Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Natural Language Processing
Title: Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
Abstract: Abstract The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions. The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and was organized in two tasks: (i) document triage task, focused on identifying scientific literature containing experimentally verified protein–protein interactions (PPIs) affected by genetic mutations and (ii) relation extraction task, focused on extracting the affected interactions (protein pairs). To assist system developers and task participants, a large-scale corpus of PubMed documents was manually annotated for this task. Ten teams worldwide contributed 22 distinct text-mining models for the document triage task, and six teams worldwide contributed 14 different text-mining systems for the relation extraction task. When comparing the text-mining system predictions with human annotations, for the triage task, the best F-score was 69.06%, the best precision was 62.89%, the best recall was 98.0% and the best average precision was 72.5%. For the relation extraction task, when taking homologous genes into account, the best F-score was 37.73%, the best precision was 46.5% and the best recall was 54.1%. Submitted systems explored a wide range of methods, from traditional rule-based, statistical and machine learning systems to state-of-the-art deep learning methods. Given the level of participation and the individual team results we find the precision medicine track to be successful in engaging the text-mining research community. In the meantime, the track produced a manually annotated corpus of 5509 PubMed documents developed by BioGRID curators and relevant for precision medicine. The data set is freely available to the community, and the specific interactions have been integrated into the BioGRID data set. In addition, this challenge provided the first results of automatically identifying PubMed articles that describe PPI affected by mutations, as well as extracting the affected relations from those articles. Still, much progress is needed for computer-assisted precision medicine text mining to become mainstream. Future work should focus on addressing the remaining technical challenges and incorporating the practical benefits of text-mining tools into real-world precision medicine information-related curation.
Extracted statement — subtasks: document triage task
Research field: Natural Language Processing
Title: End-to-end Neural Coreference Resolution
Abstract: We introduce the first end-to-end coreference resolution model and show that it significantly outperforms all previous work without using a syntactic parser or hand-engineered mention detector. The key idea is to directly consider all spans in a document as potential mentions and learn distributions over possible antecedents for each. The model computes span embeddings that combine context-dependent boundary representations with a head-finding attention mechanism. It is trained to maximize the marginal likelihood of gold antecedent spans from coreference clusters and is factored to enable aggressive pruning of potential mentions. Experiments demonstrate state-of-the-art performance, with a gain of 1.5 F1 on the OntoNotes benchmark and by 3.1 F1 using a 5-model ensemble, despite the fact that this is the first approach to be successfully trained with no external resources.
Extracted statement — model: end-to-end coreference resolution model
Research field: Natural Language Processing
Title: Character-aware neural language models
Abstract: We describe a simple neural language model that relies only on character-level inputs. Predictions are still made at the word-level. Our model employs a convolutional neural network (CNN) and a highway network over characters, whose output is given to a long short-term memory (LSTM) recurrent neural network language model (RNN-LM). On the English Penn Treebank the model is on par with the existing state-of-the-art despite having 60% fewer parameters. On languages with rich morphology (Arabic, Czech, French, German, Spanish, Russian), the model outperforms word-level/morpheme-level LSTM baselines, again with fewer parameters. The results suggest that on many languages, character inputs are sufficient for language modeling. Analysis of word representations obtained from the character composition part of the model reveals that the model is able to encode, from characters only, both semantic and orthographic information.
Extracted statement — Material: English Penn Treebank
Research field: Natural Language Processing
Title: WWW'18 Open Challenge: Financial Opinion Mining and Question Answering
Abstract: The growing maturity of Natural Language Processing (NLP) techniques and resources is dramatically changing the landscape of many application domains which are dependent on the analysis of unstructured data at scale. The finance domain, with its reliance on the interpretation of multiple unstructured and structured data sources and its demand for fast and comprehensive decision making is already emerging as a primary ground for the experimentation of NLP, Web Mining and Information Retrieval (IR) techniques for the automatic analysis of financial news and opinions online. This challenge focuses on advancing the state-of-the-art of aspect-based sentiment analysis and opinion-based Question Answering for the financial domain.
Extracted statement — Domain: financial domain
Research field: Natural Language Processing
Title: Evaluation of BioCreAtIvE assessment of task 2
Abstract: Abstract Background Molecular Biology accumulated substantial amounts of data concerning functions of genes and proteins. Information relating to functional descriptions is generally extracted manually from textual data and stored in biological databases to build up annotations for large collections of gene products. Those annotation databases are crucial for the interpretation of large scale analysis approaches using bioinformatics or experimental techniques. Due to the growing accumulation of functional descriptions in biomedical literature the need for text mining tools to facilitate the extraction of such annotations is urgent. In order to make text mining tools useable in real world scenarios, for instance to assist database curators during annotation of protein function, comparisons and evaluations of different approaches on full text articles are needed. Results The Critical Assessment for Information Extraction in Biology (BioCreAtIvE) contest consists of a community wide competition aiming to evaluate different strategies for text mining tools, as applied to biomedical literature. We report on task two which addressed the automatic extraction and assignment of Gene Ontology (GO) annotations of human proteins, using full text articles. The predictions of task 2 are based on triplets of protein – GO term – article passage . The annotation-relevant text passages were returned by the participants and evaluated by expert curators of the GO annotation (GOA) team at the European Institute of Bioinformatics (EBI). Each participant could submit up to three results for each sub-task comprising task 2. In total more than 15,000 individual results were provided by the participants. The curators evaluated in addition to the annotation itself, whether the protein and the GO term were correctly predicted and traceable through the submitted text fragment. Conclusion Concepts provided by GO are currently the most extended set of terms used for annotating gene products, thus they were explored to assess how effectively text mining tools are able to extract those annotations automatically. Although the obtained results are promising, they are still far from reaching the required performance demanded by real world applications. Among the principal difficulties encountered to address the proposed task, were the complex nature of the GO terms and protein names (the large range of variants which are used to express proteins and especially GO terms in free text), and the lack of a standard training set. A range of very different strategies were used to tackle this task. The dataset generated in line with the BioCreative challenge is publicly available and will allow new possibilities for training information extraction methods in the domain of molecular biology.
Extracted statement — Other resources: Gene Ontology
Research field: Natural Language Processing
Title: Evaluation of BioCreAtIvE assessment of task 2
Abstract: Abstract Background Molecular Biology accumulated substantial amounts of data concerning functions of genes and proteins. Information relating to functional descriptions is generally extracted manually from textual data and stored in biological databases to build up annotations for large collections of gene products. Those annotation databases are crucial for the interpretation of large scale analysis approaches using bioinformatics or experimental techniques. Due to the growing accumulation of functional descriptions in biomedical literature the need for text mining tools to facilitate the extraction of such annotations is urgent. In order to make text mining tools useable in real world scenarios, for instance to assist database curators during annotation of protein function, comparisons and evaluations of different approaches on full text articles are needed. Results The Critical Assessment for Information Extraction in Biology (BioCreAtIvE) contest consists of a community wide competition aiming to evaluate different strategies for text mining tools, as applied to biomedical literature. We report on task two which addressed the automatic extraction and assignment of Gene Ontology (GO) annotations of human proteins, using full text articles. The predictions of task 2 are based on triplets of protein – GO term – article passage . The annotation-relevant text passages were returned by the participants and evaluated by expert curators of the GO annotation (GOA) team at the European Institute of Bioinformatics (EBI). Each participant could submit up to three results for each sub-task comprising task 2. In total more than 15,000 individual results were provided by the participants. The curators evaluated in addition to the annotation itself, whether the protein and the GO term were correctly predicted and traceable through the submitted text fragment. Conclusion Concepts provided by GO are currently the most extended set of terms used for annotating gene products, thus they were explored to assess how effectively text mining tools are able to extract those annotations automatically. Although the obtained results are promising, they are still far from reaching the required performance demanded by real world applications. Among the principal difficulties encountered to address the proposed task, were the complex nature of the GO terms and protein names (the large range of variants which are used to express proteins and especially GO terms in free text), and the lack of a standard training set. A range of very different strategies were used to tackle this task. The dataset generated in line with the BioCreative challenge is publicly available and will allow new possibilities for training information extraction methods in the domain of molecular biology.
Extracted statement — Ontology used: Gene Ontology (GO)
Research field: Natural Language Processing
Title: Overview of the Bacteria Biotope Task at BioNLP Shared Task 2016
Abstract: This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (biotopes and geographical places) of bacteria from PubMe abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.
Extracted statement — Entity types: Geographical places
Research field: Natural Language Processing
Title: Incorporating non-local information into information extraction systems by Gibbs sampling
Abstract: Most current statistical natural language processing models use only local features so as to permit dynamic programming in inference, but this makes them unable to fully account for the long distance structure that is prevalent in language use. We show how to solve this dilemma with Gibbs sampling, a simple Monte Carlo method used to perform approximate inference in factored probabilistic models. By using simulated annealing in place of Viterbi decoding in sequence models such as HMMs, CMMs, and CRFs, it is possible to incorporate non-local structure while preserving tractable inference. We use this technique to augment an existing CRF-based information extraction system with long-distance dependency models, enforcing label consistency and extraction template consistency constraints. This technique results in an error reduction of up to 9% over state-of-the-art systems on two established information extraction tasks.
Extracted statement — Method: Gibbs sampling
Research field: Natural Language Processing
Title: BC4GO: a full-text corpus for the BioCreative IV GO task
Abstract: Gene function curation via Gene Ontology (GO) annotation is a common task among Model Organism Database groups. Owing to its manual nature, this task is considered one of the bottlenecks in literature curation. There have been many previous attempts at automatic identification of GO terms and supporting information from full text. However, few systems have delivered an accuracy that is comparable with humans. One recognized challenge in developing such systems is the lack of marked sentence-level evidence text that provides the basis for making GO annotations. We aim to create a corpus that includes the GO evidence text along with the three core elements of GO annotations: (i) a gene or gene product, (ii) a GO term and (iii) a GO evidence code. To ensure our results are consistent with real-life GO data, we recruited eight professional GO curators and asked them to follow their routine GO annotation protocols. Our annotators marked up more than 5000 text passages in 200 articles for 1356 distinct GO terms. For evidence sentence selection, the inter-annotator agreement (IAA) results are 9.3% (strict) and 42.7% (relaxed) in F1-measures. For GO term selection, the IAAs are 47% (strict) and 62.9% (hierarchical). Our corpus analysis further shows that abstracts contain ∼10% of relevant evidence sentences and 30% distinct GO terms, while the Results/Experiment section has nearly 60% relevant sentences and >70% GO terms. Further, of those evidence sentences found in abstracts, less than one-third contain enough experimental detail to fulfill the three core criteria of a GO annotation. This result demonstrates the need of using full-text articles for text mining GO annotations. Through its use at the BioCreative IV GO (BC4GO) task, we expect our corpus to become a valuable resource for the BioNLP research community. Database URL: http://www.biocreative.org/resources/corpora/bc-iv-go-task-corpus/.
Extracted statement — Coarse-grained Entity type: GO Term
Research field: Natural Language Processing
Title: Character-aware neural language models
Abstract: We describe a simple neural language model that relies only on character-level inputs. Predictions are still made at the word-level. Our model employs a convolutional neural network (CNN) and a highway network over characters, whose output is given to a long short-term memory (LSTM) recurrent neural network language model (RNN-LM). On the English Penn Treebank the model is on par with the existing state-of-the-art despite having 60% fewer parameters. On languages with rich morphology (Arabic, Czech, French, German, Spanish, Russian), the model outperforms word-level/morpheme-level LSTM baselines, again with fewer parameters. The results suggest that on many languages, character inputs are sufficient for language modeling. Analysis of word representations obtained from the character composition part of the model reveals that the model is able to encode, from characters only, both semantic and orthographic information.
Extracted statement — Method: Highway network
Research field: Natural Language Processing
Title: Overview of the BioCreative VI text-mining services for Kinome Curation Track
Abstract: Abstract The text-mining services for kinome curation track, part of BioCreative VI, proposed a competition to assess the effectiveness of text mining to perform literature triage. The track has exploited an unpublished curated data set from the neXtProt database. This data set contained comprehensive annotations for 300 human protein kinases. For a given protein and a given curation axis [diseases or gene ontology (GO) biological processes], participants’ systems had to identify and rank relevant articles in a collection of 5.2 M MEDLINE citations (task 1) or 530 000 full-text articles (task 2). Explored strategies comprised named-entity recognition and machine-learning frameworks. For that latter approach, participants developed methods to derive a set of negative instances, as the databases typically do not store articles that were judged as irrelevant by curators. The supervised approaches proposed by the participating groups achieved significant improvements compared to the baseline established in a previous study and compared to a basic PubMed search.
Extracted statement — Concept types: human protein kinase
Research field: Natural Language Processing
Title: The ACL RD-TEC 2.0: A Language Resource for Evaluating Term Extraction and Entity Recognition Methods
Abstract: This paper introduces the ACL Reference Dataset for Terminology Extraction and Classification, version 2.0 (ACL RD-TEC 2.0). The ACL RD-TEC 2.0 has been developed with the aim of providing a benchmark for the evaluation of term and entity recognition tasks based on specialised text from the computational linguistics domain. This release of the corpus consists of 300 abstracts from articles in the ACL Anthology Reference Corpus, published between 1978–2006. In these abstracts, terms (i.e., single or multi-word lexical units with a specialised meaning) are manually annotated. In addition to their boundaries in running text, annotated terms are classified into one of the seven categories method, tool, language resource (LR), LR product, model, measures and measurements, and other. To assess the quality of the annotations and to determine the difficulty of this annotation task, more than 171 of the abstracts are annotated twice, independently, by each of the two annotators. In total, 6,818 terms are identified and annotated in more than 1300 sentences, resulting in a specialised vocabulary made of 3,318 lexical forms, mapped to 3,471 concepts. We explain the development of the annotation guidelines and discuss some of the challenges we encountered in this annotation task.
Extracted statement — Concept types: Language Resource
Research field: Natural Language Processing
Title: Relationship extraction for knowledge graph creation from biomedical literature
Abstract: Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare a few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT and T5-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets, showing that transformer-based models handle well both small datasets, due to pre-training on large C4 dataset, as well as unbalanced data. The best performing model was the DistilBERT-based model ﬁne-tuned on balanced data, with a reported F1-score of 0.89.
Extracted statement — Method: machine learning method
Research field: Natural Language Processing
Title: Overview of the BioCreative VII LitCovid Track: multi-label topic classification for COVID-19 literature annotation
Abstract: The BioCreative LitCovid track calls for a community effort to tackle automated topic annotation for COVID-19 literature. The number of COVID-19-related articles in the literature is growing by about 10,000 articles per month, significantly challenging curation efforts and downstream interpretation. LitCovid is a literature database of COVID-19related articles in PubMed, which has accumulated more than 180,000 articles with millions of accesses each month by users worldwide. The rapid literature growth significantly increases the burden of LitCovid curation, especially for topic annotations. Topic annotation in LitCovid assigns one or more (up to eight) labels to articles. The annotated topics have been widely used both directly in LitCovid (e.g., accounting for ~20% of total uses) and downstream studies such as knowledge network generation and citation analysis. It is, therefore, important to develop innovative text mining methods to tackle the challenge. We organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. This article summarizes the BioCreative LitCovid track in terms of data collection and team participation. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/. It consists of over 30K PubMed articles, one of the largest multilabel classification datasets on biomedical literature. There were 80 submissions in total from 19 teams worldwide. The highestperforming submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. We look forward to further participation in developing biomedical text mining methods in response to the rapid growth of the COVID-19 literature. Keywords—biomedical text mining; natural language processing; artificial intelligence; machine learning; deep learning; multi-label classification; COVID-19; LitCovid;
Extracted statement — Evaluation metrics: Macro F1