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.