Doctor of Philosophy

dissertationElectronic Health Records (EHRs) provide a wealth of information for secondary uses. Methods are developed to improve usefulness of free text query and text processing and demonstrate advantages to using these methods for clinical research, specifically cohort identification and enhancement. Cohort identification is a critical early step in clinical research. Problems may arise when too few patients are identified, or the cohort consists of a nonrepresentative sample. Methods of improving query formation through query expansion are described. Inclusion of free text search in addition to structured data search is investigated to determine the incremental improvement of adding unstructured text search over structured data search alone. Query expansion using topic- and synonym-based expansion improved information retrieval performance. An ensemble method was not successful. The addition of free text search compared to structured data search alone demonstrated increased cohort size in all cases, with dramatic increases in some. Representation of patients in subpopulations that may have been underrepresented otherwise is also shown. We demonstrate clinical impact by showing that a serious clinical condition, scleroderma renal crisis, can be predicted by adding free text search. A novel information extraction algorithm is developed and evaluated (Regular Expression Discovery for Extraction, or REDEx) for cohort enrichment. The REDEx algorithm is demonstrated to accurately extract information from free text clinical iv narratives. Temporal expressions as well as bodyweight-related measures are extracted. Additional patients and additional measurement occurrences are identified using these extracted values that were not identifiable through structured data alone. The REDEx algorithm transfers the burden of machine learning training from annotators to domain experts. We developed automated query expansion methods that greatly improve performance of keyword-based information retrieval. We also developed NLP methods for unstructured data and demonstrate that cohort size can be greatly increased, a more complete population can be identified, and important clinical conditions can be detected that are often missed otherwise. We found a much more complete representation of patients can be obtained. We also developed a novel machine learning algorithm for information extraction, REDEx, that efficiently extracts clinical values from unstructured clinical text, adding additional information and observations over what is available in structured text alone

What Works Better? A Study of Classifying Requirements

Classifying requirements into functional requirements (FR) and non-functional ones (NFR) is an important task in requirements engineering. However, automated classification of requirements written in natural language is not straightforward, due to the variability of natural language and the absence of a controlled vocabulary. This paper investigates how automated classification of requirements into FR and NFR can be improved and how well several machine learning approaches work in this context. We contribute an approach for preprocessing requirements that standardizes and normalizes requirements before applying classification algorithms. Further, we report on how well several existing machine learning methods perform for automated classification of NFRs into sub-categories such as usability, availability, or performance. Our study is performed on 625 requirements provided by the OpenScience tera-PROMISE repository. We found that our preprocessing improved the performance of an existing classification method. We further found significant differences in the performance of approaches such as Latent Dirichlet Allocation, Biterm Topic Modeling, or Naive Bayes for the sub-classification of NFRs.Comment: 7 pages, the 25th IEEE International Conference on Requirements Engineering (RE'17

Substring filtering for low-cost linked data interfaces

Recently, Triple Pattern Fragments (TPFS) were introduced as a low-cost server-side interface when high numbers of clients need to evaluate SPARQL queries. Scalability is achieved by moving part of the query execution to the client, at the cost of elevated query times. Since the TPFS interface purposely does not support complex constructs such as SPARQL filters, queries that use them need to be executed mostly on the client, resulting in long execution times. We therefore investigated the impact of adding a literal substring matching feature to the TPFS interface, with the goal of improving query performance while maintaining low server cost. In this paper, we discuss the client/server setup and compare the performance of SPARQL queries on multiple implementations, including Elastic Search and case-insensitive FM-index. Our evaluations indicate that these improvements allow for faster query execution without significantly increasing the load on the server. Offering the substring feature on TPF servers allows users to obtain faster responses for filter-based SPARQL queries. Furthermore, substring matching can be used to support other filters such as complete regular expressions or range queries

Regular Expression Search on Compressed Text

We present an algorithm for searching regular expression matches in compressed text. The algorithm reports the number of matching lines in the uncompressed text in time linear in the size of its compressed version. We define efficient data structures that yield nearly optimal complexity bounds and provide a sequential implementation --zearch-- that requires up to 25% less time than the state of the art.Comment: 10 pages, published in Data Compression Conference (DCC'19

An Efficient Algorithm for Mining Frequent Sequence with Constraint Programming

The main advantage of Constraint Programming (CP) approaches for sequential pattern mining (SPM) is their modularity, which includes the ability to add new constraints (regular expressions, length restrictions, etc). The current best CP approach for SPM uses a global constraint (module) that computes the projected database and enforces the minimum frequency; it does this with a filtering algorithm similar to the PrefixSpan method. However, the resulting system is not as scalable as some of the most advanced mining systems like Zaki's cSPADE. We show how, using techniques from both data mining and CP, one can use a generic constraint solver and yet outperform existing specialized systems. This is mainly due to two improvements in the module that computes the projected frequencies: first, computing the projected database can be sped up by pre-computing the positions at which an symbol can become unsupported by a sequence, thereby avoiding to scan the full sequence each time; and second by taking inspiration from the trailing used in CP solvers to devise a backtracking-aware data structure that allows fast incremental storing and restoring of the projected database. Detailed experiments show how this approach outperforms existing CP as well as specialized systems for SPM, and that the gain in efficiency translates directly into increased efficiency for other settings such as mining with regular expressions.Comment: frequent sequence mining, constraint programmin

Video Synthesis from the StyleGAN Latent Space

Generative models have shown impressive results in generating synthetic images. However, video synthesis is still difficult to achieve, even for these generative models. The best videos that generative models can currently create are a few seconds long, distorted, and low resolution. For this project, I propose and implement a model to synthesize videos at 1024x1024x32 resolution that include human facial expressions by using static images generated from a Generative Adversarial Network trained on the human facial images. To the best of my knowledge, this is the first work that generates realistic videos that are larger than 256x256 resolution from single starting images. This model improves the video synthesis in both quantitative and qualitative ways compared to two state-of-the-art models: TGAN and MocoGAN. In a quantitative comparison, this project reaches a best Average Content Distance (ACD) score of 0.167, as compared to 0.305 and 0.201 of TGAN and MocoGAN, respectively