoyan Zhu, Yuqian Liu, Yang Shao, Li Zhang, Wenfeng Fangwork_okawp6o4jnhl5kfb2vt7hocp2uThu, 04 Aug 2022 00:00:00 GMTExtremes of Markov random fields on block graphs: max-stable limits and structured Hüsler-Reiss distributions
https://scholar.archive.org/work/p3yirohfljfc3k55hukm5rymje
We study the joint occurrence of large values of a Markov random field or undirected graphical model associated to a block graph. On such graphs, containing trees as special cases, we aim to generalize recent results for extremes of Markov trees. Every pair of nodes in a block graph is connected by a unique shortest path. These paths are shown to determine the limiting distribution of the properly rescaled random field given that a fixed variable exceeds a high threshold. The latter limit relation implies that the random field is multivariate regularly varying and it determines the max-stable distribution to which component-wise maxima of independent random samples from the field are attracted. When the sub-vectors induced by the blocks have certain limits parametrized by H\"usler-Reiss distributions, the global Markov property of the original field induces a particular structure on the parameter matrix of the limiting max-stable H\"usler-Reiss distribution. The multivariate Pareto version of the latter turns out to be an extremal graphical model according to the original block graph. Thanks to these algebraic relations, the parameters are still identifiable even if some variables are latent.Stefka Asenova, Johan Segerswork_p3yirohfljfc3k55hukm5rymjeThu, 04 Aug 2022 00:00:00 GMTSoftIGA: soft isogeometric analysis
https://scholar.archive.org/work/m53vvqgagjd3zpifwpp7rrlsfe
We extend the softFEM idea to isogeometric analysis (IGA) to reduce the stiffness (consequently, the condition numbers) of the IGA discretized problem. We refer to the resulting approximation technique as softIGA. We obtain the resulting discretization by first removing the IGA spectral outliers to reduce the system's stiffness. We then add high-order derivative-jump penalization terms (with negative penalty parameters) to the standard IGA bilinear forms. The penalty parameter seeks to minimize spectral/dispersion errors while maintaining the coercivity of the bilinear form. We establish dispersion errors for both outlier-free IGA (OF-IGA) and softIGA elements. We also derive analytical eigenpairs for the resulting matrix eigenvalue problems and show that the stiffness and condition numbers of the IGA systems significantly improve (reduce). We prove a superconvergent result of order h^2p+4 for eigenvalues where h characterizes the mesh size and p specifies the order of the B-spline basis functions. To illustrate the main idea and derive the analytical results, we focus on uniform meshes in 1D and tensor-product meshes in multiple dimensions. For the eigenfunctions, softIGA delivers the same optimal convergence rates as the standard IGA approximation. Various numerical examples demonstrate the advantages of softIGA over IGA.Quanling Deng and Pouria Behnoudfar and Victor M. Calowork_m53vvqgagjd3zpifwpp7rrlsfeThu, 04 Aug 2022 00:00:00 GMTA Comparative Study of Design of Active Fault-Tolerant Control System for Air–Fuel Ratio Control of Internal Combustion Engine Using Particle Swarm Optimization, Genetic Algorithm, and Nonlinear Regression-Based Observer Model
https://scholar.archive.org/work/5zlz7kqsrvhnfoiw6jdzfv5ovy
In this article, three distinct strategies for designing an Active Fault-Tolerant Control System (AFTCS) for Air-Fuel Ratio (AFR) control of an Internal Combustion (IC) engine in a process plant to avoid engine shutdown, are presented. The proposed AFTCS employs a Genetic Algorithm (GA), Particle Swarm Optimization (PSO), and a Nonlinear Regression (NLR)-based observer model in the Fault Detection and Isolation (FDI) unit for analytical redundancy. A comparison between these three proposed techniques is carried out to determine the least expensive and most accurate approach. The results show that the nonlinear regression produces highly accurate results by consuming very low computational power, and its response time is also very low as compared to GA and PSO. The results obtained show that NLR requires 99.6% and 93.1% less computational time for throttle and MAP estimation, respectively, by reducing the estimation error to as low as 0.01. The simulation of the proposed system is carried out in the MATLAB/Simulink environment. The results prove the superior fault tolerance performance for sensor faults of the AFR control system, especially for the Manifold Absolute Pressure (MAP) sensor in terms of less oscillatory response as compared to that reported in existing literature.Turki Alsuwian, Muhammad Sajid Iqbal, Arslan Ahmed Amin, Muhammad Bilal Qadir, Saleh Almasabi, Mohammed Jalalahwork_5zlz7kqsrvhnfoiw6jdzfv5ovyThu, 04 Aug 2022 00:00:00 GMT