arXiv subjects

Alan Kuhnle

Publications and source records attributed to Alan Kuhnle.

33 records · Page 2Linked to original sources

arXiv2023

RELS-DQN: A Robust and Efficient Local Search Framework for Combinatorial Optimization

Combinatorial optimization (CO) aims to efficiently find the best solution to NP-hard problems ranging from statistical physics to social media marketing. A wide range of CO applications can benefit from local search methods because they allow reversible action over greedy policies. Deep Q-learning (DQN) using message-passing neural networks (MPNN) has shown promise in replicating the local search behavior and obtaining comparable results to the local search algorithms. However, the over-smoothing and the information loss during the iterations of message passing limit its robustness across applications, and the large message vectors result in memory inefficiency. Our paper introduces RELS-DQN, a lightweight DQN framework that exhibits the local search behavior while providing practical scalability. Using the RELS-DQN model trained on one application, it can generalize to various applications by providing solution values higher than or equal to both the local search algorithms and the existing DQN models while remaining efficient in runtime and memory.

cs.LG↗

arXiv2021

Quick Streaming Algorithms for Maximization of Monotone Submodular Functions in Linear Time

We consider the problem of monotone, submodular maximization over a ground set of size $n$ subject to cardinality constraint $k$. For this problem, we introduce the first deterministic algorithms with linear time complexity; these algorithms are streaming algorithms. Our single-pass algorithm obtains a constant ratio in $\lceil n / c \rceil + c$ oracle queries, for any $c \ge 1$. In addition, we propose a deterministic, multi-pass streaming algorithm with a constant number of passes that achieves nearly the optimal ratio with linear query and time complexities. We prove a lower bound that implies no constant-factor approximation exists using $o(n)$ queries, even if queries to infeasible sets are allowed. An empirical analysis demonstrates that our algorithms require fewer queries (often substantially less than $n$) yet still achieve better objective value than the current state-of-the-art algorithms, including single-pass, multi-pass, and non-streaming algorithms.

cs.DS↗

arXiv2020

Simultaenous Sieves: A Deterministic Streaming Algorithm for Non-Monotone Submodular Maximization

In this work, we present a combinatorial, deterministic single-pass streaming algorithm for the problem of maximizing a submodular function, not necessarily monotone, with respect to a cardinality constraint (SMCC). In the case the function is monotone, our algorithm reduces to the optimal streaming algorithm of Badanidiyuru et al. (2014). In general, our algorithm achieves ratio $α/ (1 + α) - \varepsilon$, for any $\varepsilon > 0$, where $α$ is the ratio of an offline (deterministic) algorithm for SMCC used for post-processing. Thus, if exponential computation time is allowed, our algorithm deterministically achieves nearly the optimal $1/2$ ratio. These results nearly match those of a recently proposed, randomized streaming algorithm that achieves the same ratios in expectation. For a deterministic, single-pass streaming algorithm, our algorithm achieves in polynomial time an improvement of the best approximation factor from $1/9$ of previous literature to $\approx 0.2689$.

cs.DS↗

arXiv2019

Interlaced Greedy Algorithm for Maximization of Submodular Functions in Nearly Linear Time

A deterministic approximation algorithm is presented for the maximization of non-monotone submodular functions over a ground set of size $n$ subject to cardinality constraint $k$; the algorithm is based upon the idea of interlacing two greedy procedures. The algorithm uses interlaced, thresholded greedy procedures to obtain tight ratio $1/4 - ε$ in $O \left( \frac{n}ε \log \left( \frac{k}ε \right) \right)$ queries of the objective function, which improves upon both the ratio and the quadratic time complexity of the previously fastest deterministic algorithm for this problem. The algorithm is validated in the context of two applications of non-monotone submodular maximization, on which it outperforms the fastest deterministic and randomized algorithms in prior literature.

cs.DS↗

arXiv2019

Matching reads to many genomes with the $r$-index

The $r$-index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a genome in the database or to find seeds for reads that do not. This paper shows how to download and install the programs ri-buildfasta and ri-align; how to call ri-buildfasta on a FASTA file to build an $r$-index for that file; and how to query that index with ri-align. Availability: The source code for these programs is released under GPLv3 and available at https://github.com/alshai/r-index .

cs.DS↗

arXiv2019

Submodular Cost Submodular Cover with an Approximate Oracle

In this work, we study the Submodular Cost Submodular Cover problem, which is to minimize the submodular cost required to ensure that the submodular benefit function exceeds a given threshold. Existing approximation ratios for the greedy algorithm assume a value oracle to the benefit function. However, access to a value oracle is not a realistic assumption for many applications of this problem, where the benefit function is difficult to compute. We present two incomparable approximation ratios for this problem with an approximate value oracle and demonstrate that the ratios take on empirically relevant values through a case study with the Influence Threshold problem in online social networks.

cs.DS↗

arXiv2019

A Note on Submodular Maximization over Independence Systems

In this work, we consider the maximization of submodular functions constrained by independence systems. Because of the wide applicability of submodular functions, this problem has been extensively studied in the literature, on specialized independence systems. For general independence systems, even when all of the bases of the independence system have the same size, we show that for any $ε> 0$, the problem is hard to approximate within $(2/n)^{1-ε}$, where $n$ is the size of the ground set. In the same context, we show the greedy algorithm does obtain a ratio of $2/n$ under an additional mild additional assumption. Finally, we provide the first nearly linear-time algorithm for maximization of non-monotone submodular functions over $p$-extendible independence systems.

cs.DS↗

arXiv2018

Prefix-Free Parsing for Building Big BWTs

High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such indexes is a challenge. Fortunately, many of these genomic databases are highly-repetitive---a characteristic that can be exploited to ease the computation of the Burrows-Wheeler Transform (BWT), which underlies many popular indexes. In this paper, we introduce a preprocessing algorithm, referred to as {\em prefix-free parsing}, that takes a text $T$ as input, and in one-pass generates a dictionary $D$ and a parse $P$ of $T$ with the property that the BWT of $T$ can be constructed from $D$ and $P$ using workspace proportional to their total size and $O (|T|)$-time. Our experiments show that $D$ and $P$ are significantly smaller than $T$ in practice, and thus, can fit in a reasonable internal memory even when $T$ is very large. In particular, we show that with prefix-free parsing we can build an 131-megabyte run-length compressed FM-index (restricted to support only counting and not locating) for 1000 copies of human chromosome 19 in 2 hours using 21 gigabytes of memory, suggesting that we can build a 6.73 gigabyte index for 1000 complete human-genome haplotypes in approximately 102 hours using about 1 terabyte of memory.

cs.DS↗

arXiv2018

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the main components of the FM-index in more detail, which is a rank data structure over the Burrows-Wheeler Transform (BWT) of the string that will allow us to find the interval in the string's suffix array (SA) containing pointers to starting positions of occurrences of a given pattern; second, a sample of the SA that --- when used with the rank data structure --- allows us access the SA. The rank data structure can be kept small even for large genomic databases, by run-length compressing the BWT, but until recently there was no means known to keep the SA sample small without greatly slowing down access to the SA. Now that Gagie et al. (SODA 2018) have defined an SA sample that takes about the same space as the run-length compressed BWT --- we have the design for efficient FM-indexes of genomic databases but are faced with the problem of building them. In 2018 we showed how to build the BWT of large genomic databases efficiently (WABI 2018) but the problem of building Gagie et al.'s SA sample efficiently was left open. We compare our approach to state-of-the-art methods for constructing the SA sample, and demonstrate that it is the fastest and most space-efficient method on highly repetitive genomic databases. Lastly, we apply our method for indexing partial and whole human genomes, and show that it improves over Bowtie with respect to both memory and time.

cs.DS↗

arXiv2018

Fast Maximization of Non-Submodular, Monotonic Functions on the Integer Lattice

The optimization of submodular functions on the integer lattice has received much attention recently, but the objective functions of many applications are non-submodular. We provide two approximation algorithms for maximizing a non-submodular function on the integer lattice subject to a cardinality constraint; these are the first algorithms for this purpose that have polynomial query complexity. We propose a general framework for influence maximization on the integer lattice that generalizes prior works on this topic, and we demonstrate the efficiency of our algorithms in this context.

cs.DS↗

arXiv2018

Multiplex Influence Maximization in Online Social Networks with Heterogeneous Diffusion Models

Motivated by online social networks that are linked together through overlapping users, we study the influence maximization problem on a multiplex, with each layer endowed with its own model of influence diffusion. This problem is a novel version of the influence maximization problem that necessitates new analysis incorporating the type of propagation on each layer of the multiplex. We identify a new property, generalized deterministic submodular, which when satisfied by the propagation in each layer, ensures that the propagation on the multiplex overall is submodular -- for this case, we formulate ISF, the greedy algorithm with approximation ratio $(1 - 1/e)$. Since the size of a multiplex comprising multiple OSNs may encompass billions of users, we formulate an algorithm KSN that runs on each layer of the multiplex in parallel. KSN takes an $α$-approximation algorithm A for the influence maximization problem on a single-layer network as input, and has approximation ratio $\frac{(1-ε)α}{(o+1)k}$ for arbitrary $ε> 0$, $o$ is the number of overlapping users, and $k$ is the number of layers in the multiplex. Experiments on real and synthesized multiplexes validate the efficacy of the proposed algorithms for the problem of influence maximization in the heterogeneous multiplex. Implementations of ISF and KSN are available at http://www.alankuhnle.com/papers/mim/mim.html.

cs.SI↗

arXiv2017

Pseudo-Separation for Assessment of Structural Vulnerability of a Network

Based upon the idea that network functionality is impaired if two nodes in a network are sufficiently separated in terms of a given metric, we introduce two combinatorial \emph{pseudocut} problems generalizing the classical min-cut and multi-cut problems. We expect the pseudocut problems will find broad relevance to the study of network reliability. We comprehensively analyze the computational complexity of the pseudocut problems and provide three approximation algorithms for these problems. Motivated by applications in communication networks with strict Quality-of-Service (QoS) requirements, we demonstrate the utility of the pseudocut problems by proposing a targeted vulnerability assessment for the structure of communication networks using QoS metrics; we perform experimental evaluations of our proposed approximation algorithms in this context.

cs.DS↗

arXiv2017

Vulnerability of Clustering under Node Failure in Complex Networks

Robustness in response to unexpected events is always desirable for real-world networks. To improve the robustness of any networked system, it is important to analyze vulnerability to external perturbation such as random failures or adversarial attacks occurring to elements of the network. In this paper, we study an emerging problem in assessing the robustness of complex networks: the vulnerability of the clustering of the network to the failure of network elements. Specifically, we identify vertices whose failures will critically damage the network by degrading its clustering, evaluated through the average clustering coefficient. This problem is important because any significant change made to the clustering, resulting from element-wise failures, could degrade network performance such as the ability for information to propagate in a social network. We formulate this vulnerability analysis as an optimization problem, prove its NP-completeness and non-monotonicity, and we offer two algorithms to identify the vertices most important to clustering. Finally, we conduct comprehensive experiments in synthesized social networks generated by various well-known models as well as traces of real social networks. The empirical results over other competitive strategies show the efficacy of our proposed algorithms.

cs.SI↗

arXiv2017

Scalable Bicriteria Algorithms for the Threshold Activation Problem in Online Social Networks

We consider the Threshold Activation Problem (TAP): given social network $G$ and positive threshold $T$, find a minimum-size seed set $A$ that can trigger expected activation of at least $T$. We introduce the first scalable, parallelizable algorithm with performance guarantee for TAP suitable for datasets with millions of nodes and edges; we exploit the bicriteria nature of solutions to TAP to allow the user to control the running time versus accuracy of our algorithm through a parameter $α\in (0,1)$: given $η> 0$, with probability $1 - η$ our algorithm returns a solution $A$ with expected activation greater than $T - 2 αT$, and the size of the solution $A$ is within factor $1 + 4 αT + \log ( T )$ of the optimal size. The algorithm runs in time $O \left( α^{-2}\log \left( n / η\right) (n + m) |A| \right)$, where $n$, $m$, refer to the number of nodes, edges in the network. The performance guarantee holds for the general triggering model of internal influence and also incorporates external influence, provided a certain condition is met on the cost-effectivity of seed selection.

cs.SI↗