Yuqi Wu

Yuqi Wu, Wenzhao Zheng, Sicheng Zuo et al.

3D occupancy prediction provides a comprehensive description of the surrounding scenes and has become an essential task for 3D perception. Most existing methods focus on offline perception from one or a few views and cannot be applied to embodied agents that demand to gradually perceive the scene through progressive embodied exploration. In this paper, we formulate an embodied 3D occupancy prediction task to target this practical scenario and propose a Gaussian-based EmbodiedOcc framework to accomplish it. We initialize the global scene with uniform 3D semantic Gaussians and progressively update local regions observed by the embodied agent. For each update, we extract semantic and structural features from the observed image and efficiently incorporate them via deformable cross-attention to refine the regional Gaussians. Finally, we employ Gaussian-to-voxel splatting to obtain the global 3D occupancy from the updated 3D Gaussians. Our EmbodiedOcc assumes an unknown (i.e., uniformly distributed) environment and maintains an explicit global memory of it with 3D Gaussians. It gradually gains knowledge through the local refinement of regional Gaussians, which is consistent with how humans understand new scenes through embodied exploration. We reorganize an EmbodiedOcc-ScanNet benchmark based on local annotations to facilitate the evaluation of the embodied 3D occupancy prediction task. Our EmbodiedOcc outperforms existing methods by a large margin and accomplishes the embodied occupancy prediction with high accuracy and efficiency. Code: https://github.com/YkiWu/EmbodiedOcc.

Ricardo Loor-Torres, Yuqi Wu, Esteban Cabezas et al.

Background We aim to use Natural Language Processing (NLP) to automate the extraction and classification of thyroid cancer risk factors from pathology reports. Methods We analyzed 1,410 surgical pathology reports from adult papillary thyroid cancer patients at Mayo Clinic, Rochester, MN, from 2010 to 2019. Structured and non-structured reports were used to create a consensus-based ground truth dictionary and categorized them into modified recurrence risk levels. Non-structured reports were narrative, while structured reports followed standardized formats. We then developed ThyroPath, a rule-based NLP pipeline, to extract and classify thyroid cancer features into risk categories. Training involved 225 reports (150 structured, 75 unstructured), with testing on 170 reports (120 structured, 50 unstructured) for evaluation. The pipeline's performance was assessed using both strict and lenient criteria for accuracy, precision, recall, and F1-score. Results In extraction tasks, ThyroPath achieved overall strict F-1 scores of 93% for structured reports and 90 for unstructured reports, covering 18 thyroid cancer pathology features. In classification tasks, ThyroPath-extracted information demonstrated an overall accuracy of 93% in categorizing reports based on their corresponding guideline-based risk of recurrence: 76.9% for high-risk, 86.8% for intermediate risk, and 100% for both low and very low-risk cases. However, ThyroPath achieved 100% accuracy across all thyroid cancer risk categories with human-extracted pathology information. Conclusions ThyroPath shows promise in automating the extraction and risk recurrence classification of thyroid pathology reports at large scale. It offers a solution to laborious manual reviews and advancing virtual registries. However, it requires further validation before implementation.

Alice Rueda, Argyrios Perivolaris, Niloy Roy et al. · utoronto

Engagement between client and therapist is a critical determinant of therapeutic success. We propose a multi-dimensional natural language processing (NLP) framework that objectively classifies engagement quality in counseling sessions based on textual transcripts. Using 253 motivational interviewing transcripts (150 high-quality, 103 low-quality), we extracted 42 features across four domains: conversational dynamics, semantic similarity as topic alignment, sentiment classification, and question detection. Classifiers, including Random Forest (RF), Cat-Boost, and Support Vector Machines (SVM), were hyperparameter tuned and trained using a stratified 5-fold cross-validation and evaluated on a holdout test set. On balanced (non-augmented) data, RF achieved the highest classification accuracy (76.7%), and SVM achieved the highest AUC (85.4%). After SMOTE-Tomek augmentation, performance improved significantly: RF achieved up to 88.9% accuracy, 90.0% F1-score, and 94.6% AUC, while SVM reached 81.1% accuracy, 83.1% F1-score, and 93.6% AUC. The augmented data results reflect the potential of the framework in future larger-scale applications. Feature contribution revealed conversational dynamics and semantic similarity between clients and therapists were among the top contributors, led by words uttered by the client (mean and standard deviation). The framework was robust across the original and augmented datasets and demonstrated consistent improvements in F1 scores and recall. While currently text-based, the framework supports future multimodal extensions (e.g., vocal tone, facial affect) for more holistic assessments. This work introduces a scalable, data-driven method for evaluating engagement quality of the therapy session, offering clinicians real-time feedback to enhance the quality of both virtual and in-person therapeutic interactions.

Karisa Parkington, Bazen G. Teferra, Marianne Rouleau-Tang et al. · utoronto

Thematic analysis provides valuable insights into participants' experiences through coding and theme development, but its resource-intensive nature limits its use in large healthcare studies. Large language models (LLMs) can analyze text at scale and identify key content automatically, potentially addressing these challenges. However, their application in mental health interviews needs comparison with traditional human analysis. This study evaluates out-of-the-box and knowledge-base LLM-based thematic analysis against traditional methods using transcripts from a stress-reduction trial with healthcare workers. OpenAI's GPT-4o model was used along with the Role, Instructions, Steps, End-Goal, Narrowing (RISEN) prompt engineering framework and compared to human analysis in Dedoose. Each approach developed codes, noted saturation points, applied codes to excerpts for a subset of participants (n = 20), and synthesized data into themes. Outputs and performance metrics were compared directly. LLMs using the RISEN framework developed deductive parent codes similar to human codes, but humans excelled in inductive child code development and theme synthesis. Knowledge-based LLMs reached coding saturation with fewer transcripts (10-15) than the out-of-the-box model (15-20) and humans (90-99). The out-of-the-box LLM identified a comparable number of excerpts to human researchers, showing strong inter-rater reliability (K = 0.84), though the knowledge-based LLM produced fewer excerpts. Human excerpts were longer and involved multiple codes per excerpt, while LLMs typically applied one code. Overall, LLM-based thematic analysis proved more cost-effective but lacked the depth of human analysis. LLMs can transform qualitative analysis in mental healthcare and clinical research when combined with human oversight to balance participant perspectives and research resources.