Medical device surveillance with electronic health records

Post-market medical device surveillance is a challenge facing manufacturers, regulatory agencies, and health care providers. Electronic health records are valuable sources of real world evidence to assess device safety and track device-related patient outcomes over time. However, distilling this evidence remains challenging, as information is fractured across clinical notes and structured records. Modern machine learning methods for machine reading promise to unlock increasingly complex information from text, but face barriers due to their reliance on large and expensive hand-labeled training sets. To address these challenges, we developed and validated state-of-the-art deep learning methods that identify patient outcomes from clinical notes without requiring hand-labeled training data. Using hip replacements as a test case, our methods accurately extracted implant details and reports of complications and pain from electronic health records with up to 96.3% precision, 98.5% recall, and 97.4% F1, improved classification performance by 12.7- 53.0% over rule-based methods, and detected over 6 times as many complication events compared to using structured data alone. Using these events to assess complication-free survivorship of different implant systems, we found significant variation between implants, including for risk of revision surgery, which could not be detected using coded data alone. Patients with revision surgeries had more hip pain mentions in the post-hip replacement, pre-revision period compared to patients with no evidence of revision surgery (mean hip pain mentions 4.97 vs. 3.23; t = 5.14; p < 0.001). Some implant models were associated with higher or lower rates of hip pain mentions. Our methods complement existing surveillance mechanisms by requiring orders of magnitude less hand-labeled training data, offering a scalable solution for national medical device surveillance

WikiM: Metapaths based Wikification of Scientific Abstracts

In order to disseminate the exponential extent of knowledge being produced in the form of scientific publications, it would be best to design mechanisms that connect it with already existing rich repository of concepts -- the Wikipedia. Not only does it make scientific reading simple and easy (by connecting the involved concepts used in the scientific articles to their Wikipedia explanations) but also improves the overall quality of the article. In this paper, we present a novel metapath based method, WikiM, to efficiently wikify scientific abstracts -- a topic that has been rarely investigated in the literature. One of the prime motivations for this work comes from the observation that, wikified abstracts of scientific documents help a reader to decide better, in comparison to the plain abstracts, whether (s)he would be interested to read the full article. We perform mention extraction mostly through traditional tf-idf measures coupled with a set of smart filters. The entity linking heavily leverages on the rich citation and author publication networks. Our observation is that various metapaths defined over these networks can significantly enhance the overall performance of the system. For mention extraction and entity linking, we outperform most of the competing state-of-the-art techniques by a large margin arriving at precision values of 72.42% and 73.8% respectively over a dataset from the ACL Anthology Network. In order to establish the robustness of our scheme, we wikify three other datasets and get precision values of 63.41%-94.03% and 67.67%-73.29% respectively for the mention extraction and the entity linking phase

A Concept-Centered Hypertext Approach to Case-Based Retrieval

The goal of case-based retrieval is to assist physicians in the clinical decision making process, by finding relevant medical literature in large archives. We propose a research that aims at improving the effectiveness of case-based retrieval systems through the use of automatically created document-level semantic networks. The proposed research tackles different aspects of information systems and leverages the recent advancements in information extraction and relational learning to revisit and advance the core ideas of concept-centered hypertext models. We propose a two-step methodology that in the first step addresses the automatic creation of document-level semantic networks, then in the second step it designs methods that exploit such document representations to retrieve relevant cases from medical literature. For the automatic creation of documents' semantic networks, we design a combination of information extraction techniques and relational learning models. Mining concepts and relations from text, information extraction techniques represent the core of the document-level semantic networks' building process. On the other hand, relational learning models have the task of enriching the graph with additional connections that have not been detected by information extraction algorithms and strengthening the confidence score of extracted relations. For the retrieval of relevant medical literature, we investigate methods that are capable of comparing the documents' semantic networks in terms of structure and semantics. The automatic extraction of semantic relations from documents, and their centrality in the creation of the documents' semantic networks, represent our attempt to go one step further than previous graph-based approaches

IDEL: In-Database Entity Linking with Neural Embeddings

We present a novel architecture, In-Database Entity Linking (IDEL), in which we integrate the analytics-optimized RDBMS MonetDB with neural text mining abilities. Our system design abstracts core tasks of most neural entity linking systems for MonetDB. To the best of our knowledge, this is the first defacto implemented system integrating entity-linking in a database. We leverage the ability of MonetDB to support in-database-analytics with user defined functions (UDFs) implemented in Python. These functions call machine learning libraries for neural text mining, such as TensorFlow. The system achieves zero cost for data shipping and transformation by utilizing MonetDB's ability to embed Python processes in the database kernel and exchange data in NumPy arrays. IDEL represents text and relational data in a joint vector space with neural embeddings and can compensate errors with ambiguous entity representations. For detecting matching entities, we propose a novel similarity function based on joint neural embeddings which are learned via minimizing pairwise contrastive ranking loss. This function utilizes a high dimensional index structures for fast retrieval of matching entities. Our first implementation and experiments using the WebNLG corpus show the effectiveness and the potentials of IDEL.Comment: This manuscript is a preprint for a paper submitted to VLDB201

Linking Sequences of Events with Sparse or No Common Occurrence across Data Sets

Data of practical interest - such as personal records, transaction logs, and medical histories - are sequential collections of events relevant to a particular source entity. Recent studies have attempted to link sequences that represent a common entity across data sets to allow more comprehensive statistical analyses and to identify potential privacy failures. Yet, current approaches remain tailored to their specific domains of application, and they fail when co-referent sequences in different data sets contain sparse or no common events, which occurs frequently in many cases. To address this, we formalize the general problem of "sequence linkage" and describe "LDA-Link," a generic solution that is applicable even when co-referent event sequences contain no common items at all. LDA-Link is built upon "Split-Document" model, a new mixed-membership probabilistic model for the generation of event sequence collections. It detects the latent similarity of sequences and thus achieves robustness particularly when co-referent sequences share sparse or no event overlap. We apply LDA-Link in the context of social media profile reconciliation where users make no common posts across platforms, comparing to the state-of-the-art generic solution to sequence linkage

Maximal frequent sequences applied to drug-drug interaction extraction

A drug-drug interaction (DDI) occurs when the effects of a drug are modified by the presence of other drugs. DDIs can decrease therapeutic benefit or efficacy of treatments and this could have very harmful consequences in the patient's health that could even cause the patient's death. Knowing the interactions between prescribed drugs is of great clinical importance, it is very important to keep databases up-to-date with respect to new DDI. In this thesis we aim to build a system to assist healthcare professionals to be updated about published drug-drug interactions. The goal of this thesis is to study a method based on maximal frequent sequences (MFS) and machine learning techniques in order to automatically detect interactions between drugs in pharmacological and medical literature. With the study of these methods, the IT community will assist healthcare community to update their drug interactions database in a fast and semi-automatic way. In a first solution, we classify pharmacological sentences depending on whether or not they are describing a drug-drug interaction. This would enable to automatically find sentences containing drug-drug interactions. This solution is completely based in maximal frequent sequences (MFS) extracted from a set of test documents. In a second solution based in machine learning, we go further in the search and perform DDI extraction, determining if two specific drugs appearing in a sentence interact or not. This can be used as an assisting tool to populate databases with drug-drug interactions. The machine learning classifier is trained with several features i.e., bag of words, word categories, MFS, token and char level features and drug level features. The classifier we used was a Random Forest. This system was sent to the DDIExtraction 2011 competition and reached the 6th position. Finally, we introduce Maximal Frequent Discriminative Sequences (MFDS), a novel method of sequential pattern discovery that extends the concept of MFS to adapt it to classification tasks.García Blasco, S. (2012). Maximal frequent sequences applied to drug-drug interaction extraction. http://hdl.handle.net/10251/15342Archivo delegad

Correlation via synthesis: end-to-end nodule image generation and radiogenomic map learning based on generative adversarial network

Radiogenomic map linking image features and gene expression profiles is useful for noninvasively identifying molecular properties of a particular type of disease. Conventionally, such map is produced in three separate steps: 1) gene-clustering to "metagenes", 2) image feature extraction, and 3) statistical correlation between metagenes and image features. Each step is independently performed and relies on arbitrary measurements. In this work, we investigate the potential of an end-to-end method fusing gene data with image features to generate synthetic image and learn radiogenomic map simultaneously. To achieve this goal, we develop a generative adversarial network (GAN) conditioned on both background images and gene expression profiles, synthesizing the corresponding image. Image and gene features are fused at different scales to ensure the realism and quality of the synthesized image. We tested our method on non-small cell lung cancer (NSCLC) dataset. Results demonstrate that the proposed method produces realistic synthetic images, and provides a promising way to find gene-image relationship in a holistic end-to-end manner

Visual Relationship Detection using Scene Graphs: A Survey

Understanding a scene by decoding the visual relationships depicted in an image has been a long studied problem. While the recent advances in deep learning and the usage of deep neural networks have achieved near human accuracy on many tasks, there still exists a pretty big gap between human and machine level performance when it comes to various visual relationship detection tasks. Developing on earlier tasks like object recognition, segmentation and captioning which focused on a relatively coarser image understanding, newer tasks have been introduced recently to deal with a finer level of image understanding. A Scene Graph is one such technique to better represent a scene and the various relationships present in it. With its wide number of applications in various tasks like Visual Question Answering, Semantic Image Retrieval, Image Generation, among many others, it has proved to be a useful tool for deeper and better visual relationship understanding. In this paper, we present a detailed survey on the various techniques for scene graph generation, their efficacy to represent visual relationships and how it has been used to solve various downstream tasks. We also attempt to analyze the various future directions in which the field might advance in the future. Being one of the first papers to give a detailed survey on this topic, we also hope to give a succinct introduction to scene graphs, and guide practitioners while developing approaches for their applications

Entity-centric knowledge discovery for idiosyncratic domains

Technical and scientific knowledge is produced at an ever-accelerating pace, leading to increasing issues when trying to automatically organize or process it, e.g., when searching for relevant prior work. Knowledge can today be produced both in unstructured (plain text) and structured (metadata or linked data) forms. However, unstructured content is still themost dominant formused to represent scientific knowledge. In order to facilitate the extraction and discovery of relevant content, new automated and scalable methods for processing, structuring and organizing scientific knowledge are called for. In this context, a number of applications are emerging, ranging fromNamed Entity Recognition (NER) and Entity Linking tools for scientific papers to specific platforms leveraging information extraction techniques to organize scientific knowledge. In this thesis, we tackle the tasks of Entity Recognition, Disambiguation and Linking in idiosyncratic domains with an emphasis on scientific literature. Furthermore, we study the related task of co-reference resolution with a specific focus on named entities. We start by exploring Named Entity Recognition, a task that aims to identify the boundaries of named entities in textual contents. We propose a newmethod to generate candidate named entities based on n-gram collocation statistics and design several entity recognition features to further classify them. In addition, we show how the use of external knowledge bases (either domain-specific like DBLP or generic like DBPedia) can be leveraged to improve the effectiveness of NER for idiosyncratic domains. Subsequently, we move to Entity Disambiguation, which is typically performed after entity recognition in order to link an entity to a knowledge base. We propose novel semi-supervised methods for word disambiguation leveraging the structure of a community-based ontology of scientific concepts. Our approach exploits the graph structure that connects different terms and their definitions to automatically identify the correct sense that was originally picked by the authors of a scientific publication. We then turn to co-reference resolution, a task aiming at identifying entities that appear using various forms throughout the text. We propose an approach to type entities leveraging an inverted index built on top of a knowledge base, and to subsequently re-assign entities based on the semantic relatedness of the introduced types. Finally, we describe an application which goal is to help researchers discover and manage scientific publications. We focus on the problem of selecting relevant tags to organize collections of research papers in that context. We experimentally demonstrate that the use of a community-authored ontology together with information about the position of the concepts in the documents allows to significantly increase the precision of tag selection over standard methods

Slot Filling

Slot filling (SF) is the task of automatically extracting facts about particular entities from unstructured text, and populating a knowledge base (KB) with these facts. These structured KBs enable applications such as structured web queries and question answering. SF is typically framed as a query-oriented setting of the related task of relation extraction. Throughout this thesis, we reflect on how SF is a task with many distinct problems. We demonstrate that recall is a major limiter on SF system performance. We contribute an analysis of typical SF recall loss, and find a substantial amount of loss occurs early in the SF pipeline. We confirm that accurate NER and coreference resolution are required for high-recall SF. We measure upper bounds using a naïve graph-based semi-supervised bootstrapping technique, and find that only 39% of results are reachable using a typical feature space. We expect that this graph-based technique will be directly useful for extraction, and this leads us to frame SF as a label propagation task. We focus on a detailed graph representation of the task which reflects the behaviour and assumptions we want to model based on our analysis, including modifying the label propagation process to model multiple types of label interaction. Analysing the graph, we find that a large number of errors occur in very close proximity to training data, and identify that this is of major concern for propagation. While there are some conflicts caused by a lack of sufficient disambiguating context—we explore adding additional contextual features to address this—many of these conflicts are caused by subtle annotation problems. We find that lack of a standard for how explicit expressions of relations must be in text makes consistent annotation difficult. Using a strict definition of explicitness results in 20% of correct annotations being removed from a standard dataset. We contribute several annotation-driven analyses of this problem, exploring the definition of slots and the effect of the lack of a concrete definition of explicitness: annotation schema do not detail how explicit expressions of relations need to be, and there is large scope for disagreement between annotators. Additionally, applications may require relatively strict or relaxed evidence for extractions, but this is not considered in annotation tasks. We demonstrate that annotators frequently disagree on instances, dependent on differences in annotator world knowledge and thresholds on making probabilistic inference. SF is fundamental to enabling many knowledge-based applications, and this work motivates modelling and evaluating SF to better target these tasks