What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way

From 2017 to 2019 the Text REtrieval Conference (TREC) held a challenge task on precision medicine using documents from medical publications (PubMed) and clinical trials. Despite lots of performance measurements carried out in these evaluation campaigns, the scientific community is still pretty unsure about the impact individual system features and their weights have on the overall system performance. In order to overcome this explanatory gap, we first determined optimal feature configurations using the Sequential Model-based Algorithm Configuration (SMAC) program and applied its output to a BM25-based search engine. We then ran an ablation study to systematically assess the individual contributions of relevant system features: BM25 parameters, query type and weighting schema, query expansion, stop word filtering, and keyword boosting. For evaluation, we employed the gold standard data from the three TREC-PM installments to evaluate the effectiveness of different features using the commonly shared infNDCG metric.Comment: Accepted for SIGIR2020, 10 page

A Vertical PRF Architecture for Microblog Search

In microblog retrieval, query expansion can be essential to obtain good search results due to the short size of queries and posts. Since information in microblogs is highly dynamic, an up-to-date index coupled with pseudo-relevance feedback (PRF) with an external corpus has a higher chance of retrieving more relevant documents and improving ranking. In this paper, we focus on the research question:how can we reduce the query expansion computational cost while maintaining the same retrieval precision as standard PRF? Therefore, we propose to accelerate the query expansion step of pseudo-relevance feedback. The hypothesis is that using an expansion corpus organized into verticals for expanding the query, will lead to a more efficient query expansion process and improved retrieval effectiveness. Thus, the proposed query expansion method uses a distributed search architecture and resource selection algorithms to provide an efficient query expansion process. Experiments on the TREC Microblog datasets show that the proposed approach can match or outperform standard PRF in MAP and NDCG@30, with a computational cost that is three orders of magnitude lower.Comment: To appear in ICTIR 201

Utilizing Knowledge Bases In Information Retrieval For Clinical Decision Support And Precision Medicine

Accurately answering queries that describe a clinical case and aim at finding articles in a collection of medical literature requires utilizing knowledge bases in capturing many explicit and latent aspects of such queries. Proper representation of these aspects needs knowledge-based query understanding methods that identify the most important query concepts as well as knowledge-based query reformulation methods that add new concepts to a query. In the tasks of Clinical Decision Support (CDS) and Precision Medicine (PM), the query and collection documents may have a complex structure with different components, such as disease and genetic variants that should be transformed to enable an effective information retrieval. In this work, we propose methods for representing domain-specific queries based on weighted concepts of different types whether exist in the query itself or extracted from the knowledge bases and top retrieved documents. Besides, we propose an optimization framework, which allows unifying query analysis and expansion by jointly determining the importance weights for the query and expansion concepts depending on their type and source. We also propose a probabilistic model to reformulate the query given genetic information in the query and collection documents. We observe significant improvement of retrieval accuracy will be obtained for our proposed methods over state-of-the-art baselines for the tasks of clinical decision support and precision medicine

VoMBaT: A Tool for Visualising Evaluation Measure Behaviour in High-Recall Search Tasks

The objective of High-Recall Information Retrieval (HRIR) is to retrieve as many relevant documents as possible for a given search topic. One approach to HRIR is Technology-Assisted Review (TAR), which uses information retrieval and machine learning techniques to aid the review of large document collections. TAR systems are commonly used in legal eDiscovery and systematic literature reviews. Successful TAR systems are able to find the majority of relevant documents using the least number of assessments. Commonly used retrospective evaluation assumes that the system achieves a specific, fixed recall level first, and then measures the precision or work saved (e.g., precision at r% recall). This approach can cause problems related to understanding the behaviour of evaluation measures in a fixed recall setting. It is also problematic when estimating time and money savings during technology-assisted reviews. This paper presents a new visual analytics tool to explore the dynamics of evaluation measures depending on recall level. We implemented 18 evaluation measures based on the confusion matrix terms, both from general IR tasks and specific to TAR. The tool allows for a comparison of the behaviour of these measures in a fixed recall evaluation setting. It can also simulate savings in time and money and a count of manual vs automatic assessments for different datasets depending on the model quality. The tool is open-source, and the demo is available under the following URL: https://vombat.streamlit.app