Works Published in 2021
Displaying works 1 - 20 of 29 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2021 conference paper
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition
SIAM Conference on Applied and Computational Discrete Algorithms (ACDA21), 111–122.
Contributors: B. Sullivan*
TL;DR:
A new combinatorial model for identifying regulatory modules in gene co-expression data using a decomposition into weighted cliques is presented, and two new algorithms for finding these decompositions are presented, using linear programming and integer partitioning to determine the clique weights.
(via Semantic Scholar)
epubs.siam.org (publisher PDF)
Source: ORCID
Added: August 6, 2022
2021 article
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
BioRxiv.
Contributors: M. Pividori *, S. Lu*, B. Li *, C. Su *, M. Johnson *, W. Wei*, Q. Feng *, B. Namjou *
TL;DR:
PhenoPLIER is introduced, a computational approach that maps gene-trait associations and pharmacological perturbation data into a common latent representation for a joint analysis that is accurate in predicting known drug-disease pairs and inferring mechanisms of action.
(via Semantic Scholar)
Source: ORCID
Added: August 6, 2022
2021 journal article
An Updated Experimental Evaluation of Graph Bipartization Methods
ACM Journal of Experimental Algorithmics, 26.
Contributors: T. Goodrich n, E. Horton n & B. Sullivan n
TL;DR:
It is found that for heuristic solutions with time constraints under a second, iterative compression routines jump-started with a heuristic solution perform best, after which point using a highly tuned solver like CPLEX is worthwhile.
(via Semantic Scholar)
Source: ORCID
Added: August 6, 2022
2021 article
Sparse dominating sets and balanced neighborhood partitioning
ArXiv. http://www.scopus.com/inward/record.url?eid=2-s2.0-85121833484&partnerID=MN8TOARS
Contributors: Y. Mizutani, A. Staker & B. Sullivan
Source: ORCID
Added: August 6, 2022
2021 chapter
Secondary Structure Ensemble Analysis via Community Detection
In Association for Women in Mathematics Series (Vol. 22, pp. 55–81).
Contributors: H. Du *, M. Ferrari *, C. Heitsch*, F. Hurley n, C. Mennicke n, B. Sullivan* , B. Xu *
Source: ORCID
Added: August 6, 2022
2021 article
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition
ArXiv. http://www.scopus.com/inward/record.url?eid=2-s2.0-85108789587&partnerID=MN8TOARS
Contributors: M. Cooley, C. Greene, D. Issac, M. Pividori & B. Sullivan
Source: ORCID
Added: August 6, 2022
2021 article
Hardness of the Generalized Coloring Numbers
ArXiv. http://www.scopus.com/inward/record.url?eid=2-s2.0-85121786987&partnerID=MN8TOARS
Contributors: M. Breen-McKay, B. Lavallee & B. Sullivan
Source: ORCID
Added: August 6, 2022
2021 article
Seeds of SEED: New Security Challenges for Persistent Memory
2021 INTERNATIONAL SYMPOSIUM ON SECURE AND PRIVATE EXECUTION ENVIRONMENT DESIGN (SEED 2021), pp. 83–88.
author keywords: Persistent memory objects; Security attacks; PMO vulnerability
TL;DR:
Security implications of using the PMO, highlighting sample PMO-based attacks and potential strategies to defend against them, and threat vulnerabilities that are either new or increased in intensity under PMO programming model are discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: June 20, 2022
2021 article
Recurrent Neural Networks Meet Context-Free Grammar: Two Birds with One Stone
2021 21ST IEEE INTERNATIONAL CONFERENCE ON DATA MINING (ICDM 2021), pp. 1078–1083.
author keywords: recurrent neural networks; data compression; context free grammar; tokenization
TL;DR:
This work introduces CFG-guided compressed learning, an approach that creatively integrates Context-Free Grammar (CFG) and online tokenization into RNN learning and inference for streaming inputs through a hierarchical compression algorithm.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
4. Quality Education
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: May 2, 2022
2021 article
HPCFAIR: Enabling FAIR AI for HPC Applications
PROCEEDINGS OF THE WORKSHOP ON MACHINE LEARNING IN HIGH PERFORMANCE COMPUTING ENVIRONMENTS (MLHPC 2021), pp. 58–68.
author keywords: HPC; FAIR; AI models; datasets; neural networks
TL;DR:
HPCFAIR is proposed, a modular, extensible framework to enable AI models to be Findable, Accessible, Interoperable and Reproducible (FAIR), which enables users with a structured approach to search, load, save and reuse the models in their codes.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: March 21, 2022
2021 article
HPC Ontology: Towards a Unified Ontology for Managing Training Datasets and AI Models for High-Performance Computing
PROCEEDINGS OF THE WORKSHOP ON MACHINE LEARNING IN HIGH PERFORMANCE COMPUTING ENVIRONMENTS (MLHPC 2021), pp. 69–80.
author keywords: Ontology; HPC; FAIR; datasets; AI models
TL;DR:
This paper's ongoing work of designing an ontology for high-performance computing (named HPC ontology) in order to make training datasets and AI models FAIR provides controlled vocabularies, explicit semantics, and formal knowledge representations.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: March 21, 2022
2021 article
Toward Efficient Interactions between Python and Native Libraries
PROCEEDINGS OF THE 29TH ACM JOINT MEETING ON EUROPEAN SOFTWARE ENGINEERING CONFERENCE AND SYMPOSIUM ON THE FOUNDATIONS OF SOFTWARE ENGINEERING (ESEC/FSE '21), pp. 1117–1128.
author keywords: Python; profiling; PMU; debug register
TL;DR:
PieProf, a lightweight profiler, is developed to pinpoint interaction inefficiencies in Python applications and associate inefficiences with high-level Python code to provide a holistic view, and optimization of 17 realworld applications is guided.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: March 7, 2022
2021 article
Revisit the Scalability of Deep Auto-Regressive Models for Graph Generation
2021 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN).
TL;DR:
It is concluded that the perceived “inherent” scalability limitation is a misperception; with the right design and implementation, deep auto-regressive graph generation can be applied to graphs much larger than the device memory.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: January 10, 2022
2021 journal article
UDF to SQL Translation through Compositional Lazy Inductive Synthesis
PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 5(OOPSLA).
author keywords: program synthesis; source-to-source compiler; query optimization
TL;DR:
A new technique for translating SQL queries with UDFs to pure SQL expressions using a novel compositional strategy that decomposes the synthesis task into simpler sub-problems and scales significantly better than traditional CEGIS.
(via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 2, 2022
2021 journal article
Coarsening Optimization for Differentiable Programming
PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 5(OOPSLA).
author keywords: differentiable programming; compiler; program optimizations; SSA; Calculus
TL;DR:
This work introduces phi-calculus, a novel method to allow symbolic reasoning and differentiation of computations that involve branches and loops and avoids "expression swell" in symbolic differentiation and balance reuse and coarsening through the design of reuse-centric segment of interest identification.
(via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 2, 2022
2021 article
Brief Industry Paper: Towards Real-Time 3D Object Detection for Autonomous Vehicles with Pruning Search
2021 IEEE 27TH REAL-TIME AND EMBEDDED TECHNOLOGY AND APPLICATIONS SYMPOSIUM (RTAS 2021), pp. 425–428.
author keywords: 3D object detection; real-time; point cloud
TL;DR:
It is demonstrated in experiments that for the first time, the pruning search framework can achieve real-time 3D object detection on mobile with state-of-the-art detection performance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 29, 2021
2021 journal article
How to "DODGE" Complex Software Analytics
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING, 47(10), 2182–2194.
author keywords: Tuning; Text mining; Software; Task analysis; Optimization; Software engineering; Tools; Software analytics; hyperparameter optimization; defect prediction; text mining
TL;DR:
By ignoring redundant tunings, ODGE, a tuning tool, runs orders of magnitude faster, while also generating learners with more accurate predictions than seen in prior state-of-the-art approaches.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: November 1, 2021
2021 article
Supporting Legacy Libraries on Non-Volatile Memory: A User-Transparent Approach
2021 ACM/IEEE 48TH ANNUAL INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE (ISCA 2021), pp. 443–455.
TL;DR:
A new concept that allows programmers to reference a persistent object in the same way as reference a normal (volatile) object is presented, and compiler and simple architecture support for keeping performance overheads very low is described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 26, 2021
2021 article
G-TADOC: Enabling Efficient GPU-Based Text Analytics without Decompression
2021 IEEE 37TH INTERNATIONAL CONFERENCE ON DATA ENGINEERING (ICDE 2021), pp. 1679–1690.
author keywords: TADOC; GPU; parallelism; analytics on compressed data
TL;DR:
G-TADOC is described, the first framework that provides GPU-based text analytics directly on compression, effectively enabling efficient text analytics on GPUs without decompressing the input data and develops a novel fine-grained thread-level workload scheduling strategy for GPU threads.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: September 20, 2021
2021 article
Hardware-Based Address-Centric Acceleration of Key-Value Store
2021 27TH IEEE INTERNATIONAL SYMPOSIUM ON HIGH-PERFORMANCE COMPUTER ARCHITECTURE (HPCA 2021), pp. 736–748.
TL;DR:
This paper introduces an address-centric approach to speed up the addressing by creating a shortcut for the translation of a key to the physical address of the value, using a novel in-memory table, STLT, a virtual-physical address buffer, and two new instructions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 26, 2021
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