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PAC Learning with Bandit Feedback: Sharp Sample Complexity in the Realizable Setting Algorithms with Polynomially-Improved Approximation Factors for the $2 \rightarrow q$ Norm, and Applications A computational phase transition for learning-to-sample from Ising models Covering vertices by sequential stars Fermi-Dirac machines as quantizations of neurons A Comprehensive Evaluation of Vertex Elimination Algorithms for Algorithmic Differentiation A Tight Bound on Localization of Electrical Flows Optimal Dimension-Free Sampling for Regularized Classification Reducing the Randomness in Partition Oracles for Bounded Degree Minor-Free Graphs Beyond the Half-Approximation: Fair and Efficient Online Class Matching Efficient Uniform Sampling of Surjections via their Profiles Tractable Maximization of Budgeted Phylogenetic Diversity on Networks Utilizing Node Scanwidth Fairness in Aggregation: Optimal Top-$k$ and Improved Full Ranking Learning-Augmented Online Scheduling with Parsimonious Preemption Entropy Equivalence Testing Lumberjack: Better Differentially Private Random Forests through Heavy Hitter Detection in Trees The Secretary Problem with a Stochastic Precursor Polynomial-Time Robust Multiclass Linear Classification under Gaussian Marginals Efficient Banzhaf-Based Data Valuation for $k$-Nearest Neighbors Classification Block-Sphere Vector Quantization An Approximation Algorithm for Graph Label Selection Iterative Chow Filtering for Learning with Distribution Shift Complexity of Non-Log-Concave Sampling in Fisher Information Stochastic Matching via Local Sparsification Finite Sample Bounds for Learning with Score Matching What is Learnable in Valiant's Theory of the Learnable? Provable Quantization with Randomized Hadamard Transform Min-Max Optimization Requires Exponentially Many Queries Fast and Compact Graph Cuts for the Boykov-Kolmogorov Algorithm A proximal gradient algorithm for composite log-concave sampling
Joint alignment of multiple protein-protein interaction n...
Somaye Hashemifar, Qixing Huang, Jinbo XU · 2016-04-13 · via cs.DS updates on arXiv.org

Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps identify conserved sub-networks and provides extra information for functional annotations. Although a few methods have been developed for multiple PPI network alignment, the alignment quality is still far away from perfect and thus, new network alignment methods are needed. Result: In this paper, we present a novel method, denoted as ConvexAlign, for joint alignment of multiple PPI networks by convex optimization of a scoring function composed of sequence similarity, topological score and interaction conservation score. In contrast to existing methods that generate multiple alignments in a greedy or progressive manner, our convex method optimizes alignments globally and enforces consistency among all pairwise alignments, resulting in much better alignment quality. Tested on both synthetic and real data, our experimental results show that ConvexAlign outperforms several popular methods in producing functionally coherent alignments. ConvexAlign even has a larger advantage over the others in aligning real PPI networks. ConvexAlign also finds a few conserved complexes among 5 species which cannot be detected by the other methods.