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arXiv 2025年

作者： Li, Wenran Cadet, Xavier F. Medina-Ortiz, David Davari, Mehdi D. Sowdhamini, Ramanathan Damour, Cedric Li, Yu Miranville, Alain Cadet, Frederic University of Paris City University of Reunion INSERM BIGR DSIMB ParisF-75015 France Department of Computing Imperial College London United Kingdom Department of Computer Engineering University of Magallanes Punta Arenas Chile Centre for Biotechnology and Bioengineering Universidad de Chile Santiago Chile Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry Halle06120 Germany National Centre for Biological Science TIFR Bangalore India Molecular Biophysics Unit Indian Institute of Science Bangalore India Institute of Bioinformatics and Applied Biotechnology Bangalore India EnergyLab EA 4079 Faculty of Sciences and Technology University of Reunion France School of Information Science and Technology Beijing Institute of Artificial Intelligence China Laboratoire de Mathématiques Appliquées University Le Havre Normandie le Havre France PEACCEL Artificial Intelligence Department AI for Bi-ologics Paris75013 France

Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion models stand out for their robust math.matical foundations and impressive generative capabilities, offering unique advantages in certain applications such as protein design. In this review, we first give the definition and characteristics of diffusion models and then focus on two strategies: Denoising Diffusion Probabilistic Models (DDPM) and Score-based Generative Models (SGM), where DDPM is the discrete form of SGM. Furthermore, we discuss their applications in protein design, peptide generation, drug discovery, and protein-ligand interaction. Finally, we outline the future perspectives of diffusion models to advance autonomous protein design and engineering. The E(3) group consists of all rotations, reflections, and translations in three-dimensions. The equivariance in the E(3) group can maintain the physical stability of the N − Cα − C frame of each amino acid as much as possible, and we reflect on how to keep the diffusion model E(3) equivariant for protein generation. © 2025, CC BY.

关键词： Biomolecules

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Facility design using iterative heuristic algorithm

Facility design using iterative heuristic algorithm

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17th International Conference on Software Engineering and Data Engineering, SEDE 2008

作者： Bhowmik, Rekha Lee, Ilhyun Department of Computer Science Sam Houston State University Huntsville TX 77341 United States Department of Math. and Computer Science University of Texas of the Permian Basin Odessa TX 79762 United States

This paper presents an Iterative Heuristic Algorithm for optimal location of departments on a level. A behavioral aspect of the optimum solution: the sensitivity of the solution to variations in the problem is also pr... 详细信息

ISBN: (纸本)9781605603360

关键词： Sensitivity analysis

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Inducing approximately optimal flow using truthful mediators 15

Inducing approximately optimal flow using truthful mediators

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16th ACM Conference on Economics and Computation, EC 2015

作者： Rogers, Ryan Roth, Aaron Ullman, Jonathan Wu, Zhiwei Steven Applied Math and Computational Science Department University of Pennsylvania United States Department of Computer Science Columbia University United States

ISBN: (纸本)9781450334105

We revisit a classic coordination problem from the perspective of mechanism design: how can we coordinate a social welfare maximizing flow in a network congestion game with selfish players? The classical approach, which computes tolls as a function of known demands, fails when the demands are unknown to the mechanism designer, and naively eliciting them does not necessarily yield a truthful mechanism. Instead, we introduce a weak mediator that can provide suggested routes to players and set tolls as a function of reported demands. However, players can choose to ignore or misreport their type to this mediator. Using techniques from differential privacy, we show how to design a weak mediator such that it is an asymptotic ex-post Nash equilibrium for all players to truthfully report their types to the mediator and faithfully follow its suggestion, and that when they do, they end up playing a nearly optimal flow. Notably, our solution works in settings of incomplete information even in the absence of a prior distribution on player types. Along the way, we develop new techniques for privately solving convex programs which may be of independent interest.

关键词： algorithms differential privacy mechanism design

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Analytical modelling of a refined FCFS queueing discipline in multiprogrammed parallel processing systems

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International Journal of Modelling and Simulation 2000年第3期20卷 248-254页

作者： Li, Keqin Dept. of Math. and Computer Science State University of New York New Paltz NY 12561-2499 United States Tsinghua University China University of Houston Department of Computer Science State University of New York New Paltz NY United States IEEE IEEE Computer Society ACM SIGACT

A multiprogrammed (or partitionable) parallel computer system can be partitioned into subsystems which are allocated to independent jobs. The performance of such a parallel processing system is determined by the system partitioning strategy and the job scheduling policy adopted. In this paper, we consider the impact of a job scheduling algorithm on the system performance, mainly the average job response time. A refined First-Come-First-Serve (FCFS) queueing discipline called FCFS/SJE is studied, which, when there are not enough processors available for large jobs in the front of a waiting queue, schedules small jobs behind these large jobs earlier. We develop a multi-server queueing system for modelling multiprogrammed parallel processing systems. A system is specified by the number of processors and jobs are characterized by a probability distribution of the number of processors requested, a Poisson arrival process, and an exponential distribution of execution time. Our analysis as well as simulation indicate that FCFS/SJE results in a noticeable improvement on system performance compared with FCFS.

关键词： Queueing networks

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A COMPETITIVE AND PREY-PREDATOR MODEL WITH STAGE-STRUCTURE

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Annals of Differential Equations 2004年第1期20卷 49-58页

作者：罗桂烈刘丙辰李锋杰 Math. and Computer Science College Guangzi Normal University Guilin 541004 Dept. of Applied Math. Dalian University of Technology Dalian 116024

The uniform persistence is proved for a non-autonomous competitive and prey-predator model with ratio-dependent functional response and stage-structure. By constructing a Liapunov functional, we establish the conditions of existence and uniqueness for the positive periodic solution, which is globally asymptotically stable. We get a unique almost periodic solution for an almost periodic system as well under corresponding conditions .by means of the Razumikhin function method.

关键词： time-delay Liapunov functional Razumikhin function

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Building a Good Team: Secretary Problems and the Supermodular Degree 17

Building a Good Team: Secretary Problems and the Supermodula...

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Annual ACM-Society for Industrial and applied math.atics Symposium on Discrete Algorithms

作者： Moran Feldman Rani Izsak Department of Mathematics and Computer Science The Open University of Israel Department of Computer Science and Applied Math. Weizmann Institute of Science

ISBN: (纸本)9781510836358

In the (classical) SECRETARY PROBLEM, one has to hire the best among n candidates. The candidates are interviewed, one at a time, at a uniformly random order, and one has to decide on the spot, whether to hire a candidate or continue interviewing. It is well known that the best candidate can be hired with a probability of 1/e (Dynkin, 1963). Recent works extend this problem to settings in which multiple candidates can be hired, subject to some constraint. Here, one wishes to hire a set of candidates maximizing a given objective set function. Almost all extensions considered in the literature assume the objective set function is either linear or submodular. Unfortunately, real world functions might not have either of these properties. Consider, for example, a scenario where one hires researchers for a project. Indeed, it can be that some researchers can substitute others for that matter. However, it can also be that some combinations of researchers result in synergy (see, e.g., Woolley et al., science 2010, for a study on collective intelligence). The first phenomenon can be modeled by a submoudlar set function, while the latter cannot. In this work, we study the secretary problem with an arbitrary non-negative monotone valuation function, subject to a general matroid constraint. One can prove that, generally, only very poor results can be obtained for this class of objective functions. We tackle this hardness by combining the following: (1) Parametrizing our algorithms by the supermodular degree of the objective function (defined by Feige and Izsak, ITCS 2013), which, roughly speaking, measures the distance of a function from being submodular. (2) Suggesting an (arguably) natural model that permits approximation guarantees that are polynomial in the supermodular degree (as opposed to the standard model which allows only exponential guarantees). Our algorithms learn the input by running a non-trivial estimation algorithm on a portion of it whose size depends on the s

关键词： secretary Objective function algorithms Function solidification Matroid candidate species Standard model Researchers Nonnegative

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The effectiveness of Lloyd-type methods for the k-means problem

The effectiveness of Lloyd-type methods for the k-means prob...

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47th Annual IEEE Symposium on Foundations of computer science, FOCS 2006

作者： Ostrovsky, Rafail Rabani, Yuval Schulman, Leonard J. Swamy, Chaitanya Computer Science Department UCLA Computer Science Department Technion - Israel Institute of Technology Haifa 32000 Israel Caltech Pasadena CA 91125 Center for the Math. of Information Caltech Pasadena CA 91125

ISBN: (纸本)0769527205

We investigate variants of Lloyd's heuristic for clustering high dimensional data in an attempt to explain its popularity (a half century after its introduction) among practitioners, and in order to suggest improvements in its application. We propose and justify a clusterability criterion for data sets. We present variants of Lloyd's heuristic that quickly lead to provably near-optimal clustering solutions when applied to well-clusterable instances. This is the first performance guarantee for a variant of Lloyd's heuristic. The provision of a guarantee on output quality does not come at the expense of speed: some of our algorithms are candidates for being faster in practice than currently used variants of Lloyd's method. In addition, our other algorithms are faster on well-clusterable instances than recently proposed approximation algorithms, while maintaining similar guarantees on clustering quality. Our main algorithmic contribution is a novel probabilistic seeding process for the starting configuration of a Lloyd-type iteration. © 2006 IEEE.

关键词： Heuristic algorithms

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Warping Indexes with Envelope Transforms for Query by Humming 03

Warping Indexes with Envelope Transforms for Query by Hummin...

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2003 ACM SIGMOD International Conference on Management of Data

作者： Zhu, Yunyue Shasha, Dennis Department of Computer Science Courant Inst. of Math. Sciences New York University New York NY 10012 United States

ISBN: (纸本)9781581136340

A Query by Humming system allows the user to find a song by humming part of the tune. No musical training is needed. Previous query by humming systems have not provided satisfactory results for various reasons. Some systems have low retrieval precision because they rely on melodic contour information from the hum tune, which in turn relies on the error-prone note segmentation process. Some systems yield better precision when matching the melody directly from audio, but they are slow because of their extensive use of Dynamic Time Warping (DTW). Our approach improves both the retrieval precision and speed compared to previous approaches. We treat music as a time series and exploit and improve well-developed techniques from time series databases to index the music for fast similarity queries. We improve on existing DTW indexes technique by introducing the concept of envelope transforms, which gives a general guideline for extending existing dimensionality reduction methods to DTW indexes. The net result is high scalability. We confirm our claims through extensive experiments.

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Improving TCP performance over mobile ad hoc networks by exploiting cross-layer information awareness 04

Improving TCP performance over mobile ad hoc networks by exp...

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MobiCom 2004 - Proceedings of the Tenth Annual International Conference on Mobile Computing and Networking

作者： Yu, Xin Department of Computer Science Courant Inst. of Math. Sciences New York University New York NY 10012 United States

ISBN: (纸本)9781581138689

TCP performance degrades significantly in mobile ad hoc networks because most of packet losses occur as a result of route failures. Prior work proposed to provide link failure feedback to TCP so that TCP can avoid responding to route failures as if congestion had occurred. However, after a link failure is detected, several packets will be dropped from the network interface queue;TCP will time out because of these losses. It will also time out for ACK losses caused by route failures. In this paper, we propose to make routing protocols aware of lost data packets and ACKs and help reduce TCP timeouts for mobility-induced losses. Toward this end, we present two mechanisms: early packet loss notification (EPLN) and best-effort ACK delivery (BEAD). EPLN seeks to notify TCP senders about lost data packets. For lost ACKs, BEAD attempts to retransmit ACKs at either intermediate nodes or TCP receivers. Both mechanisms extensively use cached routes, without initiating route discoveries at any intermediate node. We evaluate TCP-ELFN enhanced with the two mechanisms using two caching strategies for DSR, path caches and a distributed cache update algorithm proposed in our prior work. We show that TCP-ELFN with EPLN and BEAD significantly outperforms TCP-ELFN under both caching strategies. We conclude that cross-layer information awareness is key to making TCP efficient in the presence of mobility.

关键词： Telecommunication networks

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Editorial

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Fuzzy Sets and Systems 2015年 281卷 1-3页

作者： De Baets, Bernard Dubois, Didier Hüllermeier, Eyke KERMIT Dept. of Math. Modeling Statistics and Bioinformatics Ghent University Belgium IRIT CNRS Université de Toulouse France Intelligent Systems Group Department of Computer Science University of Paderborn Germany

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