Natural Language Processing–Assisted Literature Retrieval and Analysis for Combination Therapy in Cancer

2022 ◽  
Author(s):  
Jia Zeng ◽  
Christian X. Cruz-Pico ◽  
Turçin Saridogan ◽  
Md Abu Shufean ◽  
Michael Kahle ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Combination Therapy ◽  
Natural Language ◽  
Search Engine ◽  
Language Processing ◽  
Biomedical Literature ◽  
Antitumor Efficacy ◽  
Domain Specific ◽  
Validation Experiment

PURPOSE Despite advances in molecular therapeutics, few anticancer agents achieve durable responses. Rational combinations using two or more anticancer drugs have the potential to achieve a synergistic effect and overcome drug resistance, enhancing antitumor efficacy. A publicly accessible biomedical literature search engine dedicated to this domain will facilitate knowledge discovery and reduce manual search and review. METHODS We developed RetriLite, an information retrieval and extraction framework that leverages natural language processing and domain-specific knowledgebase to computationally identify highly relevant papers and extract key information. The modular architecture enables RetriLite to benefit from synergizing information retrieval and natural language processing techniques while remaining flexible to customization. We customized the application and created an informatics pipeline that strategically identifies papers that describe efficacy of using combination therapies in clinical or preclinical studies. RESULTS In a small pilot study, RetriLite achieved an F 1 score of 0.93. A more extensive validation experiment was conducted to determine agents that have enhanced antitumor efficacy in vitro or in vivo with poly (ADP-ribose) polymerase inhibitors: 95.9% of the papers determined to be relevant by our application were true positive and the application's feature of distinguishing a clinical paper from a preclinical paper achieved an accuracy of 97.6%. Interobserver assessment was conducted, which resulted in a 100% concordance. The data derived from the informatics pipeline have also been made accessible to the public via a dedicated online search engine with an intuitive user interface. CONCLUSION RetriLite is a framework that can be applied to establish domain-specific information retrieval and extraction systems. The extensive and high-quality metadata tags along with keyword highlighting facilitate information seekers to more effectively and efficiently discover knowledge in the combination therapy domain.

Report on the 4th Joint Workshop on Bibliometric-Enhanced Information Retrieval and Natural Language Processing for Digital Libraries at SIGIR 2019

2019 ◽  
Vol 53 (2) ◽  
pp. 3-10
Author(s):  
Muthu Kumar Chandrasekaran ◽  
Philipp Mayr
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Natural Language ◽  
Research And Development ◽  
Language Processing ◽  
Digital Libraries ◽  
State Of The Art ◽  
Shared Task ◽  
Processing Information ◽  
Joint Workshop

The 4 th joint BIRNDL workshop was held at the 42nd ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2019) in Paris, France. BIRNDL 2019 intended to stimulate IR researchers and digital library professionals to elaborate on new approaches in natural language processing, information retrieval, scientometrics, and recommendation techniques that can advance the state-of-the-art in scholarly document understanding, analysis, and retrieval at scale. The workshop incorporated different paper sessions and the 5 th edition of the CL-SciSumm Shared Task.

scholarly journals Implementation of a Cohort Retrieval System for Clinical Data Repositories Using the Observational Medical Outcomes Partnership Common Data Model: Proof-of-Concept System Validation (Preprint)

2019 ◽  
Author(s):  
Sijia Liu ◽  
Yanshan Wang ◽  
Andrew Wen ◽  
Liwei Wang ◽  
Na Hong ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Data Model ◽  
Structured Data ◽  
Common Data Model ◽  
Concept System ◽  
Unstructured Text ◽  
Electronic Health

BACKGROUND Widespread adoption of electronic health records has enabled the secondary use of electronic health record data for clinical research and health care delivery. Natural language processing techniques have shown promise in their capability to extract the information embedded in unstructured clinical data, and information retrieval techniques provide flexible and scalable solutions that can augment natural language processing systems for retrieving and ranking relevant records. OBJECTIVE In this paper, we present the implementation of a cohort retrieval system that can execute textual cohort selection queries on both structured data and unstructured text—Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records (CREATE). METHODS CREATE is a proof-of-concept system that leverages a combination of structured queries and information retrieval techniques on natural language processing results to improve cohort retrieval performance using the Observational Medical Outcomes Partnership Common Data Model to enhance model portability. The natural language processing component was used to extract common data model concepts from textual queries. We designed a hierarchical index to support the common data model concept search utilizing information retrieval techniques and frameworks. RESULTS Our case study on 5 cohort identification queries, evaluated using the precision at 5 information retrieval metric at both the patient-level and document-level, demonstrates that CREATE achieves a mean precision at 5 of 0.90, which outperforms systems using only structured data or only unstructured text with mean precision at 5 values of 0.54 and 0.74, respectively. CONCLUSIONS The implementation and evaluation of Mayo Clinic Biobank data demonstrated that CREATE outperforms cohort retrieval systems that only use one of either structured data or unstructured text in complex textual cohort queries.

scholarly journals Exact Expected Average Precision of the Random Baseline for System Evaluation

2015 ◽  
Vol 103 (1) ◽  
pp. 131-138 ◽  
Author(s):  
Yves Bestgen
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
System Evaluation ◽  
Average Precision ◽  
The Difference

Abstract Average precision (AP) is one of the most widely used metrics in information retrieval and natural language processing research. It is usually thought that the expected AP of a system that ranks documents randomly is equal to the proportion of relevant documents in the collection. This paper shows that this value is only approximate, and provides a procedure for efficiently computing the exact value. An analysis of the difference between the approximate and the exact value shows that the discrepancy is large when the collection contains few documents, but becomes very small when it contains at least 600 documents.

BUILD KNOWLEDGE GRAPH FROM HETEROGENEOUS DOCUMENTS

2021 ◽  
Vol 47 (05) ◽  
Author(s):  
NGUYỄN CHÍ HIẾU
Keyword(s):  
Information Retrieval ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Question Answering ◽  
Semantic Analysis ◽  
Knowledge Graph ◽  
Question Answering Systems ◽  
Knowledge Graphs

Knowledge Graphs are applied in many fields such as search engines, semantic analysis, and question answering in recent years. However, there are many obstacles for building knowledge graphs as methodologies, data and tools. This paper introduces a novel methodology to build knowledge graph from heterogeneous documents.  We use the methodologies of Natural Language Processing and deep learning to build this graph. The knowledge graph can use in Question answering systems and Information retrieval especially in Computing domain

LIS4: Lesk Inspired Sense Specific Semantic Similarity using WordNet

2021 ◽  
pp. 2150006
Author(s):  
Saravanakumar Kandasamy ◽  
Aswani Kumar Cherukuri
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Natural Language ◽  
Semantic Similarity ◽  
Language Processing ◽  
Gold Standard ◽  
Question Answering ◽  
Knowledge Based ◽  
Benchmark Datasets ◽  
Processing Information

Semantic similarity quantification between concepts is one of the inevitable parts in domains like Natural Language Processing, Information Retrieval, Question Answering, etc. to understand the text and their relationships better. Last few decades, many measures have been proposed by incorporating various corpus-based and knowledge-based resources. WordNet and Wikipedia are two of the Knowledge-based resources. The contribution of WordNet in the above said domain is enormous due to its richness in defining a word and all of its relationship with others. In this paper, we proposed an approach to quantify the similarity between concepts that exploits the synsets and the gloss definitions of different concepts using WordNet. Our method considers the gloss definitions, contextual words that are helping in defining a word, synsets of contextual word and the confidence of occurrence of a word in other word’s definition for calculating the similarity. The evaluation based on different gold standard benchmark datasets shows the efficiency of our system in comparison with other existing taxonomical and definitional measures.

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