Joint prediction of travel mode choice and purpose from travel surveys: A multitask deep learning approach

The prediction and behavioural analysis of travel mode choice and purpose are critical for transport planning and have attracted increasing interest in research. Traditionally, the prediction of travel mode choice and trip purpose has been tackled separately, which fail to fully leverage the shared information between travel mode and purpose. This study addresses this gap by proposing a multitask learning deep neural network framework (MTLDNN) to jointly predict mode choice and purpose. We empirically evaluate and validate this framework using the household travel survey data in Greater London, UK. The results show that this framework has significantly lower cross-entropy loss than multinomial logit models (MNL) and single-task-learning deep neural network models (STLDNN). On the other hand, the predictive accuracy of MTLDNN is similar to STLDNN and is significantly higher than MNL. Moreover, in terms of behaviour analysis, the substitution pattern and choice probability of MTLDNN regarding input variables largely agree with MNL and STLDNN. This work demonstrates that MTLDNN is efficient in utilising the information shared by travel mode choice and purpose, and is capable of producing behaviourally reasonable substitution patterns across travel modes. Future research would develop more advanced MTLDNN frameworks for travel behaviour analysis and generalise MTLDNN to other travel behaviour topics

Automated clinical coding:What, why, and where we are?

Funding Information: The work is supported by WellCome Trust iTPA Awards (PIII009, PIII032), Health Data Research UK National Phenomics and Text Analytics Implementation Projects, and the United Kingdom Research and Innovation (grant EP/S02431X/1), UKRI Centre for Doctoral Training in Biomedical AI at the University of Edinburgh, School of Informatics. H.D. and J.C. are supported by the Engineering and Physical Sciences Research Council (EP/V050869/1) on “ConCur: Knowledge Base Construction and Curation”. HW was supported by Medical Research Council and Health Data Research UK (MR/S004149/1, MR/S004149/2); British Council (UCL-NMU-SEU international collaboration on Artificial Intelligence in Medicine: tackling challenges of low generalisability and health inequality); National Institute for Health Research (NIHR202639); Advanced Care Research Centre at the University of Edinburgh. We thank constructive comments from Murray Bell and Janice Watson in Terminology Service in Public Health Scotland, and information provided by Allison Reid in the coding department in NHS Lothian, Paul Mitchell, Nicola Symmers, and Barry Hewit in Edinburgh Cancer Informatics, and staff in Epic Systems Corporation. Thanks for the suggestions from Dr. Emma Davidson regarding clinical research. Thanks to the discussions with Dr. Kristiina Rannikmäe regarding the research on clinical coding and with Ruohua Han regarding the social and qualitative aspects of this research. In Fig. , the icon of “Clinical Coders” was from Freepik in Flaticon, https://www.flaticon.com/free-icon/user_747376 ; the icon of “Automated Coding System” was from Free Icon Library, https://icon-library.com/png/272370.html . Funding Information: The work is supported by WellCome Trust iTPA Awards (PIII009, PIII032), Health Data Research UK National Phenomics and Text Analytics Implementation Projects, and the United Kingdom Research and Innovation (grant EP/S02431X/1), UKRI Centre for Doctoral Training in Biomedical AI at the University of Edinburgh, School of Informatics. H.D. and J.C. are supported by the Engineering and Physical Sciences Research Council (EP/V050869/1) on “ConCur: Knowledge Base Construction and Curation”. HW was supported by Medical Research Council and Health Data Research UK (MR/S004149/1, MR/S004149/2); British Council (UCL-NMU-SEU international collaboration on Artificial Intelligence in Medicine: tackling challenges of low generalisability and health inequality); National Institute for Health Research (NIHR202639); Advanced Care Research Centre at the University of Edinburgh. We thank constructive comments from Murray Bell and Janice Watson in Terminology Service in Public Health Scotland, and information provided by Allison Reid in the coding department in NHS Lothian, Paul Mitchell, Nicola Symmers, and Barry Hewit in Edinburgh Cancer Informatics, and staff in Epic Systems Corporation. Thanks for the suggestions from Dr. Emma Davidson regarding clinical research. Thanks to the discussions with Dr. Kristiina Rannikmäe regarding the research on clinical coding and with Ruohua Han regarding the social and qualitative aspects of this research. In Fig. 1 , the icon of “Clinical Coders” was from Freepik in Flaticon, https://www.flaticon.com/free-icon/user_747376 ; the icon of “Automated Coding System” was from Free Icon Library, https://icon-library.com/png/272370.html. Publisher Copyright: © 2022, The Author(s).Clinical coding is the task of transforming medical information in a patient’s health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019–early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable processof a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.Peer reviewe

Automated Clinical Coding:What, Why, and Where We Are?

Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019 - early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.Comment: accepted for npj Digital Medicin

Edge-aware Hard Clustering Graph Pooling for Brain Imaging Data

Graph Convolutional Networks (GCNs) can capture non-Euclidean spatial dependence between different brain regions, and the graph pooling operator in GCNs is key to enhancing the representation learning capability and acquiring abnormal brain maps. However, the majority of existing research designs graph pooling operators only from the perspective of nodes while disregarding the original edge features, in a way that not only confines graph pooling application scenarios, but also diminishes its ability to capture critical substructures. In this study, a clustering graph pooling method that first supports multidimensional edge features, called Edge-aware hard clustering graph pooling (EHCPool), is developed. EHCPool proposes the first 'Edge-to-node' score evaluation criterion based on edge features to assess node feature significance. To more effectively capture the critical subgraphs, a novel Iteration n-top strategy is further designed to adaptively learn sparse hard clustering assignments for graphs. Subsequently, an innovative N-E Aggregation strategy is presented to aggregate node and edge feature information in each independent subgraph. The proposed model was evaluated on multi-site brain imaging public datasets and yielded state-of-the-art performance. We believe this method is the first deep learning tool with the potential to probe different types of abnormal functional brain networks from data-driven perspective. Core code is at: https://github.com/swfen/EHCPool

Ontology-driven and weakly supervised rare disease identification from clinical notes

BACKGROUND: Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. METHODS: We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. RESULTS: The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). CONCLUSION: The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies

Knowledge Driven Phenotyping

Extracting patient phenotypes from routinely collected health data (such as Electronic Health Records) requires translating clinically-sound phenotype definitions into queries/computations executable on the underlying data sources by clinical researchers. This requires significant knowledge and skills to deal with heterogeneous and often imperfect data. Translations are time-consuming, error-prone and, most importantly, hard to share and reproduce across different settings. This paper proposes a knowledge driven framework that (1) decouples the specification of phenotype semantics from underlying data sources; (2) can automatically populate and conduct phenotype computations on heterogeneous data spaces. We report preliminary results of deploying this framework on five Scottish health datasets

Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic

AimsCardiovascular diseases (CVDs) increase mortality risk from coronavirus infection (COVID-19). There are also concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both 'direct', through infection, and 'indirect', through changes in healthcare.Methods and resultsWe used (i) national mortality data for England and Wales to investigate trends in non-COVID-19 and CVD excess deaths; (ii) routine data from hospitals in England (n = 2), Italy (n = 1), and China (n = 5) to assess indirect pandemic effects on referral, diagnosis, and treatment services for CVD; and (iii) population-based electronic health records from 3 862 012 individuals in England to investigate pre- and post-COVID-19 mortality for people with incident and prevalent CVD. We incorporated pre-COVID-19 risk (by age, sex, and comorbidities), estimated population COVID-19 prevalence, and estimated relative risk (RR) of mortality in those with CVD and COVID-19 compared with CVD and non-infected (RR: 1.2, 1.5, 2.0, and 3.0).Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous (peak RR 1.14). CVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy, and England. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown and is still reduced in Italy and England. For total CVD (incident and prevalent), at 10% COVID-19 prevalence, we estimated direct impact of 31 205 and 62 410 excess deaths in England (RR 1.5 and 2.0, respectively), and indirect effect of 49 932 to 99 865 deaths.ConclusionSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the pandemic

Fluid Inclusion Constrained Multiple Petroleum Chargings in the Lithologic Reservoirs of the Late Eocene Shahejie Formation in the Minfeng Sag, Bohai Bay Basin, East China

The fluid inclusion technique was utilized to reveal the petroleum charging events in the lithologic reservoirs embraced in the Late Eocene Shahejie Formation of the Minfeng sag, Bohai Bay Basin, East China. Petrography, fluorescence microspectrometry, and microthermometry were systematically carried out on 15 double-polished thin sections handled from reservoir core samples of the third Member of the Shahejie Formation. The results show that three generations of petroleum inclusions with fluorescence colors of yellow, yellowish green and bright blue were entrapped along the healed fractures in detrital quartz grains of these samples. The fluorescence features of petroleum inclusions illustrate that inclusion oils have different maturities and were products of source rocks at different stages. In addition, the trapping time of petroleum inclusions was determined by combining the homogenization temperatures of their coeval aqueous inclusions with thermal-burial histories. By integrating the petrographic occurrence, characteristics of petroleum inclusions, and the maturity and the trapping time of the studied inclusion oils, it is jointly constrained that the lithologic reservoirs of the Late Eocene Shahejie Formation in the Minfeng sag underwent three petroleum chargings, which occurred during 37.8~25 Ma, 11.7~3.5 Ma and 1.4~0.1 Ma, respectively. The petroleum from each charging period migrated from the center of the sag to the edge, and the lower the maturity of the migrating petroleum, the longer the migration duration

Fluid Inclusion Constrained Multiple Petroleum Chargings in the Lithologic Reservoirs of the Late Eocene Shahejie Formation in the Minfeng Sag, Bohai Bay Basin, East China

The fluid inclusion technique was utilized to reveal the petroleum charging events in the lithologic reservoirs embraced in the Late Eocene Shahejie Formation of the Minfeng sag, Bohai Bay Basin, East China. Petrography, fluorescence microspectrometry, and microthermometry were systematically carried out on 15 double-polished thin sections handled from reservoir core samples of the third Member of the Shahejie Formation. The results show that three generations of petroleum inclusions with fluorescence colors of yellow, yellowish green and bright blue were entrapped along the healed fractures in detrital quartz grains of these samples. The fluorescence features of petroleum inclusions illustrate that inclusion oils have different maturities and were products of source rocks at different stages. In addition, the trapping time of petroleum inclusions was determined by combining the homogenization temperatures of their coeval aqueous inclusions with thermal-burial histories. By integrating the petrographic occurrence, characteristics of petroleum inclusions, and the maturity and the trapping time of the studied inclusion oils, it is jointly constrained that the lithologic reservoirs of the Late Eocene Shahejie Formation in the Minfeng sag underwent three petroleum chargings, which occurred during 37.8~25 Ma, 11.7~3.5 Ma and 1.4~0.1 Ma, respectively. The petroleum from each charging period migrated from the center of the sag to the edge, and the lower the maturity of the migrating petroleum, the longer the migration duration