Demo Data from VLDB 2026 / reviewers in the wild / expert
Mark Coletti
dblp:21/4602 · also Mark A. Coletti
· DBLP profile ↗
8ranked-venue papers
2as first author
4since 2021 · last 2024
0000-0003-1020-531XORCID · verified
Domains — the database's venue-derived domains; a paper can count in several
Artificial intelligence and machine learning · 5 · 2 first-author · 2 since 2021Applied, interdisciplinary, general and emerging computing · 2 · 2 since 2021Systems, architecture and hardware · 1Software engineering, systems software and programming languages · 1 · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 3 heaviest of 3, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology
protein structure prediction |
0.7 | 1 | 2023 | Predicted structural proteome of Sphagnum divinum and proteome-scale annotation · Bioinform. 2023 |
Bioinformatics and computational biology › proteomics
structural proteomics |
0.7 | 1 | 2023 | Predicted structural proteome of Sphagnum divinum and proteome-scale annotation · Bioinform. 2023 |
Bioinformatics and computational biology › protein function prediction › enzyme function prediction
enzyme classification |
0.2 | 1 | 2023 | Predicted structural proteome of Sphagnum divinum and proteome-scale annotation · Bioinform. 2023 |
Methods — techniques the papers use, named apart from their topics
structural alignment · 0.7alphafold · 0.7
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | Workflow Provenance in the Computing Continuum for Responsible, Trustworthy, and Energy-Efficient AIabstractAs Artificial Intelligence (AI) becomes more pervasive in our society, it is crucial to develop, deploy, and assess Responsible and Trustworthy AI (RTAI) models, i.e., those that consider not only accuracy but also other aspects, such as explainability, fairness, and energy efficiency. Workflow provenance data have historically enabled critical capabilities towards RTAI. Provenance data derivation paths contribute to responsible workflows through transparency in tracking artifacts and resource consumption. Provenance data are well-known for their trustworthiness helping explainability, reproducibility, and accountability. However, there are complex challenges to achieve RTAI, which are further complicated by the heterogeneous infrastructure in the computing continuum (Edge-Cloud-HPC) used to develop and deploy models. As a result, a significant research and development gap remains between workflow provenance data management and RTAI. In this paper, we present a vision of the pivotal role of workflow provenance in supporting RTAI and discuss related challenges. We present a schematic view between RTAI and provenance, and highlight open research directions. Renan Souza 0001, Silvina Caíno-Lores, Mark Coletti, Tyler J. Skluzacek, Alexandru Costan, Frédéric Suter, Marta Mattoso, Rafael Ferreira da Silva |
e-Science | 3 |
| 2023 | Predicted structural proteome of Sphagnum divinum and proteome-scale annotationabstractMOTIVATION: Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. RESULTS: We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation. AVAILABILITY AND IMPLEMENTATION: All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv. Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova |
Bioinform. | 2 |
| 2023 | Avoiding excess computation in asynchronous evolutionary algorithmsabstractAbstract Asynchronous evolutionary algorithms are becoming increasingly popular as a means of making full use of many processors while solving computationally expensive search and optimization problems. These algorithms excel at keeping large clusters fully utilized, but may sometimes inefficiently sample an excess of fast‐evaluating solutions at the expense of higher‐quality, slow‐evaluating ones. We have previously introduced a steady‐state parent selection strategy, SWEET (“Selection whilE EvaluaTing”), that sometimes selects individuals that are still being evaluated and allows them to reproduce early. We perform a takeover‐time analysis that confirms that this strategy gives slow‐evaluating individuals that have higher fitnesses an increased ability to multiply in the population. We also find that SWEET appears effective at improving optimization performance on problems in which solution quality is positively correlated with evaluation time. We evaluate our approach on six simulated real‐valued optimization problems and three real‐world applications: an autonomous vehicle controller problem that involves tuning a spiking neural network and two adversarial EA problems. We further evaluate SWEET versus a basic asynchronous process in a simulated setting. We present evidence that SWEET outperforms basic asynchronous processes in a use‐case in which performance is positively correlated with evaluation time, and performs comparably (and often better) than basic asynchronous processes in several use‐cases where performance is negatively correlated with evaluation time. That said, in the cases where performance and evaluation time are negatively correlated the variance of outcomes for SWEET is notably high. Eric O. Scott, Mark Coletti, Catherine D. Schuman, Bill Kay, Shruti R. Kulkarni, Maryam Parsa, Chathika Gunaratne, Kenneth A. De Jong |
Expert Syst. J. Knowl. Eng. | 2 |
| 2021 | Multi-Objective Hyperparameter Optimization for Spiking Neural Network NeuroevolutionabstractNeuroevolution has had significant success over recent years, but there has been relatively little work applying neuroevolution approaches to spiking neural networks (SNNs). SNNs are a type of neural networks that include temporal processing component, are not easily trained using other methods because of their lack of differentiable activation functions, and can be deployed into energy-efficient neuromorphic hardware. In this work, we investigate two evolutionary approaches for training SNNs. We explore the impact of the hyperparameters of the evolutionary approaches, including tournament size, population size, and representation type, on the performance of the algorithms. We present a multi-objective Bayesian-based hyperparameter optimization approach to tune the hyperparameters to produce the most accurate and smallest SNNs. We show that the hyperparameters can significantly affect the performance of these algorithms. We also perform sensitivity analysis and demonstrate that every hyperparameter value has the potential to perform well, assuming other hyperparameter values are set correctly. Maryam Parsa, Shruti R. Kulkarni, Mark Coletti, Jeffrey K. Bassett, J. Parker Mitchell, Catherine D. Schuman |
CEC | 3 |
| 2019 | Performance analysis and optimization for scalable deployment of deep learning models for country-scale settlement mapping on Titan supercomputerabstractSummary This paper presents a scalable object detection workflow for detecting objects, such as settlements, from remotely sensed (RS) imagery. We have successfully deployed this workflow on Titan supercomputer and utilized it for the task of mapping human settlement at a country scale. The performance of various stages in the workflow was analyzed before making it operational. The workflow implemented various strategies to address issues such as suboptimal resource utilization and long‐tail effects due to unbalanced image workload, data loss due to runtime failures, and maximum wall‐time constraints imposed by Titan's job scheduling policy. A mean shift clustering–based static load balancing strategy was implemented, which partitions the image load such that each partition contained similar‐sized images. Furthermore, a checkpoint‐restart strategy was added in the workflow as a fault‐tolerance mechanism to prevent the data losses due to unforeseen runtime failures. The performance of the above‐mentioned strategies was observed in various scenarios, such as node failure, exceeding wall time, and successful completion. Using this workflow, we have processed an RS data set that has a spatial resolution of 0.31 m and is comprised of 685 675 km2 of area of the Republic of Zambia in under six hours using 5426 nodes of the Titan supercomputer. Kuldeep R. Kurte, Jibonananda Sanyal, Andy Berres, Dalton D. Lunga, Mark Coletti, Hsiuhan Lexie Yang, Daniel Graves, Benjamin Liebersohn, Amy N. Rose |
Concurr. Comput. Pract. Exp. | 5 |
| 2009 | The relationship between evolvability and bloatabstractBloat is a common problem with Evolutionary Algorithms (EAs) that use variable length representation. By creating unnecessarily large individuals it results in longer EA runtimes and solutions that are difficult to interpret. The causes of bloat are still uncertain, but one theory suggests that it occurs when the phenotype (e.g. behaviors) of the parents are not successfully inherited by their offspring. Noting the similarity to evolvability theory, which measures heritability of fitness, we hypothesize that reproductive operators with high evolvability will be less likely to cause bloat. Jeffrey K. Bassett, Mark Coletti, Kenneth A. De Jong |
GECCO | 2 |
| 2002 | A preliminary study of learnable evolution methodology implemented with C4.5abstractThe learnable evolution model (LEM) introduces a machine learning-based birth operator into an evolutionary computing algorithm. New individuals are generated from hypotheses learned by the operator from the most-fit and least-fit parent sub-populations. The LEM allows for arbitrary machine learning mechanisms, though, so far, only an AQ (Algorithm Quasi-optimal) based machine learner has been used in LEM implementations. This paper describes preliminary results using a different machine learner in a LEM implementation - C4.5. Mark Coletti |
IEEE Congress on Evolutionary Computation | 1 |
| 1999 | Comparing Performance of the Learnable Evolution Model and Genetic Algorithms
Mark Coletti, Thomas D. Lash, Ryszard S. Michalski, Craig Mandsager, Rida E. Moustafa |
GECCO | 1 |