Anqi Li
Publications
OrganLens: Organ-Specific Representation Learning for CT Foundation Models
A CT examination captures multiple organs, but many biomedical questions concern abnormalities, prognosis, or longitudinal change in a specific organ. These questions require a separate representation for each organ within the same CT volume. Existing CT foundation models commonly produce a single volume-level representation, while recent anatomy-aware methods either encode pre-separated organ volumes or explicitly disentangle images into organ token groups. The former may remove clinically relevant surrounding context, while the latter does not condition a shared encoder on a selected organ before its features are formed. We introduce OrganLens for organ-specific representation learning through self-supervision. An organ identity conditions a shared CT encoder, while organ-specific distillation and anatomy-mask supervision shape features for anatomy-weighted pooling into organ-specific representations. At inference, the shared model produces 11 organ-specific representations without external segmentation masks. We evaluate OrganLens on CT-RATE, RAD-ChestCT, INSPECT, and NLST across diverse acquisitions and downstream evaluations. Relative to CT-pretrained DINOv2, heart representations raise CT-RATE cardiomegaly AUROC from 0.910 to 0.953, while lung representations improve the Harrell C-index for NLST lung-cancer mortality by 14.2\%. The global representation reaches INSPECT Recall@10 of 33.09\% and 32.04\% for text-to-image and image-to-text retrieval, respectively. Across organ-related tasks, anatomically matched representations provide stronger task-relevant signal, while the global representation retains broad utility. OrganLens offers a scalable approach to organ-specific CT representation learning with a shared encoder. More broadly, it provides the medical research community with a reusable framework for studying organ-specific disease across cohorts and clinical endpoints.
DRScaffold: Boosting Dense-Scene Reasoning in Lightweight Vision Language Models
Lightweight vision-language models perform competitively on standard benchmarks yet fail systematically in dense-scene reasoning, where multiple objects, attributes, and relations must be jointly grounded and resolved through multi-step inference. Such capability is critical for real-world applications where models must reliably interpret cluttered environments. Yet existing training signals provide no explicit grounding between reasoning steps and the underlying visual entities and relations, leaving lightweight models free to generate fluent but visually unanchored reasoning chains. To address this gap, we first introduce DRBench, a benchmark of 14,573 questions across 2,943 images, organized into five task categories spanning three progressive reasoning layers. Building on DRBench, we propose DRScaffold, a supervised fine-tuning framework that decomposes the supervision target into four causally ordered stages, enforcing grounded reasoning without architectural modification. Experiments on three lightweight VLMs demonstrate substantial gains on DRBench while preserving or improving performance on general-purpose benchmarks. Notably, Qwen2.5-VL-3B trained with DRScaffold surpasses the frozen Qwen2.5-VL-32B on DRBench, demonstrating that structured supervision can substitute for a significant portion of model scale in dense-scene reasoning. Our code and models are available at https://github.com/irene-shi/DRScaffold .