I am interested in all aspects of software engineering and
practical applications of natural language processing and applied
machine learning,
especially involving clinical / medical texts and data.
I studied Computer Science with a focus in Artificial Intelligence
and a minor subject in Physics
at the University
of
Koblenz-Landau, Germany and finished with the degree
Diplom-Informatiker.
Publications
2020
Tomasz Oliwa, Brian Furner, Jessica Schmitt, John Schneider,
Jessica P Ridgway, Development of a predictive model
for retention in HIV care using natural language processing of
clinical notes, Journal of the American Medical Informatics Association, ,
ocaa220, https://doi.org/10.1093/jamia/ocaa220 PubMed-Link
2019
Obtaining Knowledge in Pathology Reports Through a Natural
Language Processing Approach
With Classification, Named-Entity Recognition, and
Relation-Extraction Heuristics
Tomasz Oliwa, Steven B. Maron, Leah M. Chase, Samantha Lomnicki,
Daniel V.T. Catenacci, Brian Furner, and Samuel L. Volchenboum JCO Clinical Cancer Informatics 2019 :3, 1-8, DOI:
10.1200/CCI.19.00008 , PMID: 31365274 LinkPubMed-Link
2018
Steven Brad Maron, Smita Suhas Joshi, S Lomnicki, Tomasz Oliwa,
Stacie Landron, Julie Johnson,
Lesli Ann Kiedrowski, Rebecca J Nagy, Richard B. Lanman, Yelena
Yuriy Janjigian, Kaitlyn J. Kelly, Seung Tae Kim,
Jeeyun Lee, Daniel V.T. Catenacci, "Circulating tumor DNA (ctDNA)
landscape and prognostic implications in
advanced gastroesophageal adenocarcinoma (GEC).", Journal of Clinical Oncology 36, no. 4_suppl (February
2018) 45-45., DOI: 10.1200/JCO.2018.36.4_suppl.45 Abstract Link
2015
Tomasz Oliwa and Yang Shen, "cNMA: a framework of encounter
complex-based normal mode analysis
to model conformational changes in protein interactions." Bioinformatics 31.12 (2015):
i151-i160.
Published by Oxford University
Press. Link
2014
Tomasz Oliwa and Yang
Shen, "A complex-based normal mode analysis for conformational
changes upon
protein binding", 3DSIG 2014
Poster Abstract, Structural Bioinformatics and
Computational Biophysics, ISMB Satellite Meeting, Boston, USA, 2014.
2013
Tomasz Oliwa and Khaled Rasheed, "An overlapping variable linkage
benchmark suite".
Proceedings of the 15th annual conference companion on Genetic and
evolutionary computation
(GECCO '13 Companion),
Christian Blum (Ed.). ACM, New York, NY, USA, 127-128. BibTex - ACM
Link - ACM
Author-Izer PDF
2012
Tomasz Oliwa and Khaled Rasheed, "A Surrogate-Assisted and
Informed Linkage Aware GA",
Proceedings of the 14th annual conference companion on Genetic and
evolutionary computation
(GECCO Companion '12),
Terence Soule (Ed.). ACM, New York, NY, USA, 1467-1468. BibTex - ACM
Link - ACM
Author-Izer PDF
2011
Tomasz Oliwa and Khaled Rasheed, "A surrogate-assisted linkage
inference approach in genetic algorithms",
Proceedings of the 13th annual conference on Genetic and
evolutionary computation (GECCO
2011),
Natalio Krasnogor (Ed.). ACM, New York, NY, USA, 997-1004. BibTex - ACM
Link - ACM
Author-Izer PDF
2010
Tomasz Oliwa and Khaled Rasheed, "A Machine Learning Approach for
Sensitivity Inference in Genetic Algorithms",
Proceedings of the 2010 International Conference on Genetic and
Evolutionary Methods (GEM'2010),
Las Vegas, USA, 2010. BibTeX
2008
Tomasz Oliwa, "Genetic Algorithms and the abc Music Notation
Language for Rock Music Composition",
Proceedings of the 10th annual conference on Genetic and
evolutionary computation (GECCO
2008),
ACM, New York, NY, 1603-1610. BibTeX - ACM
Link - ACM
Author-Izer PDF
Tomasz Oliwa and Markus Wagner, "Composing Music with Neural
Networks and Probabilistic Finite-State Machines",
Proceedings of the Sixth European Workshop on Evolutionary and
Biologically Inspired Music, Sound, Art and Design
(EvoMUSART 2008), Springer
Berlin / Heidelberg, Springer, 503-508. BibTeX - Springer
LNCS
4974 - PDF
The final publication is available at www.springerlink.com.
Other
Conference/Symposium Presentations
2019
Presentation
Brian Furner and Tomasz Oliwa, "Using NLP in Clinical Data
Analytics", presented at the CRI Seminar Series
2017
Presentation
Brian Furner and Tomasz Oliwa, "Using NLP in Clinical Data
Analytics", presented at the CRI Seminar Series
2014
Presentation
Tomasz Oliwa and Yang Shen, "On conformational changes associated
with protein-protein interactions:
Normal mode analysis for encounter complexes", presented at the Protein Folding Conference 2014,
Punta Cana, Dominican Republic, July 2014
2013
Presentation
Tomasz Oliwa, "Introduction to Evolutionary Computation",
presented at the Center for
Simulational Physics
seminar, Athens, GA, USA, March 2013
2012
Presentation
Tomasz Oliwa and Khaled Rasheed, "A surrogate-assisted and
informed linkage aware GA",
presented at the Computer Science Advisory Board Poster Session,
Athens, GA, USA, October 2012
1st place: Best Poster Award
(from 41 accepted posters) Best Poster Award, Tomasz Oliwa,
"Music Composition with Artificial Intelligence", poster
presentation at the UGA Computer
Science Research Day, Athens, GA, USA.
Presentation
Tomasz Oliwa, "Machine Learning techniques utilized for Prediction
and Classification on the Alzheimer's
Disease Neuroimaging Initiative (ADNI) dataset", presented at the
Graduate Student Conference, Athens, GA, USA.
2008
Presentation
Tomasz Oliwa, "Introducing Structures for Music Composition with
Probabilistic Finite-State Machines", presented at the
8th Annual Georgia Graduate Student Interdisciplinary Conference (GGSIC 2008), Athens, GA, USA.
2006
Presentation
Tomasz Oliwa, "Understand the Java Memory Model", presented at the
5th KeY Symposium 2006,
Speyer, Germany.
Selected Projects
Natural language processing
(NLP) • Stanford CoreNLP Extensions at
https://github.com/toliwa/CoreNLP-jMWE This Stanford CoreNLP
annotator is able to capture Multi-Word Expressions (MWE) /
collocations from plain text. Under the hood, it integrates jMWE,
which itself employs a database generated through processing WordNet.
• Applications of information
retrieval from clinical texts.
Machine Learning
I am interested in developing and applying machine learning
techniques in various domains:
• Applications
of named-entity recognition, document and sentence
level classification, deep learning and topic modeling on
clinical texts.
• Music composition based on inductive learning with
time-delay neural networks, you can get an overview by looking at
this poster.
• Multi-agent predator-prey simulators with feed-forward neural
network trained agents.
• Multi-model based predictors of Alzheimer's disease based on
medical data sets.
Evolutionary Computation
• Evolutionary creativity in the domain of music composition.
Formal Methods, Verification
At the University of Koblenz-Landau, Germany I was a graduate
research assistant in the KeY
Project, a formal methods
tool for specification and verification of object oriented
software.
Virtual/Simulated GNU/Linux
Networks
During my project internship at the University of Koblenz, Germany
I worked on an implementation of NIS and NFS
in Virtual Network
User Mode Linux (VNUML).
Teaching
I have held guest lectures in the following courses:
Fall 2013
CSCI/ARTI 8950 Machine Learning
Spring 2013
CSCI/ARTI 8950 Machine Learning
Fall 2012
CSCI 4560/6560 Evolutionary Computation
Fall 2011
CSCI 4560/6560 Evolutionary Computation
Reviews
•
Reviewer, American Medical Informatics Association 2020
Virtual Annual Symposium (AMIA 2020 Virtual Annual Symposium) • Reviewer, American Medical Informatics
Association 2018 Annual Symposium (AMIA 2018 Annual
Symposium) • Reviewer, Evolutionary
Constrained Optimization, R. Datta and K. Deb (eds.), Springer,
2015 • Program committee, Genetic
and Evolutionary Computation Conference 2018 (GECCO 2018) • Program committee, Genetic and Evolutionary
Computation Conference 2017 (GECCO 2017)
• Program committee, Genetic and Evolutionary Computation
Conference 2016 (GECCO 2016) • Program committee,
Genetic and Evolutionary Computation Conference 2015 (GECCO 2015) • Program committee,
Genetic and Evolutionary Computation Conference 2014 (GECCO 2014)
• Program committee, Genetic and Evolutionary Computation
Conference 2012 (GECCO 2012) •
Reviewer, IEEE Congress on Evolutionary Computation 2020 (CEC
2020) • Reviewer, IEEE
Congress on Evolutionary Computation 2019 (CEC 2019) • Reviewer, IEEE Congress
on Evolutionary Computation 2018 (CEC 2018) • Reviewer, IEEE Congress on
Evolutionary Computation 2017 (CEC 2017) • Reviewer, IEEE
Congress on Evolutionary Computation 2016 (CEC 2016) • Reviewer, IEEE Congress
on Evolutionary Computation 2014 (CEC 2014)
• Reviewer, IEEE Congress on Evolutionary Computation 2013 (CEC
2013)
• Reviewer, IEEE Congress on Evolutionary Computation 2012 (CEC
2012)
• Reviewer, IEEE Symposium Series on Computational Intelligence
2013 (SSCI 2013)
Interests
outside of Computer Science and Artificial Intelligence
Electric Guitar
Download one of my songs/recordings here.
This hard rock instrumental was recorded under GNU/Linux with
audacity
for the guitar recording and hydrogen for the drums. To listen to
it, you will need the Ogg Vorbis sound lib (Open source).
Tae Kwon Do
I used to workout Tae Kwon Do sport at the University of Georgia.
Literature
I enjoy reading some 19th-century German literature and
philosophy.
I also like novels written by Stanislaw Lem and Franz Kafka, and
comparatively modern experimental works such as "House of Leaves"
by Mark Z. Danielewski.
