Objective: To develop and validate a natural language processing (NLP) pipeline that detects 18 conditions in French clinical notes, including 16 comorbidities of the Charlson index, while exploring a collaborative and privacy-enhancing workflow. Materials and Methods: The detection pipeline relied both on rule-based and machine learning algorithms, respectively, for named entity recognition and entity qualification, respectively. We used a large language model pre-trained on millions of clinical notes along with annotated clinical notes in the context of 3 cohort studies related to oncology, cardiology, and rheumatology. The overall workflow was conceived to foster collaboration between studies while respecting the privacy constraints of the data warehouse. We estimated the added values of the advanced technologies and of the collaborative setting. Results: The pipeline reached macro-averaged F1-score positive predictive value, sensitivity, and specificity of 95.7 (95%CI 94.5-96.3), 95.4 (95%CI 94.0-96.3), 96.0 (95%CI 94.0-96.7), and 99.2 (95%CI 99.0-99.4), respectively. F1-scores were superior to those observed using alternative technologies or non-collaborative settings. The models were shared through a secured registry. Conclusions: We demonstrated that a community of investigators working on a common clinical data warehouse could efficiently and securely collaborate to develop, validate and use sensitive artificial intelligence models. In particular, we provided an efficient and robust NLP pipeline that detects conditions mentioned in clinical notes.

Prior research suggests that psychiatric disorders could be linked to increased mortality among patients with COVID-19. However, whether all or specific psychiatric disorders are intrinsic risk factors of death in COVID-19 or whether these associations reflect the greater prevalence of medical risk factors in people with psychiatric disorders has yet to be evaluated. We performed an observational, multicenter, retrospective cohort study to examine the association between psychiatric disorders and mortality among patients hospitalized for laboratory-confirmed COVID-19 at 36 Greater Paris University hospitals. Of 15,168 adult patients, 857 (5.7%) had an ICD-10 diagnosis of psychiatric disorder. Over a mean follow-up period of 14.6 days (SD = 17.9), 326 of 857 (38.0%) patients with a diagnosis of psychiatric disorder died compared with 1276 of 14,311 (8.9%) patients without such a diagnosis (odds ratio 6.27, 95% CI 5.40–7.28, p < .01). When adjusting for age, sex, hospital, current smoking status, and medications according to compassionate use or as part of a clinical trial, this association remained significant (adjusted odds ratio 3.27, 95% CI 2.78–3.85, p < .01). However, additional adjustments for obesity and number of medical conditions resulted in a nonsignificant association (adjusted odds ratio 1.02, 95% CI 0.84–1.23, p = .86). Exploratory analyses after the same adjustments suggested that a diagnosis of mood disorders was significantly associated with reduced mortality, which might be explained by the use of antidepressants. These findings suggest that the increased risk of COVID-19–related mortality in individuals with psychiatric disorders hospitalized for COVID-19 might be explained by the greater number of medical conditions and the higher prevalence of obesity in this population and not by the underlying psychiatric disease.

Purpose: To assess the feasibility of a three-dimensional deep convolutional neural network (3D-CNN) for the general triage of whole-body FDG PET in daily clinical practice. Methods: An institutional clinical data warehouse working environment was devoted to this PET imaging purpose. Dedicated request procedures and data processing workflows were specifically developed within this infrastructure and applied retrospectively to a monocentric dataset as a proof of concept. A custom-made 3D-CNN was first trained and tested on an “unambiguous” well-balanced data sample, which included strictly normal and highly pathological scans. For the training phase, 90% of the data sample was used (learning set: 80%; validation set: 20%, 5-fold cross validation) and the remaining 10% constituted the test set. Finally, the model was applied to a “real-life” test set which included any scans taken. Text mining of the PET reports systematically combined with visual rechecking by an experienced reader served as the standard-of-truth for PET labeling. Results: From 8125 scans, 4963 PETs had processable cross-matched medical reports. For the “unambiguous” dataset (1084 PETs), the 3D-CNN’s overall results for sensitivity, specificity, positive and negative predictive values and likelihood ratios were 84%, 98%, 98%, 85%, 42.0 and 0.16, respectively (F1 score of 90%). When applied to the “real-life” dataset (4963 PETs), the sensitivity, NPV, LR+, LR− and F1 score substantially decreased (61%, 40%, 2.97, 0.49 and 73%, respectively), whereas the specificity and PPV remained high (79% and 90%). Conclusion: An AI-based triage of whole-body FDG PET is promising. Further studies are needed to overcome the challenges presented by the imperfection of real-life PET data.

Objective To develop and validate advanced natural language processing pipelines that detect 18 conditions in clinical notes written in French, among which 16 comorbidities of the Charlson index, while exploring a collaborative and privacy-preserving workflow. Materials and methods The detection pipelines relied both on rule-based and machine learning algorithms for named entity recognition and entity qualification, respectively. We used a large language model pre-trained on millions of clinical notes along with clinical notes annotated in the context of three cohort studies related to oncology, cardiology and rheumatology, respectively. The overall workflow was conceived to foster collaboration between studies while complying to the privacy constraints of the data warehouse. We estimated the added values of both the advanced technologies and the collaborative setting. Results The 18 pipelines reached macro-averaged F1-score, positive predictive value, sensitivity and specificity of 95.7 (95%CI 94.5 - 96.3), 95.4 (95%CI 94.0 - 96.3), 96.0 (95%CI 94.0 - 96.7) and 99.2 (95%CI 99.0 - 99.4), respectively. F1-scores were superior to those observed using either alternative technologies or non-collaborative settings. The models were shared through a secured registry. Conclusions We demonstrated that a community of investigators working on a common clinical data warehouse could efficiently and securely collaborate to develop, validate and use sensitive artificial intelligence models. In particular, we provided efficient and robust natural language processing pipelines that detect conditions mentioned in clinical notes.

For the second consecutive year, teams of the network "Montpellier Infectious Diseases" held their annual meeting. Whereas the 2011 meeting was focused on host-pathogen interaction and pathophysiology, the 2012 meeting was focused on the cooperation between medical and chemical sciences interdisciplinary approaches to fight against virus, bacteria and parasites. Several approaches aimed at designing new bioactive compounds were described during this meeting.