Learning to rank for biomedical information retrieval

In these years, the number of biomedical articles has increased exponentially, which becomes a problem for biologists to capture all the needed information manually. Information retrieval technologies, as the core of search engines, can deal with the problem automatically, providing users with the needed information. However, it is a great challenge to apply these technologies directly for biomedical retrieval, because of the abundance of domain specific terminologies. To enhance biomedical retrieval, we propose a novel framework based on learning to rank. Learning to rank is a series of state-of-the-art information retrieval techniques, and has been proved effective in many information retrieval tasks. In the proposed framework, we attempt to tackle the problem of the abundance of terminologies by constructing ranking models, which focus on not only retrieving the most relevant documents, but also diversifying the searching results to increase the completeness of the resulting list for a given query. In the model training, we propose two novel document labeling strategies, and combine several traditional retrieval models as learning features. Besides, we also investigate the usefulness of different learning to rank approaches in our framework. Experimental results on TREC Genomics datasets demonstrate the effectiveness of our framework for biomedical information retrieval.

The task of semantic code search is to retrieve code snippets from a source code corpus based on an information need expressed in natural language. The semantic gap between natural language and programming languages has for long been regarded as one of the most significant obstacles to the effectiveness of keyword-based information retrieval (IR) methods. It is a common assumption that “traditional” bag-of-words IR methods are poorly suited for semantic code search: our work empirically investigates this assumption. Specifically, we examine the effectiveness of two traditional IR methods, namely BM25 and RM3, on the CodeSearchNet Corpus, which consists of natural language queries paired with relevant code snippets. We find that the two keyword-based methods outperform several pre-BERT neural models. We also compare several code-specific data pre-processing strategies and find that specialized tokenization improves effectiveness.

Extracting similar terms from multiple EMR-based semantic embeddings to support chart reviews

Search Engine (SE) is the most used information retrieval tool in the present scenario. In spite of the huge involvement of users in search engines, their limited capabilities to understand the user context and emotions places high load on the user to maintain the search momentum. Thus the research is being done on the web search process including the users. The aim is to reduce the contextual and emotional mismatch between the SE's and users. Personalized user query processing, current knowledge updation on users, information retrieval effectiveness and user satisfaction are the major challenges to be addressed in this field. To meet the high level requirements of the users and to improve the intellectualization level of the search, various cognitive agent based SE models are proposed in the literature. The challenges of the cognitive agents in present search engine scenario are obtaining sufficient percepts from the environment, understanding it, gathering the knowledge and retrieving the information from the huge volume of data. Recent advancements in the field of semantic search engines, knowledge gathering techniques and information retrieval methods are discussed which can better the cognitive agent based search engines by addressing the challenges. Overall the goal is to enhance the search experience by fewer repetitions of queries and making it easier for the users to retrieve the highly relevant documents of their interest.

To improve the effectiveness and efficiency of biomedical information retrieval by proposing ranking-based methods for selecting an optimal subset of retrieval systems for data fusion, we propose three ranking-based subset selection methods SFS (Sequential Forward Search), D&P (Diversity & Performance), and P&D (Performance & Diversity). These methods were applied in combination with the Reciprocal Rank Fusion technique. Experiments were conducted on four medical datasets from TREC, using between 62 and 125 candidate retrieval systems, and selecting up to 15 for fusion. The proposed subset selection methods significantly improved retrieval performance. Fusing the selected systems using RRF yielded improvements ranging from 10% to over 60% compared to the best individual retrieval system across the datasets. They also outperform the state-of-the-art technology by a large margin. In summary, our subset selection approach offers a practical and cost-efficient solution for biomedical information retrieval, achieving substantial performance gains while reducing computational overhead.

In recent years, information retrieval technology is widely used in the medical industry. How to effectively retrieve electronic medical record has become a hot issue in the field of information retrieval. Medical terms occupy an important position in the electronic medical record (EMR) retrieval, and they are usually used to limit the retrieval conditions, so they suggest the user’s search intention. Aiming at the importance of medical terms, a method of query reformulation based on medical term reweighting is proposed to improve the performance of EMR retrieval. Firstly, the method filtrates medical terms from the origin query. Then, each medical term is weighted by its own self-information which can be estimated from the document set. Finally, the new query is constructed by combining the weighted medical terms and origin query proportionally. Experimental results on the TREC dataset show that our method performed above the baseline in three performance metrics: MAP (+ 14.2%), bpref (+ 8.0%), and P@10 (+ 9.6%).

Distributed information retrieval methods are growing rapidly because of the rising need to access and search distributed digital documents. However, the content-based information retrieval (CBIR) is concentrated to extract and retrieve the information from massive digital libraries, which require a huge amount of computing and storage resources. The grid computing provides the reliable infrastructure for effective and efficient retrieval on these large collections. In order to build an effective and efficient CBIR technique, varieties of architectures were developed based on grid technologies. The goal of such architecture is to solve interoperability and heterogeneous resource issues, and increase the efficiency and effectiveness of information retrieval (IR) techniques by harnessing the grid computing capabilities. This paper reviews and analyzes latest research carried out in the domain of large-scale dataset IR based on a grid. The evaluation is based on scalability, response time, scope, data type, search technique, middleware, and query type. The contribution is to illustrate the features, capabilities, and shortages of current solutions that can guide the researchers in this evolving area.

With the rapid development of biomedicine, the number of biomedical articles has increased accordingly, which presents a great challenge for biologists trying to keep up with the latest research. Information retrieval seeks to meet this challenge by searching among a large number of articles based on given queries and providing the most relevant ones to fulfill information needs. As an effective information retrieval technique, query expansion has some room for improvement to achieve the desired performance when directly applied for biomedical information retrieval because there exist many domain-related terms both in users' queries and in related articles. To solve this problem, we propose a biomedical query expansion framework based on learning-to-rank methods, in which we refine candidate expansion terms by training term-ranking models to select the most relevant terms. To train the term-ranking models, we first propose a pseudo-relevance feedback method based on MeSH to select candidate expansion terms and then represent the candidate terms as feature vectors by defining both the corpus-based term features and the resource-based term features. Experimental results obtained for TREC genomics datasets show that our method can capture more relevant terms to expand the original query and effectively improve biomedical information retrieval performance.

The intention of this paper was to determine usability of KOHA OPAC in information retrieval with regard to usability testing by undergraduate users at Technical University of Kenya Library (TU-KL) in Nairobi County. Usability testing can be realized by way of assigning tasks to a representative of the user population in order to determine whether users can be able to achieve the desired goal of retrieving information. To a great extent, success will depend on how users perform the tasks assigned to them. This study conducted usability test on actual users of KOHA OPAC at Technical University of Kenya Library. Qualitative data was collected using the think aloud method where study participants were required to verbalize their thought process as they performed search and retrieval tasks using KOHA OPAC. The number of errors made, time taken to complete search and retrieval activities were coded, recorded and analysed during usability testing. This helped the researcher to determine whether KOHA OPAC is easy to use and whether it saves time for the user. Undergraduate students for the study were selected using a stratified random sampling technique. The population of the study (n = 382) was determined using a simplified formula developed by Yamane. The study initiated a usability test which presented search scenarios where participants were invited to participate in searching and retrieving information resources using KOHA OPAC. The results of the usability test of KOHA OPAC at TU-KL showed that users were slow at accomplishing search tasks, they took long duration to access TU-KL website that hosts KOHA OPAC and there was inefficiency in accessing library materials. This study concluded that usability challenges may have an impact on users' overall satisfaction with KOHA OPAC and information retrieval effectiveness. In order to enhance user experience and boost the effectiveness of information retrieval, the study recommends improvement of KOHA OPAC usability by revamping its interface and enhancing its features.

Research and experimentation using Arabic WordNet in the field of information retrieval are relatively new. It is limited compared to the research that has been done using Princeton WordNet. This work attempts to study the impact of Arabic WordNet on the performance of Arabic information retrieval. We extend Lucene with Arabic WordNet to expand user's queries. The major contribution of this study is to propose an interactive query expansion (IQE) methodology using the word's part-of-speech, according to the part it plays in a query. First, the user selects the appropriate part of speech for each term in the original query, and then he reselects the appropriate synonyms. Experimental results show that our IQE strategy produces a good Mean Average Precision (MAP), it is able to improve MAP by 12.6%, but no variant of automatic query expansion (AQE) strategies did. Nevertheless, the experiments allow us to conclude that with an appropriate use of Arabic WordNet as a source of linguistic information for AQE can improve effectiveness for Arabic information retrieval.

This paper presents a multipronged approach to predict early risk of mental health issues from user-generated content in social media. Supervised learning and information retrieval methods are used to estimate the risk of depression for a user given the content of its posts in reddit. The approach presented here was evaluated on the CLEF eRisk 2017 pilot task. We describe the details of five systems submitted to the task, and compare their performance. The comparisons show that combining information retrieval and machine learning methods gives the best results.

Question Answering (QA) is a specialized subfield within Information Retrieval (IR) that focuses on providing precise answers to user queries. Recent advances in Large Language Models (LLMs) have greatly improved the speed and accuracy of question-answering (QA) systems, leading to significantly enhanced capabilities and performance. This study introduces a multi-PDF querying system designed to support automated question answering for Vietnamese students, leveraging the capabilities of LLMs. To enhance the retrieval accuracy from natural language queries, we integrate four Vietnamese-language embedding models. These models are evaluated using a dataset comprising questions related to the academic regulations of the University of Da Nang - University of Science and Technology (DUT), reflecting real-life scenarios students commonly encounter. Experimental results reveal that the top-performing Vietnamese embedding model achieves a Mean Average Precision (mAP) of 0.840 and an F1-score of 0.959, demonstrating its high effectiveness in information retrieval. This study makes significant contributions to the integration of Vietnamese embedding models into automated question-answering systems, aiming to effectively support students in the university environment.

In Electronic Commerce (EC) environment, the quality of business information directly affects the level of enterprise operations. This paper analyzes the common methods of business information retrieval in EC environment, and designs a software system which can automatically collect business information in Internet and extract business information required by enterprise from database directly. The system adopts meta-search engine to expand search scale, and applies information retrieval, web mining and agent technology to analyze and filter the business information, in order to improve the search quality of business information.

Evaluation is crucial in assessing the effectiveness of new information retrieval and human computer interaction techniques and systems. Relevance judgements are often performed by humans, which makes obtaining them expensive and time consuming. Consequently, relevance judgements are usually performed only on a subset of a given collection of data or experimental results with a focus on the top ranked documents. However, when assessing the performance of exploratory search systems, the diversity or subjective relevance of documents that the user was presented with over a search session are often of more importance than the relative ranking of top documents. In order to perform these types of assessment, all the documents in a given collection need to be judged for relevance. In this paper, we propose an approach based on topic modeling that can greatly accelerate document relevance judgment of an entire document collection with an expert assessor needing to mark only a small subset of documents from a given collection. Experimental results show a substantial overlap between relevance judgments compared to a human assessor.

As millions of consumers perform health information retrieval online, the mismatch between their terminology and the terminologies of the information sources could become a major barrier to successful retrievals. To address this problem, we studied the characteristics of consumer terminology for health information retrieval. Our study focused on consumer queries that were used on a consumer health service Web site and a consumer health information Web site. We analyzed data from the site-usage logs and conducted interviews with patients. Our findings show that consumers' information retrieval performance is very poor. There are significant mismatches at all levels (lexical, semantic and mental models) between the consumer terminology and both the information source terminology and standard medical vocabularies. Comprehensive terminology support on all levels is needed for consumer health information retrieval.