Interactive Machine Learning with Applications in Health Informatics

Recent years have witnessed unprecedented growth of health data, including millions of biomedical research publications, electronic health records, patient discussions on health forums and social media, fitness tracker trajectories, and genome sequences. Information retrieval and machine learning techniques are powerful tools to unlock invaluable knowledge in these data, yet they need to be guided by human experts. Unlike training machine learning models in other domains, labeling and analyzing health data requires highly specialized expertise, and the time of medical experts is extremely limited. How can we mine big health data with little expert effort? In this dissertation, I develop state-of-the-art interactive machine learning algorithms that bring together human intelligence and machine intelligence in health data mining tasks. By making efficient use of human expert's domain knowledge, we can achieve high-quality solutions with minimal manual effort. I first introduce a high-recall information retrieval framework that helps human users efficiently harvest not just one but as many relevant documents as possible from a searchable corpus. This is a common need in professional search scenarios such as medical search and literature review. Then I develop two interactive machine learning algorithms that leverage human expert's domain knowledge to combat the curse of "cold start" in active learning, with applications in clinical natural language processing. A consistent empirical observation is that the overall learning process can be reliably accelerated by a knowledge-driven "warm start", followed by machine-initiated active learning. As a theoretical contribution, I propose a general framework for interactive machine learning. Under this framework, a unified optimization objective explains many existing algorithms used in practice, and inspires the design of new algorithms.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147518/1/raywang_1.pd

Thematic Annotation: extracting concepts out of documents

Contrarily to standard approaches to topic annotation, the technique used in this work does not centrally rely on some sort of -- possibly statistical -- keyword extraction. In fact, the proposed annotation algorithm uses a large scale semantic database -- the EDR Electronic Dictionary -- that provides a concept hierarchy based on hyponym and hypernym relations. This concept hierarchy is used to generate a synthetic representation of the document by aggregating the words present in topically homogeneous document segments into a set of concepts best preserving the document's content. This new extraction technique uses an unexplored approach to topic selection. Instead of using semantic similarity measures based on a semantic resource, the later is processed to extract the part of the conceptual hierarchy relevant to the document content. Then this conceptual hierarchy is searched to extract the most relevant set of concepts to represent the topics discussed in the document. Notice that this algorithm is able to extract generic concepts that are not directly present in the document.Comment: Technical report EPFL/LIA. 81 pages, 16 figure

Applying Wikipedia to Interactive Information Retrieval

There are many opportunities to improve the interactivity of information retrieval systems beyond the ubiquitous search box. One idea is to use knowledge bases—e.g. controlled vocabularies, classification schemes, thesauri and ontologies—to organize, describe and navigate the information space. These resources are popular in libraries and specialist collections, but have proven too expensive and narrow to be applied to everyday webscale search. Wikipedia has the potential to bring structured knowledge into more widespread use. This online, collaboratively generated encyclopaedia is one of the largest and most consulted reference works in existence. It is broader, deeper and more agile than the knowledge bases put forward to assist retrieval in the past. Rendering this resource machine-readable is a challenging task that has captured the interest of many researchers. Many see it as a key step required to break the knowledge acquisition bottleneck that crippled previous efforts. This thesis claims that the roadblock can be sidestepped: Wikipedia can be applied effectively to open-domain information retrieval with minimal natural language processing or information extraction. The key is to focus on gathering and applying human-readable rather than machine-readable knowledge. To demonstrate this claim, the thesis tackles three separate problems: extracting knowledge from Wikipedia; connecting it to textual documents; and applying it to the retrieval process. First, we demonstrate that a large thesaurus-like structure can be obtained directly from Wikipedia, and that accurate measures of semantic relatedness can be efficiently mined from it. Second, we show that Wikipedia provides the necessary features and training data for existing data mining techniques to accurately detect and disambiguate topics when they are mentioned in plain text. Third, we provide two systems and user studies that demonstrate the utility of the Wikipedia-derived knowledge base for interactive information retrieval

Ontology-Based Quality Evaluation of Value Generalization Hierarchies for Data Anonymization

In privacy-preserving data publishing, approaches using Value Generalization Hierarchies (VGHs) form an important class of anonymization algorithms. VGHs play a key role in the utility of published datasets as they dictate how the anonymization of the data occurs. For categorical attributes, it is imperative to preserve the semantics of the original data in order to achieve a higher utility. Despite this, semantics have not being formally considered in the specification of VGHs. Moreover, there are no methods that allow the users to assess the quality of their VGH. In this paper, we propose a measurement scheme, based on ontologies, to quantitatively evaluate the quality of VGHs, in terms of semantic consistency and taxonomic organization, with the aim of producing higher-quality anonymizations. We demonstrate, through a case study, how our evaluation scheme can be used to compare the quality of multiple VGHs and can help to identify faulty VGHs.Comment: 18 pages, 7 figures, presented in the Privacy in Statistical Databases Conference 2014 (Ibiza, Spain

PersoNER: Persian named-entity recognition

© 1963-2018 ACL. Named-Entity Recognition (NER) is still a challenging task for languages with low digital resources. The main difficulties arise from the scarcity of annotated corpora and the consequent problematic training of an effective NER pipeline. To abridge this gap, in this paper we target the Persian language that is spoken by a population of over a hundred million people world-wide. We first present and provide ArmanPerosNERCorpus, the first manually-annotated Persian NER corpus. Then, we introduce PersoNER, an NER pipeline for Persian that leverages a word embedding and a sequential max-margin classifier. The experimental results show that the proposed approach is capable of achieving interesting MUC7 and CoNNL scores while outperforming two alternatives based on a CRF and a recurrent neural network

A knowledge-based approach to information extraction for semantic interoperability in the archaeology domain

The paper presents a method for automatic semantic indexing of archaeological grey-literature reports using empirical (rule-based) Information Extraction techniques in combination with domain-specific knowledge organization systems. Performance is evaluated via the Gold Standard method. The semantic annotation system (OPTIMA) performs the tasks of Named Entity Recognition, Relation Extraction, Negation Detection and Word Sense disambiguation using hand-crafted rules and terminological resources for associating contextual abstractions with classes of the standard ontology (ISO 21127:2006) CIDOC Conceptual Reference Model (CRM) for cultural heritage and its archaeological extension, CRM-EH, together with concepts from English Heritage thesauri and glossaries.Relation Extraction performance benefits from a syntactic based definition of relation extraction patterns derived from domain oriented corpus analysis. The evaluation also shows clear benefit in the use of assistive NLP modules relating to word-sense disambiguation, negation detection and noun phrase validation, together with controlled thesaurus expansion.The semantic indexing results demonstrate the capacity of rule-based Information Extraction techniques to deliver interoperable semantic abstractions (semantic annotations) with respect to the CIDOC CRM and archaeological thesauri. Major contributions include recognition of relevant entities using shallow parsing NLP techniques driven by a complimentary use of ontological and terminological domain resources and empirical derivation of context-driven relation extraction rules for the recognition of semantic relationships from phrases of unstructured text. The semantic annotations have proven capable of supporting semantic query, document study and cross-searching via the ontology framework

A statistical approach to a verb vector task classifier

A thesis submitted to the University of Bedfordshire, in fulfilment ofthe requirements for the degree of Master of Science by researchHow to enable a service robot to understand its user's intention is a hot topic of research today. Based on its understanding, the robot can coordinate and adjust its behaviours to provide desired assistance and services to the user as a capable partner. Active Robot Learning (ARL) is an approach to the development of the understanding of human intention. The task action bank is part of the ARL which can store task categories. In this approach, a robot actively performs test actions in order to obtain its user's intention from the user's response to the action. This thesis presents an approach to verbs clustering based on the basic action required of the robot, using a statistical method. A parser is established to process a corpus and analyse the probability of the verb feature vector, for example when the user says "bring me a cup of coffee", this means the same as "give me a cup of coffee". This parser could identify similar verbs between "bring" and "give" with the statistical method. Experimental results show the collocation between semantically related verbs, which can be further utilised to establish a test action bank for Active Robot Learning (ARL)

Neural correlates of the processing of co-speech gestures

In communicative situations, speech is often accompanied by gestures. For example, speakers tend to illustrate certain contents of speech by means of iconic gestures which are hand movements that bear a formal relationship to the contents of speech. The meaning of an iconic gesture is determined both by its form as well as the speech context in which it is performed. Thus, gesture and speech interact in comprehension. Using fMRI, the present study investigated what brain areas are involved in this interaction process. Participants watched videos in which sentences containing an ambiguous word (e.g. She touched the mouse) were accompanied by either a meaningless grooming movement, a gesture supporting the more frequent dominant meaning (e.g. animal) or a gesture supporting the less frequent subordinate meaning (e.g. computer device). We hypothesized that brain areas involved in the interaction of gesture and speech would show greater activation to gesture-supported sentences as compared to sentences accompanied by a meaningless grooming movement. The main results are that when contrasted with grooming, both types of gestures (dominant and subordinate) activated an array of brain regions consisting of the left posterior superior temporal sulcus (STS), the inferior parietal lobule bilaterally and the ventral precentral sulcus bilaterally. Given the crucial role of the STS in audiovisual integration processes, this activation might reflect the interaction between the meaning of gesture and the ambiguous sentence. The activations in inferior frontal and inferior parietal regions may reflect a mechanism of determining the goal of co-speech hand movements through an observation-execution matching process

Automated Coding of Under-Studied Medical Concept Domains: Linking Physical Activity Reports to the International Classification of Functioning, Disability, and Health

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.Comment: Updated final version, published in Frontiers in Digital Health, https://doi.org/10.3389/fdgth.2021.620828. 34 pages (23 text + 11 references); 9 figures, 2 table