Harvesting Entities from the Web Using Unique Identifiers -- IBEX

In this paper we study the prevalence of unique entity identifiers on the Web. These are, e.g., ISBNs (for books), GTINs (for commercial products), DOIs (for documents), email addresses, and others. We show how these identifiers can be harvested systematically from Web pages, and how they can be associated with human-readable names for the entities at large scale. Starting with a simple extraction of identifiers and names from Web pages, we show how we can use the properties of unique identifiers to filter out noise and clean up the extraction result on the entire corpus. The end result is a database of millions of uniquely identified entities of different types, with an accuracy of 73--96% and a very high coverage compared to existing knowledge bases. We use this database to compute novel statistics on the presence of products, people, and other entities on the Web.Comment: 30 pages, 5 figures, 9 tables. Complete technical report for A. Talaika, J. A. Biega, A. Amarilli, and F. M. Suchanek. IBEX: Harvesting Entities from the Web Using Unique Identifiers. WebDB workshop, 201

Information Extraction from Text for Improving Research on Small Molecules and Histone Modifications

The cumulative number of publications, in particular in the life sciences, requires efficient methods for the automated extraction of information and semantic information retrieval. The recognition and identification of information-carrying units in text – concept denominations and named entities – relevant to a certain domain is a fundamental step. The focus of this thesis lies on the recognition of chemical entities and the new biological named entity type histone modifications, which are both important in the field of drug discovery. As the emergence of new research fields as well as the discovery and generation of novel entities goes along with the coinage of new terms, the perpetual adaptation of respective named entity recognition approaches to new domains is an important step for information extraction. Two methodologies have been investigated in this concern: the state-of-the-art machine learning method, Conditional Random Fields (CRF), and an approximate string search method based on dictionaries. Recognition methods that rely on dictionaries are strongly dependent on the availability of entity terminology collections as well as on its quality. In the case of chemical entities the terminology is distributed over more than 7 publicly available data sources. The join of entries and accompanied terminology from selected resources enables the generation of a new dictionary comprising chemical named entities. Combined with the automatic processing of respective terminology – the dictionary curation – the recognition performance reached an F1 measure of 0.54. That is an improvement by 29 % in comparison to the raw dictionary. The highest recall was achieved for the class of TRIVIAL-names with 0.79. The recognition and identification of chemical named entities provides a prerequisite for the extraction of related pharmacological relevant information from literature data. Therefore, lexico-syntactic patterns were defined that support the automated extraction of hypernymic phrases comprising pharmacological function terminology related to chemical compounds. It was shown that 29-50 % of the automatically extracted terms can be proposed for novel functional annotation of chemical entities provided by the reference database DrugBank. Furthermore, they are a basis for building up concept hierarchies and ontologies or for extending existing ones. Successively, the pharmacological function and biological activity concepts obtained from text were included into a novel descriptor for chemical compounds. Its successful application for the prediction of pharmacological function of molecules and the extension of chemical classification schemes, such as the the Anatomical Therapeutic Chemical (ATC), is demonstrated. In contrast to chemical entities, no comprehensive terminology resource has been available for histone modifications. Thus, histone modification concept terminology was primary recognized in text via CRFs with a F1 measure of 0.86. Subsequent, linguistic variants of extracted histone modification terms were mapped to standard representations that were organized into a newly assembled histone modification hierarchy. The mapping was accomplished by a novel developed term mapping approach described in the thesis. The combination of term recognition and term variant resolution builds up a new procedure for the assembly of novel terminology collections. It supports the generation of a term list that is applicable in dictionary-based methods. For the recognition of histone modification in text it could be shown that the named entity recognition method based on dictionaries is superior to the used machine learning approach. In conclusion, the present thesis provides techniques which enable an enhanced utilization of textual data, hence, supporting research in epigenomics and drug discovery

Enhancing Phenotype Recognition in Clinical Notes Using Large Language Models: PhenoBCBERT and PhenoGPT

We hypothesize that large language models (LLMs) based on the transformer architecture can enable automated detection of clinical phenotype terms, including terms not documented in the HPO. In this study, we developed two types of models: PhenoBCBERT, a BERT-based model, utilizing Bio+Clinical BERT as its pre-trained model, and PhenoGPT, a GPT-based model that can be initialized from diverse GPT models, including open-source versions such as GPT-J, Falcon, and LLaMA, as well as closed-source versions such as GPT-3 and GPT-3.5. We compared our methods with PhenoTagger, a recently developed HPO recognition tool that combines rule-based and deep learning methods. We found that our methods can extract more phenotype concepts, including novel ones not characterized by HPO. We also performed case studies on biomedical literature to illustrate how new phenotype information can be recognized and extracted. We compared current BERT-based versus GPT-based models for phenotype tagging, in multiple aspects including model architecture, memory usage, speed, accuracy, and privacy protection. We also discussed the addition of a negation step and an HPO normalization layer to the transformer models for improved HPO term tagging. In conclusion, PhenoBCBERT and PhenoGPT enable the automated discovery of phenotype terms from clinical notes and biomedical literature, facilitating automated downstream tasks to derive new biological insights on human diseases

Linking social media, medical literature, and clinical notes using deep learning.

Researchers analyze data, information, and knowledge through many sources, formats, and methods. The dominant data format includes text and images. In the healthcare industry, professionals generate a large quantity of unstructured data. The complexity of this data and the lack of computational power causes delays in analysis. However, with emerging deep learning algorithms and access to computational powers such as graphics processing unit (GPU) and tensor processing units (TPUs), processing text and images is becoming more accessible. Deep learning algorithms achieve remarkable results in natural language processing (NLP) and computer vision. In this study, we focus on NLP in the healthcare industry and collect data not only from electronic medical records (EMRs) but also medical literature and social media. We propose a framework for linking social media, medical literature, and EMRs clinical notes using deep learning algorithms. Connecting data sources requires defining a link between them, and our key is finding concepts in the medical text. The National Library of Medicine (NLM) introduces a Unified Medical Language System (UMLS) and we use this system as the foundation of our own system. We recognize social media’s dynamic nature and apply supervised and semi-supervised methodologies to generate concepts. Named entity recognition (NER) allows efficient extraction of information, or entities, from medical literature, and we extend the model to process the EMRs’ clinical notes via transfer learning. The results include an integrated, end-to-end, web-based system solution that unifies social media, literature, and clinical notes, and improves access to medical knowledge for the public and experts

Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re

A Semi-Supervised Information Extraction Framework for Large Redundant Corpora

The vast majority of text freely available on the Internet is not available in a form that computers can understand. There have been numerous approaches to automatically extract information from human- readable sources. The most successful attempts rely on vast training sets of data. Others have succeeded in extracting restricted subsets of the available information. These approaches have limited use and require domain knowledge to be coded into the application. The current thesis proposes a novel framework for Information Extraction. From large sets of documents, the system develops statistical models of the data the user wishes to query which generally avoid the lim- itations and complexity of most Information Extractions systems. The framework uses a semi-supervised approach to minimize human input. It also eliminates the need for external Named Entity Recognition systems by relying on freely available databases. The final result is a query-answering system which extracts information from large corpora with a high degree of accuracy

A Semi-Supervised Information Extraction Framework for Large Redundant Corpora

The vast majority of text freely available on the Internet is not available in a form that computers can understand. There have been numerous approaches to automatically extract information from human- readable sources. The most successful attempts rely on vast training sets of data. Others have succeeded in extracting restricted subsets of the available information. These approaches have limited use and require domain knowledge to be coded into the application. The current thesis proposes a novel framework for Information Extraction. From large sets of documents, the system develops statistical models of the data the user wishes to query which generally avoid the lim- itations and complexity of most Information Extractions systems. The framework uses a semi-supervised approach to minimize human input. It also eliminates the need for external Named Entity Recognition systems by relying on freely available databases. The final result is a query-answering system which extracts information from large corpora with a high degree of accuracy

De-Identification of French Unstructured Clinical Notes for Machine Learning Tasks

Unstructured textual data are at the heart of health systems: liaison letters between doctors, operating reports, coding of procedures according to the ICD-10 standard, etc. The details included in these documents make it possible to get to know the patient better, to better manage him or her, to better study the pathologies, to accurately remunerate the associated medical acts\ldots All this seems to be (at least partially) within reach of today by artificial intelligence techniques. However, for obvious reasons of privacy protection, the designers of these AIs do not have the legal right to access these documents as long as they contain identifying data. De-identifying these documents, i.e. detecting and deleting all identifying information present in them, is a legally necessary step for sharing this data between two complementary worlds. Over the last decade, several proposals have been made to de-identify documents, mainly in English. While the detection scores are often high, the substitution methods are often not very robust to attack. In French, very few methods are based on arbitrary detection and/or substitution rules. In this paper, we propose a new comprehensive de-identification method dedicated to French-language medical documents. Both the approach for the detection of identifying elements (based on deep learning) and their substitution (based on differential privacy) are based on the most proven existing approaches. The result is an approach that effectively protects the privacy of the patients at the heart of these medical documents. The whole approach has been evaluated on a French language medical dataset of a French public hospital and the results are very encouraging