ILR Research in Progress 2011-12

The production of scholarly research continues to be one of the primary missions of the ILR School. During a typical academic year, ILR faculty members published or had accepted for publication over 25 books, edited volumes, and monographs, 170 articles and chapters in edited volumes, numerous book reviews. In addition, a large number of manuscripts were submitted for publication, presented at professional association meetings, or circulated in working paper form. Our faculty's research continues to find its way into the very best industrial relations, social science and statistics journals.Research_in_Progress_2011_12.pdf: 46 downloads, before Oct. 1, 2020

Survey of the State of the Art in Natural Language Generation: Core tasks, applications and evaluation

This paper surveys the current state of the art in Natural Language Generation (NLG), defined as the task of generating text or speech from non-linguistic input. A survey of NLG is timely in view of the changes that the field has undergone over the past decade or so, especially in relation to new (usually data-driven) methods, as well as new applications of NLG technology. This survey therefore aims to (a) give an up-to-date synthesis of research on the core tasks in NLG and the architectures adopted in which such tasks are organised; (b) highlight a number of relatively recent research topics that have arisen partly as a result of growing synergies between NLG and other areas of artificial intelligence; (c) draw attention to the challenges in NLG evaluation, relating them to similar challenges faced in other areas of Natural Language Processing, with an emphasis on different evaluation methods and the relationships between them.Comment: Published in Journal of AI Research (JAIR), volume 61, pp 75-170. 118 pages, 8 figures, 1 tabl

Discovering prescription patterns in pediatric acute-onset neuropsychiatric syndrome patients

OBJECTIVE: Pediatric acute-onset neuropsychiatric syndrome (PANS) is a complex neuropsychiatric syndrome characterized by an abrupt onset of obsessive-compulsive symptoms and/or severe eating restrictions, along with at least two concomitant debilitating cognitive, behavioral, or neurological symptoms. A wide range of pharmacological interventions along with behavioral and environmental modifications, and psychotherapies have been adopted to treat symptoms and underlying etiologies. Our goal was to develop a data-driven approach to identify treatment patterns in this cohort. MATERIALS AND METHODS: In this cohort study, we extracted medical prescription histories from electronic health records. We developed a modified dynamic programming approach to perform global alignment of those medication histories. Our approach is unique since it considers time gaps in prescription patterns as part of the similarity strategy. RESULTS: This study included 43 consecutive new-onset pre-pubertal patients who had at least 3 clinic visits. Our algorithm identified six clusters with distinct medication usage history which may represent clinician\u27s practice of treating PANS of different severities and etiologies i.e., two most severe groups requiring high dose intravenous steroids; two arthritic or inflammatory groups requiring prolonged nonsteroidal anti-inflammatory drug (NSAID); and two mild relapsing/remitting group treated with a short course of NSAID. The psychometric scores as outcomes in each cluster generally improved within the first two years. DISCUSSION AND CONCLUSION: Our algorithm shows potential to improve our knowledge of treatment patterns in the PANS cohort, while helping clinicians understand how patients respond to a combination of drugs

ILR Faculty Research in Progress, 2015-2016

The production of scholarly research continues to be one of the primary missions of the ILR School. During a typical academic year, ILR faculty members published or had accepted for publication over 25 books, edited volumes, and monographs, 170 articles and chapters in edited volumes, numerous book reviews. In addition, a large number of manuscripts were submitted for publication, presented at professional association meetings, or circulated in working paper form. Our faculty's research continues to find its way into the very best industrial relations, social science and statistics journals.ResearchinProgress_2015_16.pdf: 22 downloads, before Oct. 1, 2020

Privacy in the Genomic Era

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward

Predicting morbidity by local similarities in multi-scale patient trajectories

[EN] Patient Trajectories (PTs) are a method of representing the temporal evolution of patients. They can include information from different sources and be used in socio-medical or clinical domains. PTs have generally been used to generate and study the most common trajectories in, for instance, the development of a disease. On the other hand, healthcare predictive models generally rely on static snapshots of patient information. Only a few works about prediction in healthcare have been found that use PTs, and therefore benefit from their temporal dimension. All of them, however, have used PTs created from single-source information. Therefore, the use of longitudinal multi-scale data to build PTs and use them to obtain predictions about health conditions is yet to be explored. Our hypothesis is that local similarities on small chunks of PTs can identify similar patients concerning their future morbidities. The objectives of this work are (1) to develop a methodology to identify local similarities between PTs before the occurrence of morbidities to predict these on new query individuals; and (2) to validate this methodology on risk prediction of cardiovascular diseases (CVD) occurrence in patients with diabetes. We have proposed a novel formal definition of PTs based on sequences of longitudinal multi-scale data. Moreover, a dynamic programming methodology to identify local alignments on PTs for predicting future morbidities is proposed. Both the proposed methodology for PT definition and the alignment algorithm are generic to be applied on any clinical domain. We validated this solution for predicting CVD in patients with diabetes and we achieved a precision of 0.33, a recall of 0.72 and a specificity of 0.38. Therefore, the proposed solution in the diabetes use case can result of utmost utility to secondary screening.This work was supported by the CrowdHealth project (COLLECTIVE WISDOM DRIVING PUBLIC HEALTH POLICIES (727560)) and the MTS4up project (DPI2016-80054-R).Carrasco-Ribelles, LA.; Pardo-Más, JR.; Tortajada, S.; Sáez Silvestre, C.; Valdivieso, B.; Garcia-Gomez, JM. (2021). Predicting morbidity by local similarities in multi-scale patient trajectories. Journal of Biomedical Informatics. 120:1-9. https://doi.org/10.1016/j.jbi.2021.103837S1912

Automated methods to extract patient new information from clinical notes in electronic health record systems

University of Minnesota Ph.D. dissertation. November 2013. Major: Health Informatics. Advisor: Serguei Pakhomov. 1 computer file (PDF); xii, 102 pages.The widespread adoption of Electronic Health Record (EHR) has resulted in rapid text proliferation within clinical care. Clinicians' use of copying and pasting functions in EHR systems further compounds this by creating a large amount of redundant clinical information in clinical documents. A mixture of redundant information (especially outdated and incorrect information) and new information in a single clinical note increases clinicians' cognitive burden and results in decision-making difficulties. Moreover, replicated erroneous information can potentially cause risks to patient safety. However, automated methods to identify redundant or relevant new information in clinical texts have not been extensively investigated. The overarching goal of this research is to develop and evaluate automated methods to identify new and clinically relevant information in clinical notes using expert-derived reference standards. Modified global alignment methods were adapted to investigate the pattern of redundancy in individual longitudinal clinical notes as well as a larger group of patient clinical notes. Statistical language models were also developed to identify new and clinically relevant information in clinical notes. Relevant new information identified by automated methods will be highlighted in clinical notes to provide visualization cues to clinicians. New information proportion (NIP) was used to indicate the quantity of new information in each note and also navigate clinician notes with more new information. Classifying semantic types of new information further provides clinicians with specific types of new information that they are interested in finding. The techniques developed in this research can be incorporated into production EHR systems and could potentially aid clinicians in finding and synthesizing new information in a note more purposely, and could finally improve the efficiency of healthcare delivery

Sequential Multi-Dimensional Self-Supervised Learning for Clinical Time Series

Self-supervised learning (SSL) for clinical time series data has received significant attention in recent literature, since these data are highly rich and provide important information about a patient's physiological state. However, most existing SSL methods for clinical time series are limited in that they are designed for unimodal time series, such as a sequence of structured features (e.g., lab values and vitals signs) or an individual high-dimensional physiological signal (e.g., an electrocardiogram). These existing methods cannot be readily extended to model time series that exhibit multimodality, with structured features and high-dimensional data being recorded at each timestep in the sequence. In this work, we address this gap and propose a new SSL method -- Sequential Multi-Dimensional SSL -- where a SSL loss is applied both at the level of the entire sequence and at the level of the individual high-dimensional data points in the sequence in order to better capture information at both scales. Our strategy is agnostic to the specific form of loss function used at each level -- it can be contrastive, as in SimCLR, or non-contrastive, as in VICReg. We evaluate our method on two real-world clinical datasets, where the time series contains sequences of (1) high-frequency electrocardiograms and (2) structured data from lab values and vitals signs. Our experimental results indicate that pre-training with our method and then fine-tuning on downstream tasks improves performance over baselines on both datasets, and in several settings, can lead to improvements across different self-supervised loss functions.Comment: ICML 202