Brendan Mumey

Brendan Mumey
Montana State University | MSU · Department of Computer Science

Ph.D.

About

113
Publications
10,961
Reads
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872
Citations
Citations since 2016
39 Research Items
412 Citations
2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080
Additional affiliations
August 1998 - present
Montana State University
Position
  • Professor (Full)

Publications

Publications (113)
Preprint
A minimum path cover (MPC) of a directed acyclic graph (DAG) $G = (V,E)$ is a minimum-size set of paths that together cover all the vertices of the DAG. Computing an MPC is a basic polynomial problem, dating back to Dilworth's and Fulkerson's results in the 1950s. Since the size $k$ of an MPC (also known as the width) can be small in practical appl...
Article
Minimum flow decomposition (MFD) is an NP-hard problem asking to decompose a network flow into a minimum set of paths (together with associated weights). Variants of it are powerful models in multiassembly problems in Bioinformatics, such as RNA assembly. Owing to its hardness, practical multiassembly tools either use heuristics or solve simpler, p...
Preprint
Full-text available
Minimum flow decomposition (MFD) -- the problem of finding a minimum set of weighted source-to-sink paths that perfectly decomposes a flow -- is a classical problem in Computer Science, and variants of it are powerful models in different fields such as Bioinformatics and Transportation. Even on acyclic graphs, the problem is NP-hard, and most pract...
Preprint
Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow $X$ on directed graph $G$ into weighted source-to-sink paths whose superposition equals $X$. We focus on a common formulation of the problem where the path weights must be non-negative integers and also on a new variant where these weights...
Preprint
Full-text available
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of interest because of their prominence in virus DNA. Thus, given no restrictions on pre-processing time, how quickly a...
Article
Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms? A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species ( Pseudomonas aeruginosa , Staphylococ...
Article
Full-text available
Flow network decomposition is a natural model for problems where we are given a flow network arising from superimposing a set of weighted paths and would like to recover the underlying data, i.e., decompose the flow into the original paths and their weights. Thus, variations on flow decomposition are often used as subroutines in multiassembly probl...
Preprint
Full-text available
Minimum flow decomposition (MFD) (the problem of finding a minimum set of paths that perfectly decomposes a flow) is a classical problem in Computer Science, and variants of it are powerful models in multiassembly problems in Bioinformatics (e.g. RNA assembly). However, because this problem and its variants are NP-hard, practical multiassembly tool...
Chapter
Minimum flow decomposition (MFD)—the problem of finding a minimum set of paths that perfectly decomposes a flow—is a classical problem in Computer Science, and variants of it are powerful models in multiassembly problems in Bioinformatics (e.g. RNA assembly). However, because this problem and its variants are NP-hard, practical multiassembly tools...
Article
Full-text available
A multi-assembly problem asks to reconstruct multiple genomic sequences from mixed reads sequenced from all of them. Standard formulations of such problems model a solution as a path cover in a directed acyclic graph, namely a set of paths that together cover all vertices of the graph. Since multi-assembly problems admit multiple solutions in pract...
Chapter
The width k of a directed acyclic graph (DAG) \(G = (V, E)\) equals the largest number of pairwise non-reachable vertices. Computing the width dates back to Dilworth’s and Fulkerson’s results in the 1950s, and is doable in quadratic time in the worst case. Since k can be small in practical applications, research has also studied algorithms whose co...
Preprint
A minimum path cover (MPC) of a directed acyclic graph (DAG) $G = (V,E)$ is a minimum-size set of paths that together cover all the vertices of the DAG. Computing an MPC is a basic polynomial problem, dating back to Dilworth's and Fulkerson's results in the 1950s. Since the size $k$ of an MPC (also known as the width) can be small in practical appl...
Chapter
Job scheduling to minimize peak demand occurs in the context of smart electric power grids. Some jobs (e.g. certain household appliances) may have flexibility in their start times and so can be shifted in order to lower the peak power demand of the schedule. In this work, we consider a version of peak-demand scheduling where jobs are non-preemptibl...
Preprint
A minimum path cover (MPC) of a directed acyclic graph (DAG) G = (V,E) is a minimum-size set of paths that together cover all the vertices of the DAG. The size k of a MPC is also called the width of G. Computing a MPC is a basic problem, dating back to Dilworth's and Fulkerson's results in the 1950s, and is solvable in quadratic time in the worst c...
Article
Full-text available
Recent work provides the first method to measure the relative fitness of genomic variants within a population that scales to large numbers of genomes. A key component of the computation involves finding maximal perfect haplotype blocks from a set of genomic samples for which SNPs (single nucleotide polymorphisms) have been called. Often, due to low...
Chapter
Recent work provides the first method to measure the relative fitness of genomic variants within a population that scales to large numbers of genomes. A key component of the computation involves finding conserved haplotype blocks, which can be done in linear time. Here, we extend the notion of conserved haplotype blocks to pangenomes, which can sto...
Conference Paper
Full-text available
Connecting genetic variation (genotype) to trait variation (phenotype) is a critical but often difficult step in genetic research. A genome-wide association study (GWAS) is a common approach to connect underlying genetic variation to complex phenotypic traits, allowing for phenotypic prediction. GWAS is important in many disciplines, including iden...
Poster
Connecting genetic variation (genotype) to trait variation (phenotype) is a critical but often difficult step in genetic research. A genome-wide association study (GWAS) is a common approach to connect underlying genetic variation to complex phenotypic traits, allowing for phenotypic prediction. GWAS is important in many disciplines, including iden...
Article
Full-text available
Chondrocytes use the pathways of central metabolism to synthesize molecular building blocks and energy for cartilage homeostasis. An interesting feature of the in vivo chondrocyte environment is the cyclical loading generated in various activities (e.g., walking). However, it is unknown whether central metabolism is altered by mechanical loading. W...
Preprint
Full-text available
The {\em bottleneck distance} is a natural measure of the distance between two finite point sets of equal cardinality. In this work, we consider the problem of indexing a set of $m$ planar point sets (of varying sizes) to create a database $D$ that supports nearest bottleneck distance queries: given a query point set $Q$ of size $n$, the point sets...
Article
We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work, we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some application...
Preprint
Full-text available
Chondrocytes use the pathways of central metabolism to synthesize molecular building blocks and energy for cartilage homeostasis. An interesting feature of the in vivo chondrocyte environment is the cyclical loading generated in various activities (e.g. walking). However, it is unknown if central metabolism is altered by mechanical loading. We hypo...
Article
Full-text available
This paper examines an important problem in smart grid energy scheduling; peaks in power demand are proportionally more expensive to generate and provision for. The issue is exacerbated in local microgrids that do not benefit from the aggregate smoothing experienced by large grids. Demand-side scheduling can reduce these peaks by taking advantage o...
Preprint
This paper examines an important problem in smart grid energy scheduling; peaks in power demand are proportionally more expensive to generate and provision for. The issue is exacerbated in local microgrids that do not benefit from the aggregate smoothing experienced by large grids. Demand-side scheduling can reduce these peaks by taking advantage o...
Conference Paper
Full-text available
We consider the problem of identifying regions within a pan-genome de Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some applications...
Conference Paper
Full-text available
With the unit cost of DNA sequencing continuing on a downward trajectory, research institutions and genome sequencing consortia have proposed and implemented strategies to sequence multiple genomes per species, creating pangenomic data sets. We consider the prob- lem of mining approximate frequent subpaths (AFSs) from such data sets, where each gen...
Article
Full-text available
Osteoarthritis is a debilitating disease likely involving altered metabolism of the chondrocytes in articular cartilage. Chondrocytes can respond metabolically to mechanical loads via cellular mechanotransduction, and metabolic changes are significant because they produce the precursors to the tissue matrix necessary for cartilage health. However,...
Data
Stoichiometric matrix of central energy metabolism. The network consists of glycolysis, the TCA cyle, pentose phosphate pathway, electron transport chain, anaplerotic reactions, and transformation of pyruvate into acetyl-CoA. This file represents this network as a matrix with 38 columns representing the reactions and 52 rows representing the indivi...
Data
A list of internal and external metabolites. This list details which of the measurable and constrained metabolites were classified as internal or external to the network, along with a short rationale for each. (XLSX)
Data
ANOVA examining the effects of compression time on metabolite abundance. Samples taken at 15 and 30 minutes. The table shows the P-values for the null hypothesis when analyzed by two-factor ANOVA. (XLSX)
Data
Fluxes calculated from experimental data. Fluxes calculated using each of the biosynthesis reactions (e.g. type II collagen). Also included are the fluxes calculated without a biosynthesis reaction in the matrix. (XLSX)
Data
Precursor ratios used in synthesis reactions examining cartilage matrix synthesis. An explanation of the rationale for choosing precursors for collagen, aggrecan, lipids and albumin is given accompanied by the code used to compute the precursors. (ZIP)
Data
Stoichiometric matrix after modification to accommodate data. The original stoichiometric matrix in S1 was reduced to include only the reactions that transformed known, measurable metabolites to other known, measurable metabolites. (XLSX)
Data
Fluxes maximizing synthesis reaction flux. Fluxes calculated by solving a linear program for maximal for type II, VI collagen, aggrecan, albumin, and lipid biosynthesis using a stoichiometric matrix as constraints. (XLSX)
Data
Fluxes calculated with no biosynthesis reaction. The fluxes were calculated using a stoichiometric matrix that did not include a biosynthesis reaction. Fluxes calculated for time intervals (A) 0 to 15 min. and (B) 15 to 30 min. for compressed and uncompressed cells. Also included are fluxes calculated for (C) compressed cells for time interval 0 to...
Data
LC-MS data for chondrocytes in response to 0–30 minutes of compression. Intensity values from LC-MS analysis of targeted metabolites for central energy metabolism. Note that these values were thresholded as described in the text prior to flux calculations. (TIF)
Article
Full-text available
Given a set of datacenters and groups of application clients, well-connected datacenters can be rented as traffic proxies to reduce client latency. Rental costs must be minimized while meeting the application specific latency needs. Here, we formally define the Cooperative Group Provisioning problem and show it is NP-hard to approximate within a co...
Conference Paper
Full-text available
We propose some novel computational approaches to analyzing historical student transcript data to help improve course sequencing and generate default pathways for students to complete a college degree. Additionally, we examine whether there are “hidden prerequisites” to courses and whether there are courses which, when taken early in a student’s ca...
Article
Full-text available
Smart grid technology has the opportunity to revolutionize our control over power consumption. Currently power-requesting jobs are scheduled in an on-demand fashion; power draw begins when the consumer requests power (turns on an appliance) and ends when the job is complete (appliance is turned off). Often such jobs may have some flexibility in the...
Conference Paper
Full-text available
Peak demand scheduling aims to schedule jobs so as to minimize the peak load in the schedule. An important application of this problem comes from scheduling power jobs in the smart grid. Currently, peaks in power demand are due to the aggregation of many jobs being scheduled in an on-demand fashion. Often these have some flexibility in their starti...
Conference Paper
Full-text available
With the advancement of mobile technology, mobile sensing becomes increasingly popular for applications in environmental protection, traffic monitoring, and health care. Apart from sensing, mobile phones have also been suggested to facilitate data collection from wireless sensors in their surroundings. The idea is to use smart phones to collect dat...
Conference Paper
Full-text available
Multi-spectrum cognitive radios can be deployed in a wireless network to enhance the capacity of the network by reserving multiple channels in multiple frequencies for each link. In this paper we focus on the topology control approach for wireless networking with cognitive radios in which the network operator must lease channels that will be used i...
Conference Paper
Full-text available
Uncertainties arise in the actual transmission rates achievable over various channels available on wireless links and in the interference characteristics of those links. In this work, we examine a dynamical learning approach to link scheduling for coping with this uncertainty in multihop cognitive relay networks. We formalize a scheduling with unce...
Conference Paper
Full-text available
While extending the lifetime of a wireless sensor network (WSN) with full coverage has been extensively studied, it was found recently that the lifetime of a WSN can be prolonged significantly if partial covers are used instead. In this paper, we formally define the problem of extending the lifetime of a WSN using partial covers. (Throughout this p...
Conference Paper
Full-text available
Relay Stations (RSs) can be deployed in a wireless network to extend its coverage and improve its capacity. Smart (directional) antennas can enhance the functionalities of RSs by forming the beam only towards intended receiving Subscriber Stations (SSs). In this paper, we study a joint problem of selecting a beam width and direction for the smart a...
Conference Paper
Full-text available
In this article, we study distributed relay selection methods assuming a dual-hop Decode-and-Forward (DF) relaying protocol. We assume Uplink (UL) phase in a cellular network where multiple source nodes seek the assistance of candidate relay nodes for message delivery. Due to complexity considerations, we consider that each relay node belongs to th...
Article
Full-text available
Secondary users in a cognitive radio mesh network may select from a set of available channels, provided that they do not disrupt communications among primary users. This ability can improve the overall network performance but introduces the question of how to best use the channels. This paper first considers the problem of selecting the channels to...
Article
Full-text available
Relay stations can be deployed between mobile stations and base stations in a single-hop wireless network to extend its coverage and improve its capacity. In this paper, we exploit cooperative diversity, channel diversity and multiuser diversity gains in an OFDMA-based wireless relay network. We study a joint channel and relay assignment problem wi...
Conference Paper
Full-text available
Transparent optical networks must support dynamic traffic demands and end-to-end optical transmission. We present a new physically-aware algorithm based on dynamic programming for routing and wavelength assignment in such networks that considers both linear and nonlinear impairments that accumulated along the transmission path. We show that our alg...
Conference Paper
Full-text available
The most straightforward way to reduce network power consumption is to turn off idle links and nodes (switches/routers), which we call the power down approach. In a wired network, especially in a backbone network, many links are actually “bundles” of multiple physical cables and line cards that can be shut down independently. In this paper, we stud...
Article
Full-text available
Network power consumption can be reduced considerably by adapting link data rates to their offered traffic loads. In this paper, we exploit how to leverage rate adaptation for green networking by studying the following flow allocation problem in wired networks: Given a set of candidate paths for each end-to-end communication session, determine how...
Article
The structures of protein antigen-antibody (Ag-Ab) interfaces contain information about how Ab recognize Ag as well as how Ag are folded to present surfaces for Ag recognition. As such, the Ab surface holds information about Ag folding that resides with the Ab-Ag interface residues and how they interact. In order to gain insight into the nature of...
Conference Paper
Full-text available
Smart (directional) antennas can be deployed in a wireless network to enhance the capacity of the network by forming one or multiple beams only towards intended receivers. In this paper, we focus on the topology control approach for efficient communications in a wireless network with multi-beam smart antennas. This approach pre-computes an antenna...
Conference Paper
Full-text available
Nodes in a cognitive radio mesh network comprised of secondary users may select from a set of available channels provided they do not interfere with primary users. This ability can improve overall network performance but introduces the question of how best to use these channels. Given a routing multipath M, we would like to choose which channels ea...
Article
Full-text available
Current de novo genome sequence assemblers use paired-end read data from high throughput next-generation technology in order to reconstruct genomes. These assemblers produce longer contiguous sequences known as contigs. Using the paired-end read data it becomes possible to assess the relative order and orientation of the contigs; a process known as...
Conference Paper
Full-text available
Relay Stations (RSs) can be deployed in a wireless network to extend its coverage and improve its capacity. Smart (directional) antennas can enhance the functionalities of RSs by forming one or multiple beams only towards intended receivers. In this paper, we focus on the topology control approach for efficient communications in wireless relay netw...
Conference Paper
Full-text available
Relay stations can be deployed in a wireless network to extend its coverage and improve its capacity. In this paper, we study a scheduling problem in OFDMA-based wireless relay networks with consideration for multi-user diversity, channel diversity and spatial reuse. First, we present a Mixed Integer Linear Programming (MILP) formulation to provide...
Article
Different physical impairments can occur in optical transmission systems. Impairments such as fiber nonlinear effects are dependent on network state and vary with traffic and topology changes. In all-optical networks, impairments can accumulate along a lightpath and cause significant signal degradations. It is important to consider these impairment...
Conference Paper
Full-text available
In this paper, we exploit cooperative diversity, channel diversity and multi-user diversity gains in an OFDMA-based wireless relay network by studying a joint channel and relay assignment problem. This problem turns out to be NP-hard. First, a mixed integer linear programming formulation is presented to provide optimal solutions. We then present a...
Conference Paper
Full-text available
Nodes in a cognitive radio mesh network may select from a set of available channels to use provided they do not interfere with primary users. This ability can improve overall network performance but introduces the question of how best to use these channels. This paper addresses the following specific problem: given a routing path P , choose which c...
Conference Paper
Full-text available
MIMO links enable concurrent transmissions of multiple independent data streams between a pair of nodes, which can significantly improve network throughput. In this paper, we study the stream control and scheduling problems in multihop wireless networks with MIMO links. We present a constant factor approximation algorithm as well as an efficient he...
Article
The trend in multi-wavelength optical networks is toward dynamic route and wavelength assignment to support burst-switching or packet switching. Where erbium-doped optical amplifiers (EDFAs) are used for multi-wavelength amplifications, the time interval between traffic blocks can be long enough to induce EDFA optical power transients created by ab...
Article
Full-text available
This paper presents a performance evaluation of soliton and non-soliton-based all-optical wavelength division multiplexed (WDM) networks assuming the existing infrastructure (e.g., fiber and other physical layer components). The performance evaluation is carried out using the quality (Q) factor, which is a measure of the signal-to-noise ratio, and...
Article
Rhodopsin is the best-understood member of the large G protein–coupled receptor (GPCR) superfamily. The G-protein amplification cascade is triggered by poorly understood light-induced conformational changes in rhodopsin that are homologous to changes caused by agonists in other GPCRs. We have applied the “antibody imprint” method to light-activated...
Article
Multi-wavelength optical networks make extensive use of erbium-doped optical amplifiers (EDFAs) to offset the effects of fiber attenuation and signal power splitting. As optical networking moves towards burst and packet switching, the effects of changes of optical power levels on one wavelength, or channel, can have an impact on the behavior of oth...
Article
Full-text available
Many erbium doped fiber amplifier (EDFA) based multi-wavelength optical networks employ techniques such as burst-switching or packet switching where the time interval between traffic blocks can be long enough to induce EDFA optical power transients. The optical power transients are created by abrupt changes in the average input power to the EDFAs a...
Conference Paper
Full-text available
MIMO links can significantly improve network throughput by supporting multiple concurrent data streams between a pair of nodes and suppressing wireless interference. In this paper, we formally define a new cross-layer optimization problem for MIMO-based multihop wireless networks, which is referred to as the joint stream control and scheduling prob...
Article
We present a randomized polynomial-time approximation algorithm for the fixed linear crossing number problem (FLCNP). In this problem, the vertices of a graph are placed in a fixed order along a horizontal “node line” in the plane, each edge is drawn as an arc in one of the two half-planes (pages), and the objective is to minimize the number of edg...