Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers

Care episode retrieval: distributional semantic models for information retrieval in the clinical domain

Patients' health related information is stored in electronic health records (EHRs) by health service providers. These records include sequential documentation of care episodes in the form of clinical notes. EHRs are used throughout the health care sector by professionals, administrators and patients, primarily for clinical purposes, but also for secondary purposes such as decision support and research. The vast amounts of information in EHR systems complicate information management and increase the risk of information overload. Therefore, clinicians and researchers need new tools to manage the information stored in the EHRs. A common use case is, given a - possibly unfinished - care episode, to retrieve the most similar care episodes among the records. This paper presents several methods for information retrieval, focusing on care episode retrieval, based on textual similarity, where similarity is measured through domain-specific modelling of the distributional semantics of words. Models include variants of random indexing and the semantic neural network model word2vec. Two novel methods are introduced that utilize the ICD-10 codes attached to care episodes to better induce domain-specificity in the semantic model. We report on experimental evaluation of care episode retrieval that circumvents the lack of human judgements regarding episode relevance. Results suggest that several of the methods proposed outperform a state-of-the art search engine (Lucene) on the retrieval task

Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

An autoencoder-based neural network model for selectional preference: evidence from pseudo-disambiguation and cloze tasks

Intuitively, some predicates have a better fit with certain arguments than others. Usage-based models of language emphasize the importance of semantic similarity in shaping the structuring of constructions (form and meaning). In this study, we focus on modeling the semantics of transitive constructions in Finnish and present an autoencoder-based neural network model trained on semantic vectors based on Word2vec. This model builds on the distributional hypothesis according to which semantic information is primarily shaped by contextual information. Specifically, we focus on the realization of the object. The performance of the model is evaluated in two tasks: a pseudo-disambiguation and a cloze task. Additionally, we contrast the performance of the autoencoder with a previously implemented neural model. In general, the results show that our model achieves an excellent performance on these tasks in comparison to the other models. The results are discussed in terms of usage-based construction grammar.Kokkuvõte. Aki-Juhani Kyröläinen, M. Juhani Luotolahti ja Filip Ginter: Autokoodril põhinev närvivõrkude mudel valikulisel eelistamisel. Intuitiivselt tundub, et mõned argumendid sobivad teatud predikaatidega paremini kokku kui teised. Kasutuspõhised keelemudelid rõhutavad konstruktsioonide struktuuri (nii vormi kui tähenduse) kujunemisel tähendusliku sarnasuse olulisust. Selles uurimuses modelleerime soome keele transitiivsete konstruktsioonide semantikat ja esitame närvivõrkude mudeli ehk autokoodri. Mudel põhineb distributiivse semantika hüpoteesil, mille järgi kujuneb semantiline info peamiselt konteksti põhjal. Täpsemalt keskendume uurimuses objektile. Mudelit hindame nii valeühestamise kui ka lünkülesande abil. Kõrvutame autokoodri tulemusi varem välja töötatud neurovõrgumudelitega ja tõestame, et meie mudel töötab võrreldes teiste mudelitega väga hästi. Tulemused esitame kasutuspõhise konstruktsioonigrammatika kontekstis.Võtmesõnad: neurovõrk; autokooder; tähendusvektor; kasutuspõhine mudel; soome kee

Parsing Clinical Finnish: Experiments with Rule-Based and Statistical Dependency Parsers

Proceedings of the 17th Nordic Conference of Computational Linguistics NODALIDA 2009. Editors: Kristiina Jokinen and Eckhard Bick. NEALT Proceedings Series, Vol. 4 (2009), 65-72. © 2009 The editors and contributors. Published by Northern European Association for Language Technology (NEALT) http://omilia.uio.no/nealt . Electronically published at Tartu University Library (Estonia) http://hdl.handle.net/10062/9206

Proceedings of the 13th Conference on Language Resources and Evaluation (LREC 2022)

The prevailing practice in the academia is to evaluate the model performance on in-domain evaluation data typically set aside from the training corpus. However, in many real world applications the data on which the model is applied may very substantially differ from the characteristics of the training data. In this paper, we focus on Finnish out-of-domain parsing by introducing a novel UD Finnish-OOD out-of-domain treebank including five very distinct data sources (web documents, clinical, online discussions, tweets, and poetry), and a total of 19,382 syntactic words in 2,122 sentences released under the Universal Dependencies framework. Together with the new treebank, we present extensive out-of-domain parsing evaluation utilizing the available section-level information from three different Finnish UD treebanks (TDT, PUD, OOD). Compared to the previously existing treebanks, the new Finnish-OOD is shown include sections more challenging for the general parser, creating an interesting evaluation setting and yielding valuable information for those applying the parser outside of its training domain.</p

Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation

BACKGROUND: The ability to distinguish between genes and proteins is essential for understanding biological text. Support Vector Machines (SVMs) have been proven to be very efficient in general data mining tasks. We explore their capability for the gene versus protein name disambiguation task. RESULTS: We incorporated into the conventional SVM a weighting scheme based on distances of context words from the word to be disambiguated. This weighting scheme increased the performance of SVMs by five percentage points giving performance better than 85% as measured by the area under ROC curve and outperformed the Weighted Additive Classifier, which also incorporates the weighting, and the Naive Bayes classifier. CONCLUSION: We show that the performance of SVMs can be improved by the proposed weighting scheme. Furthermore, our results suggest that in this study the increase of the classification performance due to the weighting is greater than that obtained by selecting the underlying classifier or the kernel part of the SVM