The therapeutic working alliance is a critical factor in predicting the success of psychotherapy treatment. Traditionally, working alliance assessment relies on questionnaires completed by both therapists and patients. In this paper, we present COMPASS, a novel framework to directly infer the therapeutic working alliance from the natural language used in psychotherapy sessions. Our approach utilizes advanced large language models to analyze transcripts of psychotherapy sessions and compare them with distributed representations of statements in the working alliance inventory. Analyzing a dataset of over 950 sessions covering diverse psychiatric conditions, we demonstrate the effectiveness of our method in microscopically mapping patient-therapist alignment trajectories and providing interpretability for clinical psychiatry and in identifying emerging patterns related to the condition being treated. By employing various neural topic modeling techniques in combination with generative language prompting, we analyze the topical characteristics of different psychiatric conditions and incorporate temporal modeling to capture the evolution of topics at a turn-level resolution. This combined framework enhances the understanding of therapeutic interactions, enabling timely feedback for therapists regarding conversation quality and providing interpretable insights to improve the effectiveness of psychotherapy.

Both medical care and observational studies in oncology require a thorough understanding of a patient's disease progression and treatment history, often elaborately documented in clinical notes. Despite their vital role, no current oncology information representation and annotation schema fully encapsulates the diversity of information recorded within these notes. Although large language models (LLMs) have recently exhibited impressive performance on various medical natural language processing tasks, due to the current lack of comprehensively annotated oncology datasets, an extensive evaluation of LLMs in extracting and reasoning with the complex rhetoric in oncology notes remains understudied. We developed a detailed schema for annotating textual oncology information, encompassing patient characteristics, tumor characteristics, tests, treatments, and temporality. Using a corpus of 40 de-identified breast and pancreatic cancer progress notes at University of California, San Francisco, we applied this schema to assess the zero-shot abilities of three recent LLMs (GPT-4, GPT-3.5-turbo, and FLAN-UL2) to extract detailed oncological history from two narrative sections of clinical progress notes. Our team annotated 9028 entities, 9986 modifiers, and 5312 relationships. The GPT-4 model exhibited overall best performance, with an average BLEU score of 0.73, an average ROUGE score of 0.72, an exact-match F1-score of 0.51, and an average accuracy of 68% on complex tasks (expert manual evaluation on subset). Notably, it was proficient in tumor characteristic and medication extraction, and demonstrated superior performance in relational inference like adverse event detection. However, further improvements are needed before using it to reliably extract important facts from cancer progress notes needed for clinical research, complex population management, and documenting quality patient care.

Background: Polypharmacy, i.e. taking five drugs or more, is both a public health and an economic issue. Medication reviews are structured interviews of the patient by the community pharmacist, aiming at optimizing the drug treatment and deprescribing useless, redundant or dangerous drugs. However, they remain difficult to perform and time-consuming. Several clinical decision support systems were developed for helping clinicians to manage polypharmacy. However, most were limited to the implementation of clinical practice guidelines. In this work, our objective is to design an innovative clinical decision support system for medication reviews and polypharmacy management, named ABiMed. Methods: ABiMed associates several approaches: guidelines implementation, but the automatic extraction of patient data from the GP's electronic health record and its transfer to the pharmacist, and the visual presentation of contextualized drug knowledge using visual analytics. We performed an ergonomic assessment and qualitative evaluations involving pharmacists and GPs during focus groups and workshops. Results: We describe the proposed architecture, which allows a collaborative multi-user usage. We present the various screens of ABiMed for entering or verifying patient data, for accessing drug knowledge (posology, adverse effects, interactions), for viewing STOPP/START rules and for suggesting modification to the treatment. Qualitative evaluations showed that health professionals were highly interested by our approach, associating the automatic guidelines execution with the visual presentation of drug knowledge. Conclusions: The association of guidelines implementation with visual presentation of knowledge is a promising approach for managing polypharmacy. Future works will focus on the improvement and the evaluation of ABiMed.

Clinical decision support systems are software tools that help clinicians to make medical decisions. However, their acceptance by clinicians is usually rather low. A known problem is that they often require clinicians to manually enter lots of patient data, which is long and tedious. Existing solutions, such as the automatic data extraction from electronic health record, are not fully satisfying, because of low data quality and availability. In practice, many systems still include long questionnaire for data entry. In this paper, we propose an original solution to simplify patient data entry, using an adaptive questionnaire, i.e. a questionnaire that evolves during user interaction, showing or hiding questions dynamically. Considering a rule-based decision support systems, we designed methods for translating the system's clinical rules into display rules that determine the items to show in the questionnaire, and methods for determining the optimal order of priority among the items in the questionnaire. We applied this approach to a decision support system implementing STOPP/START v2, a guideline for managing polypharmacy. We show that it permits reducing by about two thirds the number of clinical conditions displayed in the questionnaire. Presented to clinicians during focus group sessions, the adaptive questionnaire was found "pretty easy to use". In the future, this approach could be applied to other guidelines, and adapted for data entry by patients.

Chronic disease progression is emerging as an important area of investment for healthcare providers. As the quantity and richness of available clinical data continue to increase along with advances in machine learning, there is great potential to advance our approaches to caring for patients. An ideal approach to this problem should generate good performance on at least three axes namely, a) perform across many clinical conditions without requiring deep clinical expertise or extensive data scientist effort, b) generalization across populations, and c) be explainable (model interpretability). We present SAVEHR, a self-attention based architecture on heterogeneous structured EHR data that achieves $>$ 0.51 AUC-PR and $>$ 0.87 AUC-ROC gains on predicting the onset of four clinical conditions (CHF, Kidney Failure, Diabetes and COPD) 15-months in advance, and transfers with high performance onto a new population. We demonstrate that SAVEHR model performs superior to ten baselines on all three axes stated formerly.

Early detection of Alzheimer's disease (AD) and identification of potential risk/beneficial factors are important for planning and administering timely interventions or preventive measures. In this paper, we learn a disease model for AD that combines genotypic and phenotypic profiles, and cognitive health metrics of patients. We propose a probabilistic generative subspace that describes the correlative, complementary and domain-specific semantics of the dependencies in multi-view, multi-modality medical data. Guided by domain knowledge and using the latent consensus between abstractions of multi-view data, we model the fusion as a data generating process. We show that our approach can potentially lead to i) explainable clinical predictions and ii) improved AD diagnoses.

We describe a method for parameter estimation in bipartite probabilistic graphical models for joint prediction of clinical conditions from the electronic medical record. The method does not rely on the availability of gold-standard labels, but rather uses noisy labels, called anchors, for learning. We provide a likelihood-based objective and a moments-based initialization that are effective at learning the model parameters. The learned model is evaluated in a task of assigning a heldout clinical condition to patients based on retrospective analysis of the records, and outperforms baselines which do not account for the noisiness in the labels or do not model the conditions jointly.