Machine learning model for clinical named entity recognition

To extract important concepts (named entities) from clinical notes, most widely used NLP task is named entity recognition (NER). It is found from the literature that several researchers have extensively used machine learning models for clinical NER.The most fundamental tasks among the medical data mining tasks are medical named entity recognition and normalization. Medical named entity recognition is different from general NER in various ways. Huge number of alternate spellings and synonyms create explosion of word vocabulary sizes. This reduces the medicine dictionary efficiency. Entities often consist of long sequences of tokens, making harder to detect boundaries exactly. The notes written by clinicians written notes are less structured and are in minimal grammatical form with cryptic short hand. Because of this, it poses challenges in named entity recognition. Generally, NER systems are either rule based or pattern based. The rules and patterns are not generalizable because of the diverse writing style of clinicians. The systems that use machine learning based approach to resolve these issues focus on choosing effective features for classifier building. In this work, machine learning based approach has been used to extract the clinical data in a required manne

Enhancing Timeliness of Drug Overdose Mortality Surveillance: A Machine Learning Approach

BACKGROUND: Timely data is key to effective public health responses to epidemics. Drug overdose deaths are identified in surveillance systems through ICD-10 codes present on death certificates. ICD-10 coding takes time, but free-text information is available on death certificates prior to ICD-10 coding. The objective of this study was to develop a machine learning method to classify free-text death certificates as drug overdoses to provide faster drug overdose mortality surveillance. METHODS: Using 2017–2018 Kentucky death certificate data, free-text fields were tokenized and features were created from these tokens using natural language processing (NLP). Word, bigram, and trigram features were created as well as features indicating the part-of-speech of each word. These features were then used to train machine learning classifiers on 2017 data. The resulting models were tested on 2018 Kentucky data and compared to a simple rule-based classification approach. Documented code for this method is available for reuse and extensions: https://github.com/pjward5656/dcnlp. RESULTS: The top scoring machine learning model achieved 0.96 positive predictive value (PPV) and 0.98 sensitivity for an F-score of 0.97 in identification of fatal drug overdoses on test data. This machine learning model achieved significantly higher performance for sensitivity (p \u3c 0.001) than the rule-based approach. Additional feature engineering may improve the model’s prediction. This model can be deployed on death certificates as soon as the free-text is available, eliminating the time needed to code the death certificates. CONCLUSION: Machine learning using natural language processing is a relatively new approach in the context of surveillance of health conditions. This method presents an accessible application of machine learning that improves the timeliness of drug overdose mortality surveillance. As such, it can be employed to inform public health responses to the drug overdose epidemic in near-real time as opposed to several weeks following events

Ferromagnetism in the Periodic Anderson Model - a Modified Alloy Analogy

We introduce a new aproximation scheme for the periodic Anderson model (PAM). The modified alloy approximation represents an optimum alloy approximation for the strong coupling limit, which can be solved within the CPA-formalism. Zero-temperature and finite-temperature phase diagrams are presented for the PAM in the intermediate-valence regime. The diversity of magnetic properties accessible by variation of the system parameters can be studied by means of quasiparticle densities of states: The conduction band couples either ferro- or antiferromagneticaly to the f-levels. A finite hybridization is a necessary precondition for ferromagnetism. However, too strong hybridization generally suppresses ferromagnetism, but can for certain system parameters also lead to a semi-metallic state with unusual magnetic properties. By comparing with the spectral density approximation, the influence of quasiparticle damping can be examined.Comment: 20 pages, 13 figure

Bflier's: A Novel Butterfly Inspired Multi-robotic Model in Search of Signal Sources

The diversified ecology in nature had various forms of swarm behaviors in many species. The butterfly species is one of the prominent and a bit insightful in their random flights and converting that into an artificial metaphor would lead to enormous possibilities. This paper considers one such metaphor known as Butterfly Mating Optimization (BMO). In BMO, the Bfly follows the patrolling mating phenomena and simultaneously captures all the local optima of multimodal functions. To imitate this algorithm, a mobile robot (Bflybot) was designed to meet the features of the Bfly in the BMO algorithm. Also, the multi-Bflybot swarm is designed to act like butterflies in nature and follow the algorithm's rules. The real-time experiments were performed on the BMO algorithm in the multi-robotic arena and considered the signal source as the light source. The experimental results show that the BMO algorithm is applicable to detect multiple signal sources with significant variations in their movements i.e., static and dynamic. In the case of static signal sources, with varying initial locations of Bflybots, the convergence is affected in terms of time and smoothness. Whereas the experiments with varying step-size leads to their variation in the execution time and speed of the bots. In this work, experiments were performed in a dynamic environment where the movement of the signal source in both maneuvering and non-maneuvering scenarios. The Bflybot swarm is able to detect the single and multi-signal sources, moving linearly in between two fixed points, in circular, up and down movements.To evaluate the BMO phenomenon, various ongoing and prospective works such as mid-sea ship detection, aerial search applications, and earthquake prediction were discussed.Comment: 12 pages, 17 figure

Characterizing Long COVID: Deep Phenotype of a Complex Condition

BACKGROUND: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or long COVID ), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies. METHODS: The Human Phenotype Ontology (HPO) is a widely used standard for exchange and analysis of phenotypic abnormalities in human disease but has not yet been applied to the analysis of COVID-19. FINDINGS: We identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to HPO terms. We present layperson synonyms and definitions that can be used to link patient self-report questionnaires to standard medical terminology. Long COVID clinical manifestations are not assessed consistently across studies, and most manifestations have been reported with a wide range of synonyms by different authors. Across at least 10 cohorts, authors reported 31 unique clinical features corresponding to HPO terms; the most commonly reported feature was Fatigue (median 45.1%) and the least commonly reported was Nausea (median 3.9%), but the reported percentages varied widely between studies. INTERPRETATION: Translating long COVID manifestations into computable HPO terms will improve analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared/pooled more effectively. Furthermore, mapping lay terminology to HPO will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, thereby improving the stratification, diagnosis, and treatment of long COVID. FUNDING: U24TR002306; UL1TR001439; P30AG024832; GBMF4552; R01HG010067; UL1TR002535; K23HL128909; UL1TR002389; K99GM145411

Characterizing Long COVID: Deep Phenotype of a Complex Condition.

BACKGROUND: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or long COVID ), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies. METHODS: The Human Phenotype Ontology (HPO) is a widely used standard for exchange and analysis of phenotypic abnormalities in human disease but has not yet been applied to the analysis of COVID-19. FINDINGS: We identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to HPO terms. We present layperson synonyms and definitions that can be used to link patient self-report questionnaires to standard medical terminology. Long COVID clinical manifestations are not assessed consistently across studies, and most manifestations have been reported with a wide range of synonyms by different authors. Across at least 10 cohorts, authors reported 31 unique clinical features corresponding to HPO terms; the most commonly reported feature was Fatigue (median 45.1%) and the least commonly reported was Nausea (median 3.9%), but the reported percentages varied widely between studies. INTERPRETATION: Translating long COVID manifestations into computable HPO terms will improve analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared/pooled more effectively. Furthermore, mapping lay terminology to HPO will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, thereby improving the stratification, diagnosis, and treatment of long COVID. FUNDING: U24TR002306; UL1TR001439; P30AG024832; GBMF4552; R01HG010067; UL1TR002535; K23HL128909; UL1TR002389; K99GM145411

Survival and performance of a dual tapered-wedge fully HA-coated press fit femoral stem

Introduction Fully hydroxyapatite-coated titanium alloy double-tapered stems have been successful implant designs for THA. The Novation Element Stem (Exactech, Gainesville, FL) is one of several of these implants following a modified Corail design philosophy. Although a great deal is known about the results of the Corail stem, little is known about the more recent Corail-inspired implants. The authors evaluated the clinical outcomes, radiographic findings and survival statistics of the collarless version of the Element Stem when used routinely in a diverse patient population. Methods A retrospective review was performed for all primary THR cases from 2010 to 2018. Patient demographics and HHS/OHS/patient satisfaction scores were obtained. Radiographs were evaluated for stem subsidence, radiolucencies, and bone responses to the implant. Results One hundred and fifty seven Element Stems were implanted with greater than 2 years of radiographic follow-up, while 105 Element Stems implanted during the study period had a survival of 5 years or more. Average HHS was 91.7 and average OHS was 44.0. 54 of 157 hips had radiolucencies, all of which included a proximal zonal radiolucency. Average subsidence was 3.33 mm; 18 hips had subsidence > 4 mm. There were 8 revisions for: aseptic loosening (4), trauma-related peri-prosthetic fractures, and early proximal-medial fractures. At 5 years, the all-cause survival rate is 92.4%, 96.2% based only on aseptic loosening and 98.1% based only on proximal medial fractures. Conclusion Clinical outcomes using the collarless Novation Element Stem are good, but early proximal medial fracture is still a factor in patients with poor-quality bone. Proximal radiolucencies progressing to aseptic loosening post-operatively are also a concern. The 11.5% rate of subsidence is comparable to other fully HA-coated collarless stems. This study provides a thorough critical analysis of outcomes and midterm survival data of this dual tapered-wedge fully HA-coated collarless stem used routinely in a diverse patient population