Steven Song

Fariborz Taherkhani, Aashish Rai, Quankai Gao et al.

3D face modeling has been an active area of research in computer vision and computer graphics, fueling applications ranging from facial expression transfer in virtual avatars to synthetic data generation. Existing 3D deep learning generative models (e.g., VAE, GANs) allow generating compact face representations (both shape and texture) that can model non-linearities in the shape and appearance space (e.g., scatter effects, specularities, etc.). However, they lack the capability to control the generation of subtle expressions. This paper proposes a new 3D face generative model that can decouple identity and expression and provides granular control over expressions. In particular, we propose using a pair of supervised auto-encoder and generative adversarial networks to produce high-quality 3D faces, both in terms of appearance and shape. Experimental results in the generation of 3D faces learned with holistic expression labels, or Action Unit labels, show how we can decouple identity and expression; gaining fine-control over expressions while preserving identity.

Qiang Zhang, Tong Xiao, Haroun Habeeb et al.

We present a novel system for real-time tracking of facial expressions using egocentric views captured from a set of infrared cameras embedded in a virtual reality (VR) headset. Our technology facilitates any user to accurately drive the facial expressions of virtual characters in a non-intrusive manner and without the need of a lengthy calibration step. At the core of our system is a distillation based approach to train a machine learning model on heterogeneous data and labels coming form multiple sources, \eg synthetic and real images. As part of our dataset, we collected 18k diverse subjects using a lightweight capture setup consisting of a mobile phone and a custom VR headset with extra cameras. To process this data, we developed a robust differentiable rendering pipeline enabling us to automatically extract facial expression labels. Our system opens up new avenues for communication and expression in virtual environments, with applications in video conferencing, gaming, entertainment, and remote collaboration.

Steven Song, Anirudh Subramanyam, Zhenyu Zhang et al.

The Genomic Data Commons (GDC) provides access to high quality, harmonized cancer genomics data through a unified curation and analysis platform centered around patient cohorts. While GDC users can interactively create complex cohorts through the graphical Cohort Builder, users (especially new ones) may struggle to find specific cohort descriptors across hundreds of possible fields and properties. However, users may be better able to describe their desired cohort in free-text natural language. We introduce GDC Cohort Copilot, an open-source copilot tool for curating cohorts from the GDC. GDC Cohort Copilot automatically generates the GDC cohort filter corresponding to a user-input natural language description of their desired cohort, before exporting the cohort back to the GDC for further analysis. An interactive user interface allows users to further refine the generated cohort. We develop and evaluate multiple large language models (LLMs) for GDC Cohort Copilot and demonstrate that our locally-served, open-source GDC Cohort LLM achieves better results than GPT-4o prompting in generating GDC cohorts. We implement and share GDC Cohort Copilot as a containerized Gradio app on HuggingFace Spaces, available at https://huggingface.co/spaces/uc-ctds/GDC-Cohort-Copilot. GDC Cohort LLM weights are available at https://huggingface.co/uc-ctds. All source code is available at https://github.com/uc-cdis/gdc-cohort-copilot.

Nathaniel Diamant, Erik Reinertsen, Steven Song et al.

Supervised machine learning applications in health care are often limited due to a scarcity of labeled training data. To mitigate this effect of small sample size, we introduce a pre-training approach, Patient Contrastive Learning of Representations (PCLR), which creates latent representations of ECGs from a large number of unlabeled examples. The resulting representations are expressive, performant, and practical across a wide spectrum of clinical tasks. We develop PCLR using a large health care system with over 3.2 million 12-lead ECGs, and demonstrate substantial improvements across multiple new tasks when there are fewer than 5,000 labels. We release our model to extract ECG representations at https://github.com/broadinstitute/ml4h/tree/master/model_zoo/PCLR.

Steven Song, Sahil Sethi, Brett Beaulieu-Jones et al.

In time-series domains where both predictive performance and interpretability are essential, deep neural networks achieve strong results but provide limited insight into how their predictions are made. Projection-based prototype networks address this limitation by grounding predictions in similarity to representative training examples, enabling case-based explanations and global prototype inspection. However, existing approaches rely on label supervision, tying prototypes to a specific task and requiring large labeled datasets. We introduce ProtoSSL, a novel framework for learning interpretable, projection-based prototypes from unlabeled time-series data and adapting them to downstream tasks. Our key idea is to separate motif discovery from label alignment. ProtoSSL first learns a reusable prototype bank using a self-supervised objective applied directly to prototype activations, and then aligns these prototypes to downstream tasks through an efficient assignment procedure. Across six electrocardiography (ECG) datasets, ProtoSSL improves label efficiency, outperforming supervised prototype baselines in low-data regimes with as few as 256 labeled examples; with fine-tuning, ProtoSSL outperforms supervised prototype baselines at full dataset scale. In a human evaluation study, ProtoSSL produces prototypes and prototype-based explanations that are judged more favorably than those learned with direct label supervision. We further show that the framework extends to audio classification. Thus, ProtoSSL enables both learning generalizable prototypes from unlabeled data before the downstream label space is known, and subsequent assignment of interpretable, projection-grounded prototypes to new time-series tasks.

Steven Song, Anirudh Subramanyam, Irene Madejski et al.

In the current paradigm of image captioning, deep learning models are trained to generate text from image embeddings of latent features. We challenge the assumption that fine-tuning of large, bespoke models is required to improve model generation accuracy. Here we propose Label Boosted Retrieval Augmented Generation (LaB-RAG), a small-model-based approach to image captioning that leverages image descriptors in the form of categorical labels to boost standard retrieval augmented generation (RAG) with pretrained large language models (LLMs). We study our method in the context of radiology report generation (RRG) over MIMIC-CXR and CheXpert Plus. We argue that simple classification models combined with zero-shot embeddings can effectively transform X-rays into text-space as radiology-specific labels. In combination with standard RAG, we show that these derived text labels can be used with general-domain LLMs to generate radiology reports. Without ever training our generative language model or image embedding models specifically for the task, and without ever directly "showing" the LLM an X-ray, we demonstrate that LaB-RAG achieves better results across natural language and radiology language metrics compared with other retrieval-based RRG methods, while attaining competitive results compared to other fine-tuned vision-language RRG models. We further conduct extensive ablation experiments to better understand the components of LaB-RAG. Our results suggest broader compatibility and synergy with fine-tuned methods to further enhance RRG performance.

Steven Song, Morgan Borjigin-Wang, Irene Madejski et al.

The Cancer Genome Atlas (TCGA) has enabled novel discoveries and served as a large-scale reference dataset in cancer through its harmonized genomics, clinical, and imaging data. Numerous prior studies have developed bespoke deep learning models over TCGA for tasks such as cancer survival prediction. A modern paradigm in biomedical deep learning is the development of foundation models (FMs) to derive feature embeddings agnostic to a specific modeling task. Biomedical text especially has seen growing development of FMs. While TCGA contains free-text data as pathology reports, these have been historically underutilized. Here, we investigate the ability to train classical machine learning models over multimodal, zero-shot FM embeddings of cancer data. We demonstrate the ease and additive effect of multimodal fusion, outperforming unimodal models. Further, we show the benefit of including pathology report text and rigorously evaluate the effect of model-based text summarization and hallucination. Overall, we propose an embedding-centric approach to multimodal cancer modeling.