Annotating patient clinical records with syntactic chunks and named entities: the Harvey corpus

The free text notes typed by physicians during patient consultations contain valuable information for the study of disease and treatment. These notes are difficult to process by existing natural language analysis tools since they are highly telegraphic (omitting many words), and contain many spelling mistakes, inconsistencies in punctuation, and non-standard word order. To support information extraction and classification tasks over such text, we describe a de-identified corpus of free text notes, a shallow syntactic and named entity annotation scheme for this kind of text, and an approach to training domain specialists with no linguistic background to annotate the text. Finally, we present a statistical chunking system for such clinical text with a stable learning rate and good accuracy, indicating that the manual annotation is consistent and that the annotation scheme is tractable for machine learning

Retrosynthetic reaction prediction using neural sequence-to-sequence models

We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step towards solving the challenging problem of computational retrosynthetic analysis

Harnessing Machine Learning to Improve Healthcare Monitoring with FAERS

This research study investigates the potential of machine learning techniques to improve healthcare monitoring through the utilization of data from the FDA Adverse Event Reporting System (FAERS). The objective is to explore specific applications of machine learning in healthcare monitoring with FAERS and highlight their findings. The study reveals several significant ways in which machine learning can contribute to enhancing healthcare monitoring using FAERS.Machine learning algorithms can detect potential safety signals at an early stage by analyzing FAERS data. By employing anomaly detection and temporal pattern analysis techniques, these models can identify emerging safety concerns that were previously unknown or underreported. This early detection enables timely action to mitigate risks associated with medications or medical products.Machine learning models can assist in pharmacovigilance triage, addressing the challenge posed by the large number of adverse event reports within FAERS. By developing ranking and classification models, adverse events can be prioritized based on severity, novelty, or potential impact. This automation of the triage process enables pharmacovigilance teams to efficiently identify and investigate critical safety concerns.Machine learning models can automate the classification and coding of adverse events, which are often present in unstructured text within FAERS reports. Through the application of Natural Language Processing (NLP) techniques, such as named entity recognition and text classification, relevant information can be extracted, enhancing the efficiency and accuracy of adverse event coding.Machine learning algorithms can refine and validate signals generated from FAERS data by incorporating additional data sources, such as electronic health records, social media, or clinical trials data. This integration provides a more comprehensive understanding of potential risks and helps filter out false positives, facilitating the identification of signals requiring further investigation.Machine learning enables real-time surveillance of FAERS data, allowing for the identification of safety concerns as they occur. Continuous monitoring and real-time analysis of incoming reports enable machine learning models to trigger alerts or notifications to relevant stakeholders, promoting timely intervention to minimize patient harm.The study demonstrates the use of machine learning models to conduct comparative safety analyses by combining FAERS data with other healthcare databases. These models assist in identifying safety differences between medications, patient populations, or dosing regimens, enabling healthcare providers and regulators to make informed decisions regarding treatment choices.While machine learning is a powerful tool in healthcare monitoring, its implementation should be complemented by human expertise and domain knowledge. The interpretation and validation of results generated by machine learning models necessitate the involvement of healthcare professionals and pharmacovigilance experts to ensure accurate and meaningful insights.This research study illustrates the diverse applications of machine learning in improving healthcare monitoring using FAERS data. The findings highlight the potential of machine learning in early safety signal detection, pharmacovigilance triage, adverse event classification and coding, signal refinement and validation, real-time surveillance and alerting, and comparative safety analysis. The study emphasizes the importance of combining machine learning with human expertise to achieve effective and reliable healthcare monitoring

The benefits of in silico modeling to identify possible small-molecule drugs and their off-target interactions

Accepted for publication in a future issue of Future Medicinal Chemistry.The research into the use of small molecules as drugs continues to be a key driver in the development of molecular databases, computer-aided drug design software and collaborative platforms. The evolution of computational approaches is driven by the essential criteria that a drug molecule has to fulfill, from the affinity to targets to minimal side effects while having adequate absorption, distribution, metabolism, and excretion (ADME) properties. A combination of ligand- and structure-based drug development approaches is already used to obtain consensus predictions of small molecule activities and their off-target interactions. Further integration of these methods into easy-to-use workflows informed by systems biology could realize the full potential of available data in the drug discovery and reduce the attrition of drug candidates.Peer reviewe

Processing of Electronic Health Records using Deep Learning: A review

Availability of large amount of clinical data is opening up new research avenues in a number of fields. An exciting field in this respect is healthcare, where secondary use of healthcare data is beginning to revolutionize healthcare. Except for availability of Big Data, both medical data from healthcare institutions (such as EMR data) and data generated from health and wellbeing devices (such as personal trackers), a significant contribution to this trend is also being made by recent advances on machine learning, specifically deep learning algorithms

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape