Using citation networks to evaluate the impact of text length on keyword extraction
Ontology highlight
ABSTRACT:
SUBMITTER: Tohalino J
PROVIDER: S-EPMC10681196 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:A document's keywords provide high-level descriptions of the content that summarize the document's central themes, concepts, ideas, or arguments. These descriptive phrases make it easier for algorithms to find relevant information quickly and efficiently. It plays a vital role in document processing, such as indexing, classification, clustering, and summarization. Traditional keyword extraction approaches rely on statistical distributions of key terms in a document for the most part. According to contemporary technological breakthroughs, contextual information is critical in deciding the semantics of the work at hand. Similarly, context-based features may be beneficial in the job of keyword extraction. For example, simply indicating the previous or next word of the phrase of interest might be used to describe the context of a phrase. This research presents several experiments to validate that context-based key extraction is significant compared to traditional methods. Additionally, the KeyBERT proposed methodology also results in improved results. The proposed work relies on identifying a group of important words or phrases from the document's content that can reflect the authors' main ideas, concepts, or arguments. It also uses contextual word embedding to extract keywords. Finally, the findings are compared to those obtained using older approaches such as Text Rank, Rake, Gensim, Yake, and TF-IDF. The Journals of Universal Computer (JUCS) dataset was employed in our research. Only data from abstracts were used to produce keywords for the research article, and the KeyBERT model outperformed traditional approaches in producing similar keywords to the authors' provided keywords. The average similarity of our approach with author-assigned keywords is 51%.
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Project description:With the ever-increasing abundance of biomedical articles, improving the accuracy of keyword search results becomes crucial for ensuring reproducible research. However, keyword extraction for biomedical articles is hard due to the existence of obscure keywords and the lack of a comprehensive benchmark. PubMedAKE is an author-assigned keyword extraction dataset that contains the title, abstract, and keywords of over 843,269 articles from the PubMed open access subset database. This dataset, publicly available on Zenodo, is the largest keyword extraction benchmark with sufficient samples to train neural networks. Experimental results using state-of-the-art baseline methods illustrate the need for developing automatic keyword extraction methods for biomedical literature.
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Project description:Protein phosphorylation is a reversible post-translational modification where a protein kinase adds a phosphate group to a protein, potentially regulating its function, localization and/or activity. Phosphorylation can affect protein-protein interactions (PPIs), abolishing interaction with previous binding partners or enabling new interactions. Extracting phosphorylation information coupled with PPI information from the scientific literature will facilitate the creation of phosphorylation interaction networks of kinases, substrates and interacting partners, toward knowledge discovery of functional outcomes of protein phosphorylation. Increasingly, PPI databases are interested in capturing the phosphorylation state of interacting partners. We have previously developed the eFIP (Extracting Functional Impact of Phosphorylation) text mining system, which identifies phosphorylated proteins and phosphorylation-dependent PPIs. In this work, we present several enhancements for the eFIP system: (i) text mining for full-length articles from the PubMed Central open-access collection; (ii) the integration of the RLIMS-P 2.0 system for the extraction of phosphorylation events with kinase, substrate and site information; (iii) the extension of the PPI module with new trigger words/phrases describing interactions and (iv) the addition of the iSimp tool for sentence simplification to aid in the matching of syntactic patterns. We enhance the website functionality to: (i) support searches based on protein roles (kinases, substrates, interacting partners) or using keywords; (ii) link protein entities to their corresponding UniProt identifiers if mapped and (iii) support visual exploration of phosphorylation interaction networks using Cytoscape. The evaluation of eFIP on full-length articles achieved 92.4% precision, 76.5% recall and 83.7% F-measure on 100 article sections. To demonstrate eFIP for knowledge extraction and discovery, we constructed phosphorylation-dependent interaction networks involving 14-3-3 proteins identified from cancer-related versus diabetes-related articles. Comparison of the phosphorylation interaction network of kinases, phosphoproteins and interactants obtained from eFIP searches, along with enrichment analysis of the protein set, revealed several shared interactions, highlighting common pathways discussed in the context of both diseases.
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Project description:Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services.
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Project description:ObjectiveWe implement 2 different multitask learning (MTL) techniques, hard parameter sharing and cross-stitch, to train a word-level convolutional neural network (CNN) specifically designed for automatic extraction of cancer data from unstructured text in pathology reports. We show the importance of learning related information extraction (IE) tasks leveraging shared representations across the tasks to achieve state-of-the-art performance in classification accuracy and computational efficiency.Materials and methodsMultitask CNN (MTCNN) attempts to tackle document information extraction by learning to extract multiple key cancer characteristics simultaneously. We trained our MTCNN to perform 5 information extraction tasks: (1) primary cancer site (65 classes), (2) laterality (4 classes), (3) behavior (3 classes), (4) histological type (63 classes), and (5) histological grade (5 classes). We evaluated the performance on a corpus of 95 231 pathology documents (71 223 unique tumors) obtained from the Louisiana Tumor Registry. We compared the performance of the MTCNN models against single-task CNN models and 2 traditional machine learning approaches, namely support vector machine (SVM) and random forest classifier (RFC).ResultsMTCNNs offered superior performance across all 5 tasks in terms of classification accuracy as compared with the other machine learning models. Based on retrospective evaluation, the hard parameter sharing and cross-stitch MTCNN models correctly classified 59.04% and 57.93% of the pathology reports respectively across all 5 tasks. The baseline models achieved 53.68% (CNN), 46.37% (RFC), and 36.75% (SVM). Based on prospective evaluation, the percentages of correctly classified cases across the 5 tasks were 60.11% (hard parameter sharing), 58.13% (cross-stitch), 51.30% (single-task CNN), 42.07% (RFC), and 35.16% (SVM). Moreover, hard parameter sharing MTCNNs outperformed the other models in computational efficiency by using about the same number of trainable parameters as a single-task CNN.ConclusionsThe hard parameter sharing MTCNN offers superior classification accuracy for automated coding support of pathology documents across a wide range of cancers and multiple information extraction tasks while maintaining similar training and inference time as those of a single task-specific model.
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Project description:A citation is deemed as a potential parameter to determine linkage between research articles. The parameter has extensively been employed to form multifarious academic aspects like calculating the impact factor of journals, h-Index of researchers, allocate different research grants, find the latest research trends, etc. The current state-of-the-art contends that all citations are not of equal importance. Based on this argument, the current trend in citation classification community categorizes citations into important and non-important reasons. The community has proposed different approaches to extract important citations such as citation count, context-based, metadata, and textual based approaches. The contemporary state-of-the-art in citation classification community ignores significantly potential features that can play a vital role in citation classification. This research presents a novel approach for binary citation classification by exploiting section-wise in-text citation frequencies, similarity score, and overall citation count-based features. The study also introduces machine learning algorithms based novel approach for assigning appropriate weights to the logical sections of research papers. The weights are allocated to the citations with respect to their sections. To perform the classification, we used three classification techniques, Support Vector Machine, Kernel Linear Regression, and Random Forest. The experiment was performed on two annotated benchmark datasets that contain 465 and 311 citation pairs of research articles respectively. The results revealed that the proposed approach attained an improved value of precision (i.e., 0.84 vs 0.72) from contemporary state-of-the-art approach.
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Project description:In recent years, the science of science policy has been facilitated by the greater availability of and access to digital data associated with the science, technology, and innovation enterprise. Historically, most of the studies from which such data are derived have been econometric or "scientometric" in nature, focusing on the development of quantitative data, models, and metrics of the scientific process as well as outputs and outcomes. Broader definitions of research impact, however, necessitate the use of qualitative case-study methods. For many years, U.S. federal science agencies such as the National Institutes of Health have demonstrated the impact of the research they support through tracing studies that document critical events in the development of successful technologies. A significant disadvantage and barrier of such studies is the labor-intensive nature of a case study approach. Currently, however, the same data infrastructures that have been developed to support scientometrics may also facilitate historical tracing studies. In this paper, we describe one approach we used to discover long-term, downstream outcomes of research supported in the late 1970's and early 1980's by the National Institute of General Medical Sciences, a component of the National Institutes of Health.
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Project description:Neural keyword spotting could form the basis of a speech brain-computer-interface for menu-navigation if it can be done with low latency and high specificity comparable to the "wake-word" functionality of modern voice-activated AI assistant technologies. This study investigated neural keyword spotting using motor representations of speech via invasively-recorded electrocorticographic signals as a proof-of-concept. Neural matched filters were created from monosyllabic consonant-vowel utterances: one keyword utterance, and 11 similar non-keyword utterances. These filters were used in an analog to the acoustic keyword spotting problem, applied for the first time to neural data. The filter templates were cross-correlated with the neural signal, capturing temporal dynamics of neural activation across cortical sites. Neural vocal activity detection (VAD) was used to identify utterance times and a discriminative classifier was used to determine if these utterances were the keyword or non-keyword speech. Model performance appeared to be highly related to electrode placement and spatial density. Vowel height (/a/ vs /i/) was poorly discriminated in recordings from sensorimotor cortex, but was highly discriminable using neural features from superior temporal gyrus during self-monitoring. The best performing neural keyword detection (5 keyword detections with two false-positives across 60 utterances) and neural VAD (100% sensitivity, ~1 false detection per 10 utterances) came from high-density (2 mm electrode diameter and 5 mm pitch) recordings from ventral sensorimotor cortex, suggesting the spatial fidelity and extent of high-density ECoG arrays may be sufficient for the purpose of speech brain-computer-interfaces.
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Project description:BackgroundThe increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Named entity recognition of well-defined objects, such as genes or proteins, has achieved a sufficient level of maturity such that it can form the basis for the next step: the extraction of relations that exist between the recognized entities. Whereas most early work focused on the mere detection of relations, the classification of the type of relation is also of great importance and this is the focus of this work. In this paper we describe an approach that extracts both the existence of a relation and its type. Our work is based on Conditional Random Fields, which have been applied with much success to the task of named entity recognition.ResultsWe benchmark our approach on two different tasks. The first task is the identification of semantic relations between diseases and treatments. The available data set consists of manually annotated PubMed abstracts. The second task is the identification of relations between genes and diseases from a set of concise phrases, so-called GeneRIF (Gene Reference Into Function) phrases. In our experimental setting, we do not assume that the entities are given, as is often the case in previous relation extraction work. Rather the extraction of the entities is solved as a subproblem. Compared with other state-of-the-art approaches, we achieve very competitive results on both data sets. To demonstrate the scalability of our solution, we apply our approach to the complete human GeneRIF database. The resulting gene-disease network contains 34758 semantic associations between 4939 genes and 1745 diseases. The gene-disease network is publicly available as a machine-readable RDF graph.ConclusionWe extend the framework of Conditional Random Fields towards the annotation of semantic relations from text and apply it to the biomedical domain. Our approach is based on a rich set of textual features and achieves a performance that is competitive to leading approaches. The model is quite general and can be extended to handle arbitrary biological entities and relation types. The resulting gene-disease network shows that the GeneRIF database provides a rich knowledge source for text mining. Current work is focused on improving the accuracy of detection of entities as well as entity boundaries, which will also greatly improve the relation extraction performance.
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Project description:MOTIVATION:A complete repository of gene-gene interactions is key for understanding cellular processes, human disease and drug response. These gene-gene interactions include both protein-protein interactions and transcription factor interactions. The majority of known interactions are found in the biomedical literature. Interaction databases, such as BioGRID and ChEA, annotate these gene-gene interactions; however, curation becomes difficult as the literature grows exponentially. DeepDive is a trained system for extracting information from a variety of sources, including text. In this work, we used DeepDive to extract both protein-protein and transcription factor interactions from over 100,000 full-text PLOS articles. METHODS:We built an extractor for gene-gene interactions that identified candidate gene-gene relations within an input sentence. For each candidate relation, DeepDive computed a probability that the relation was a correct interaction. We evaluated this system against the Database of Interacting Proteins and against randomly curated extractions. RESULTS:Our system achieved 76% precision and 49% recall in extracting direct and indirect interactions involving gene symbols co-occurring in a sentence. For randomly curated extractions, the system achieved between 62% and 83% precision based on direct or indirect interactions, as well as sentence-level and document-level precision. Overall, our system extracted 3356 unique gene pairs using 724 features from over 100,000 full-text articles. AVAILABILITY AND IMPLEMENTATION:Application source code is publicly available at https://github.com/edoughty/deepdive_genegene_app CONTACT:russ.altman@stanford.edu SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
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