Using Learning to Rank Approach to Promoting Diversity for Biomedical Information Retrieval with Wikipedia

In most of the traditional information retrieval (IR) models, the independent relevance assumption is taken, which assumes the relevance of a document is independent of other documents. However, the pitfall of this is the high redundancy and low diversity of retrieval result. This has been seen in many scenarios, especially in biomedical IR, where the information need of one query may refer to different aspects. Promoting diversity in IR takes the relationship between documents into account. Unlike previous studies, we tackle this problem in the learning to rank perspective. The main challenges are how to find salient features for biomedical data and how to integrate dynamic features into the ranking model. To address these challenges, Wikipedia is used to detect topics of documents for generating diversity biased features. A combined model is proposed and studied to learn a diversified ranking result. Experiment results show the proposed method outperforms baseline models

Protein interaction sentence detection using multiple semantic kernels

<p>Abstract</p> <p>Background</p> <p>Detection of sentences that describe protein-protein interactions (PPIs) in biomedical publications is a challenging and unresolved pattern recognition problem. Many state-of-the-art approaches for this task employ kernel classification methods, in particular support vector machines (SVMs). In this work we propose a novel data integration approach that utilises semantic kernels and a kernel classification method that is a probabilistic analogue to SVMs. Semantic kernels are created from statistical information gathered from large amounts of unlabelled text using lexical semantic models. Several semantic kernels are then fused into an overall composite classification space. In this initial study, we use simple features in order to examine whether the use of combinations of kernels constructed using word-based semantic models can improve PPI sentence detection.</p> <p>Results</p> <p>We show that combinations of semantic kernels lead to statistically significant improvements in recognition rates and receiver operating characteristic (ROC) scores over the plain Gaussian kernel, when applied to a well-known labelled collection of abstracts. The proposed kernel composition method also allows us to automatically infer the most discriminative kernels.</p> <p>Conclusions</p> <p>The results from this paper indicate that using semantic information from unlabelled text, and combinations of such information, can be valuable for classification of short texts such as PPI sentences. This study, however, is only a first step in evaluation of semantic kernels and probabilistic multiple kernel learning in the context of PPI detection. The method described herein is modular, and can be applied with a variety of feature types, kernels, and semantic models, in order to facilitate full extraction of interacting proteins.</p

Machine Learning Methods for Finding Textual Features of Depression from Publications

Depression is a common but serious mood disorder. In 2015, WHO reports about 322 million people were living with some form of depression, which is the leading cause of ill health and disability worldwide. In USA, there are approximately 14.8 million American adults (about 6.7% percent of the US population) affected by major depressive disorder. Most individuals with depression are not receiving adequate care because the symptoms are easily neglected and most people are not even aware of their mental health problems. Therefore, a depression prescreen system is greatly beneficial for people to understand their current mental health status at an early stage. Diagnosis of depressions, however, is always extremely challenging due to its complicated, many and various symptoms. Fortunately, publications have rich information about various depression symptoms. Text mining methods can discover the different depression symptoms from literature. In order to extract these depression symptoms from publications, machine learning approaches are proposed to overcome four main obstacles: (1) represent publications in a mathematical form; (2) get abstracts from publications; (3) remove the noisy publications to improve the data quality; (4) extract the textual symptoms from publications. For the first obstacle, we integrate Word2Vec with LDA by either representing publications with document-topic distance distributions or augmenting the word-to-topic and word-to-word vectors. For the second obstacle, we calculate a document vector and its paragraph vectors by aggregating word vectors from Word2Vec. Feature vectors are calculated by clustering word vectors. Selected paragraphs are decided by the similarity of their distances to feature vectors and the document vector to feature vectors. For the third obstacle, one class SVM model is trained by vectored publications, and outlier publications are excluded by distance measurements. For the fourth obstacle, we fully evaluate the possibility of a word as a symptom according to its frequency in entire publications, and local relationship with its surrounding words in a publication

Integrating Medical Ontology and Pseudo Relevance Feedback For Medical Document Retrieval

The purpose of this thesis is to undertake and improve the accuracy of locating the relevant documents from a large amount of Electronic Medical Data (EMD). The unique goal of this research is to propose a new idea for using medical ontology to find an easy and more reliable approach for patients to have a better understanding of their diseases and also help doctors to find and further improve the possible methods of diagnosis and treatments. The empirical studies were based on the dataset provided by CLEF focused on health care data. In this research, I have used Information Retrieval to find and obtain relevant information within the large amount of data sets provided by CLEF. I then used ranking functionality on the Terrier platform to calculate and evaluate the matching documents in the collection of data sets. BM25 was used as the base normalization method to retrieve the results and Pseudo Relevance Feedback weighting model to retrieve the information regarding patients health history and medical records in order to find more accurate results. I then used Unified Medical Language System to develop indexing of the queries while searching on the Internet and looking for health related documents. UMLS software was actually used to link the computer system with the health and biomedical terms and vocabularies into classify tools; it works as a dictionary for the patients by translating the medical terms. Later I would like to work on using medical ontology to create a relationship between the documents regarding the medical data and my retrieved results

Semantic concept extraction from electronic medical records for enhancing information retrieval performance

With the healthcare industry increasingly using EMRs, there emerges an opportunity for knowledge discovery within the healthcare domain that was not possible with paper-based medical records. One such opportunity is to discover UMLS concepts from EMRs. However, with opportunities come challenges that need to be addressed. Medical verbiage is very different from common English verbiage and it is reasonable to assume extracting any information from medical text requires different protocols than what is currently used in common English text. This thesis proposes two new semantic matching models: Term-Based Matching and CUI-Based Matching. These two models use specialized biomedical text mining tools that extract medical concepts from EMRs. Extensive experiments to rank the extracted concepts are conducted on the University of Pittsburgh BLULab NLP Repository for the TREC 2011 Medical Records track dataset that consists of 101,711 EMRs that contain concepts in 34 predefined topics. This thesis compares the proposed semantic matching models against the traditional weighting equations and information retrieval tools used in the academic world today