MC-DRE: Multi-Aspect Cross Integration for Drug Event/Entity Extraction

Extracting meaningful drug-related information chunks, such as adverse drug events (ADE), is crucial for preventing morbidity and saving many lives. Most ADEs are reported via an unstructured conversation with the medical context, so applying a general entity recognition approach is not sufficient enough. In this paper, we propose a new multi-aspect cross-integration framework for drug entity/event detection by capturing and aligning different context/language/knowledge properties from drug-related documents. We first construct multi-aspect encoders to describe semantic, syntactic, and medical document contextual information by conducting those slot tagging tasks, main drug entity/event detection, part-of-speech tagging, and general medical named entity recognition. Then, each encoder conducts cross-integration with other contextual information in three ways: the key-value cross, attention cross, and feedforward cross, so the multi-encoders are integrated in depth. Our model outperforms all SOTA on two widely used tasks, flat entity detection and discontinuous event extraction.Comment: Accepted at CIKM 202

Named Entity Recognition in Electronic Health Records: A Methodological Review

Objectives A substantial portion of the data contained in Electronic Health Records (EHR) is unstructured, often appearing as free text. This format restricts its potential utility in clinical decision-making. Named entity recognition (NER) methods address the challenge of extracting pertinent information from unstructured text. The aim of this study was to outline the current NER methods and trace their evolution from 2011 to 2022. Methods We conducted a methodological literature review of NER methods, with a focus on distinguishing the classification models, the types of tagging systems, and the languages employed in various corpora. Results Several methods have been documented for automatically extracting relevant information from EHRs using natural language processing techniques such as NER and relation extraction (RE). These methods can automatically extract concepts, events, attributes, and other data, as well as the relationships between them. Most NER studies conducted thus far have utilized corpora in English or Chinese. Additionally, the bidirectional encoder representation from transformers using the BIO tagging system architecture is the most frequently reported classification scheme. We discovered a limited number of papers on the implementation of NER or RE tasks in EHRs within a specific clinical domain. Conclusions EHRs play a pivotal role in gathering clinical information and could serve as the primary source for automated clinical decision support systems. However, the creation of new corpora from EHRs in specific clinical domains is essential to facilitate the swift development of NER and RE models applied to EHRs for use in clinical practice

Recent Developments in Smart Healthcare

Medicine is undergoing a sector-wide transformation thanks to the advances in computing and networking technologies. Healthcare is changing from reactive and hospital-centered to preventive and personalized, from disease focused to well-being centered. In essence, the healthcare systems, as well as fundamental medicine research, are becoming smarter. We anticipate significant improvements in areas ranging from molecular genomics and proteomics to decision support for healthcare professionals through big data analytics, to support behavior changes through technology-enabled self-management, and social and motivational support. Furthermore, with smart technologies, healthcare delivery could also be made more efficient, higher quality, and lower cost. In this special issue, we received a total 45 submissions and accepted 19 outstanding papers that roughly span across several interesting topics on smart healthcare, including public health, health information technology (Health IT), and smart medicine

Bruk av naturlig språkprosessering i psykiatri: En systematisk kartleggingsoversikt

Bakgrunn: Bruk av kunstig intelligens (AI) har et stadig økende fokus, også i helsevesenet. En metode som virker lovende, er naturlig språkprosessering (NLP), som kan brukes til analysering av skriftlig tekst, for eksempel tekst i elektroniske pasientjournaler. Denne undersøkelsen har som formål å undersøke forskning som er gjort på bruk av naturlig språkprosessering for analysering av elektroniske journaler fra pasienter med alvorlige psykiske lidelser, som affektive lidelser og psykoselidelser. Den overordnete hensikten med dette, er å få et inntrykk av om noe av forskningen som er gjort har fokus på forbedring av pasientenes helsesituasjon. Materiale og metode: Det ble gjennomført en systematisk kartleggingsoversikt («scoping review»). Litteratursøket ble gjort i én database for medisinsk forskning, PubMed, med søketermene «psychiatry», «electronic medical records» og «natural language processing». Søket var ikke avgrenset i tid. For at en artikkel skulle bli inkludert i undersøkelsen måtte den være empirisk, ha utført analyser på journaldata i fritekst, ha brukt elektroniske journaler fra psykiatriske pasienter med psykoselidelser og/eller affektive lidelser og være skrevet på engelsk språk. Resultater: Litteratursøket resulterte i totalt 211 unike artikler, av disse oppfylte 37 artikler inklusjonskriteriene i kartleggingsoversikten, og ble undersøkt videre. De fleste av studiene var gjennomført i Storbritannia og USA. Størrelsen på studiepopulasjonen varierte mye, fra noen hundre til flere hundre tusen inkluderte pasienter i studiene. Det var lite av forskningen som var gjort på spesifikke dokumenttyper fra pasientjournal, som for eksempel epikriser eller innkomstjournaler. Hensikten for studiene varierte mye, men kunne deles inn i noen felles kategorier: 1) identifisering av informasjon fra journal, 2) kvantitative undersøkelser av populasjonen eller journalene, 3) seleksjon av pasienter til kohorter og 4) vurdering av risiko. Fortolkning: Det trengs mer grunnforskning før teknologi for naturlig språkprosessering til analyse av elektronisk journal vil bidra med forbedring av psykiatriske pasienters helsesituasjon

Structuring the Unstructured: Unlocking pharmacokinetic data from journals with Natural Language Processing

The development of a new drug is an increasingly expensive and inefficient process. Many drug candidates are discarded due to pharmacokinetic (PK) complications detected at clinical phases. It is critical to accurately estimate the PK parameters of new drugs before being tested in humans since they will determine their efficacy and safety outcomes. Preclinical predictions of PK parameters are largely based on prior knowledge from other compounds, but much of this potentially valuable data is currently locked in the format of scientific papers. With an ever-increasing amount of scientific literature, automated systems are essential to exploit this resource efficiently. Developing text mining systems that can structure PK literature is critical to improving the drug development pipeline. This thesis studied the development and application of text mining resources to accelerate the curation of PK databases. Specifically, the development of novel corpora and suitable natural language processing architectures in the PK domain were addressed. The work presented focused on machine learning approaches that can model the high diversity of PK studies, parameter mentions, numerical measurements, units, and contextual information reported across the literature. Additionally, architectures and training approaches that could efficiently deal with the scarcity of annotated examples were explored. The chapters of this thesis tackle the development of suitable models and corpora to (1) retrieve PK documents, (2) recognise PK parameter mentions, (3) link PK entities to a knowledge base and (4) extract relations between parameter mentions, estimated measurements, units and other contextual information. Finally, the last chapter of this thesis studied the feasibility of the whole extraction pipeline to accelerate tasks in drug development research. The results from this thesis exhibited the potential of text mining approaches to automatically generate PK databases that can aid researchers in the field and ultimately accelerate the drug development pipeline. Additionally, the thesis presented contributions to biomedical natural language processing by developing suitable architectures and corpora for multiple tasks, tackling novel entities and relations within the PK domain

Natural Language Processing: Emerging Neural Approaches and Applications

This Special Issue highlights the most recent research being carried out in the NLP field to discuss relative open issues, with a particular focus on both emerging approaches for language learning, understanding, production, and grounding interactively or autonomously from data in cognitive and neural systems, as well as on their potential or real applications in different domains