Learning to Combine Representations for Medical Records Search

ABSTRACT The complexity of medical terminology raises challenges when searching medical records. For example, 'cancer', 'tumour', and 'neoplasms', which are synonyms, may prevent a traditional search system from retrieving relevant records that contain only synonyms of the query terms. Prior works use bag-of-concepts approaches, to deal with this by representing medical terms sharing the same meanings using concepts from medical resources (e.g. MeSH). The relevance scores are then combined with a traditional bag-of-words representation, when inferring the relevance of medical records. Even though the existing approaches are effective, the predicted retrieval effectiveness of either the bag-of-words or bag-ofconcepts representation, which may be used to effectively model the score combination and hence improve retrieval performance, is not taken into account. In this paper, we propose a novel learning framework that models the importance of the bag-of-words and the bag-of-concepts representations, combining their scores on a per-query basis. Our proposed framework leverages retrieval performance predictors, such as the clarity score and AvIDF, calculated on both representations as learning features. We evaluate our proposed framework using the TREC Medical Records track's test collections. As our proposed framework can significantly outperform an existing approach that linearly merges the relevance scores, we conclude that retrieval performance predictors can be effectively leveraged when combining the relevance scores

Ontology-Based MEDLINE Document Classification

An increasing and overwhelming amount of biomedical information is available in the research literature mainly in the form of free-text. Biologists need tools that automate their information search and deal with the high volume and ambiguity of free-text. Ontologies can help automatic information processing by providing standard concepts and information about the relationships between concepts. The Medical Subject Headings (MeSH) ontology is already available and used by MEDLINE indexers to annotate the conceptual content of biomedical articles. This paper presents a domain-independent method that uses the MeSH ontology inter-concept relationships to extend the existing MeSH-based representation of MEDLINE documents. The extension method is evaluated within a document triage task organized by the Genomics track of the 2005 Text REtrieval Conference (TREC). Our method for extending the representation of documents leads to an improvement of 17% over a non-extended baseline in terms of normalized utility, the metric defined for the task. The SVMlight software is used to classify documents

Learning Tasks for Multitask Learning: Heterogenous Patient Populations in the ICU

Machine learning approaches have been effective in predicting adverse outcomes in different clinical settings. These models are often developed and evaluated on datasets with heterogeneous patient populations. However, good predictive performance on the aggregate population does not imply good performance for specific groups. In this work, we present a two-step framework to 1) learn relevant patient subgroups, and 2) predict an outcome for separate patient populations in a multi-task framework, where each population is a separate task. We demonstrate how to discover relevant groups in an unsupervised way with a sequence-to-sequence autoencoder. We show that using these groups in a multi-task framework leads to better predictive performance of in-hospital mortality both across groups and overall. We also highlight the need for more granular evaluation of performance when dealing with heterogeneous populations.Comment: KDD 201

ART Neural Networks: Distributed Coding and ARTMAP Applications

ART (Adaptive Resonance Theory) neural networks for fast, stable learning and prediction have been applied in a variety of areas. Applications include airplane design and manufacturing, automatic target recognition, financial forecasting, machine tool monitoring, digital circuit design, chemical analysis, and robot vision. Supervised ART architectures, called ARTMAP systems, feature internal control mechanisms that create stable recognition categories of optimal size by maximizing code compression while minimizing predictive error in an on-line setting. Special-purpose requirements of various application domains have led to a number of ARTMAP variants, including fuzzy ARTMAP, ART-EMAP, Gaussian ARTMAP, and distributed ARTMAP. ARTMAP has been used for a variety of applications, including computer-assisted medical diagnosis. Medical databases present many of the challenges found in general information management settings where speed, efficiency, ease of use, and accuracy are at a premium. A direct goal of improved computer-assisted medicine is to help deliver quality emergency care in situations that may be less than ideal. Working with these problems has stimulated a number of ART architecture developments, including ARTMAP-IC [1]. This paper describes a recent collaborative effort, using a new cardiac care database for system development, has brought together medical statisticians and clinicians at the New England Medical Center with researchers developing expert systems and neural networks, in order to create a hybrid method for medical diagnosis. The paper also considers new neural network architectures, including distributed ART {dART), a real-time model of parallel distributed pattern learning that permits fast as well as slow adaptation, without catastrophic forgetting. Local synaptic computations in the dART model quantitatively match the paradoxical phenomenon of Markram-Tsodyks [2] redistribution of synaptic efficacy, as a consequence of global system hypotheses.Office of Naval Research (N00014-95-1-0409, N00014-95-1-0657