arXiv subjects

Emily B. Collier

Publications and source records attributed to Emily B. Collier.

6 recordsLinked to original sources

arXiv2026

Lesion Detection in CT with Frozen Self-Distilled Features: SALT, a Spatially Adaptive Label-Guided Temperature

Self-supervised pretraining objectives are spatially uniform: the teacher temperature and the per-patch loss weight are identical everywhere in the image, so a lesion a few patches wide contributes no more to the training signal than the surrounding parenchyma. Prior work biases the views toward annotated regions, which changes what the model sees but adds no pressure on the objective. We instead condition the targets of self-distillation, a method we call SALT (Spatially Adaptive Label-guided Temperature). Weak, box-derived labels, available only during pretraining, define a compact region on the encoder's patch grid, inside which the teacher's softmax temperature is sharpened and the masked-patch loss is up-weighted. The objectives, the masking policy and the centering statistics are otherwise unchanged, and at every downstream use the encoder is a plain feature extractor with no labels and no conditioning. We evaluate by freezing the encoder and training only a lightweight multi-depth CenterNet-style head, detecting lesions in 3D on four CT cohorts, and we isolate the mechanism against a backbone identical in architecture, pretraining data, schedule and label-guided cropping but with no target conditioning. We report patch-level separability, 3D detection stratified by cohort and by lesion size, box quality, and a detector-free probe in which a single frozen patch embedding re-identifies a lesion in a follow-up scan without registration, masks or fine-tuning. Because the conditioning is expressed through a spatial indicator rather than through label semantics, the formulation admits any weak spatial annotation; we instantiate and validate it for lesions.

cs.CV↗

arXiv2026

DALE-CT: Depth-Aware 2D Slice Encoders Learn an Anatomical World Model of Chest CT

Chest CT is among the highest-volume imaging exams in medicine, yet expert voxel-level annotations are scarce and costly, motivating encoders that learn directly from unlabeled scans. We present DALE-CT, a family of 2D slice-based Vision Transformers trained from scratch on chest CT with the heuristics-free LeJEPA objective. We introduce depth-aware slab sampling, which draws self-supervised views from across a physical $z$-axis slab rather than a single slice, implicitly tasking the 2D encoder with representing how anatomy changes between neighboring slices. The frozen representations trace each scan as a smooth anatomical trajectory, recover cranio-caudal slice ordering without labels, and distinguish slices by the anatomy they contain rather than by position alone. This anatomical world model emerges without any 3D or positional supervision, and an otherwise-identical encoder trained on slices in isolation never develops it. Building on this backbone, we introduce dense auxiliary supervision into the pretraining objective, using anatomical and abnormality masks to supervise patch and slice tokens alongside the self-supervised loss, and we compare the resulting variants against a DINOv2 baseline continually pretrained on CT-RATE. Among nine public and in-house models evaluated under the same protocol, DALE-CT-2S is the strongest 2D model in-domain, reaching 0.825 Macro AUROC on CT-RATE, within 0.024 of COLIPRI-CRM and without any text supervision. We subsequently scale the supervision-free configuration to a $\sim$287k-scan multi-source pool, to our knowledge the largest reported chest-CT pretraining corpus. The resulting DALE-CT-0-L posts the best 2D external-transfer point estimates, and we release it as our recommended backbone with the full model family, training code, and evaluation pipeline.

cs.CV↗

arXiv2025

Toward an AI Reasoning-Enabled System for Patient-Clinical Trial Matching

Screening patients for clinical trial eligibility remains a manual, time-consuming, and resource-intensive process. We present a secure, scalable proof-of-concept system for Artificial Intelligence (AI)-augmented patient-trial matching that addresses key implementation challenges: integrating heterogeneous electronic health record (EHR) data, facilitating expert review, and maintaining rigorous security standards. Leveraging open-source, reasoning-enabled large language models (LLMs), the system moves beyond binary classification to generate structured eligibility assessments with interpretable reasoning chains that support human-in-the-loop review. This decision support tool represents eligibility as a dynamic state rather than a fixed determination, identifying matches when available and offering actionable recommendations that could render a patient eligible in the future. The system aims to reduce coordinator burden, intelligently broaden the set of trials considered for each patient and guarantee comprehensive auditability of all AI-generated outputs.

cs.AI↗

arXiv2025

Semantic Nutrition Estimation: Predicting Food Healthfulness from Text Descriptions

Accurate nutritional assessment is critical for public health, but existing profiling systems require detailed data often unavailable or inaccessible from colloquial text descriptions of food. This paper presents a machine learning pipeline that predicts the comprehensive Food Compass Score 2.0 (FCS) from text descriptions. Our approach uses multi-headed neural networks to process hybrid feature vectors that combine semantic text embeddings, lexical patterns, and domain heuristics, alongside USDA Food and Nutrient Database for Dietary Studies (FNDDS) data. The networks estimate the nutrient and food components necessary for the FCS algorithm. The system demonstratedstrong predictive power, achieving a median R^2 of 0.81 for individual nutrients. The predicted FCS correlated strongly with published values (Pearson's r = 0.77), with a mean absolute difference of 14.0 points. While errors were largest for ambiguous or processed foods, this methodology translates language into actionable nutritional information, enabling scalable dietary assessment for consumer applications and research.

cs.LG↗

arXiv2025

Vision Foundry: A System for Training Foundational Vision AI Models

Self-supervised learning (SSL) leverages vast unannotated medical datasets, yet steep technical barriers limit adoption by clinical researchers. We introduce Vision Foundry, a code-free, HIPAA-compliant platform that democratizes pre-training, adaptation, and deployment of foundational vision models. The system integrates the DINO-MX framework, abstracting distributed infrastructure complexities while implementing specialized strategies like Magnification-Aware Distillation (MAD) and Parameter-Efficient Fine-Tuning (PEFT). We validate the platform across domains, including neuropathology segmentation, lung cellularity estimation, and coronary calcium scoring. Our experiments demonstrate that models trained via Vision Foundry significantly outperform generic baselines in segmentation fidelity and regression accuracy, while exhibiting robust zero-shot generalization across imaging protocols. By bridging the gap between advanced representation learning and practical application, Vision Foundry enables domain experts to develop state-of-the-art clinical AI tools with minimal annotation overhead, shifting focus from engineering optimization to clinical discovery.

q-bio.QM↗

arXiv2025

Leveraging LLMs for Structured Data Extraction from Unstructured Patient Records

Manual chart review remains an extremely time-consuming and resource-intensive component of clinical research, requiring experts to extract often complex information from unstructured electronic health record (EHR) narratives. We present a secure, modular framework for automated structured feature extraction from clinical notes leveraging locally deployed large language models (LLMs) on institutionally approved, Health Insurance Portability and Accountability Act (HIPPA)-compliant compute infrastructure. This system integrates retrieval augmented generation (RAG) and structured response methods of LLMs into a widely deployable and scalable container to provide feature extraction for diverse clinical domains. In evaluation, the framework achieved high accuracy across multiple medical characteristics present in large bodies of patient notes when compared against an expert-annotated dataset and identified several annotation errors missed in manual review. This framework demonstrates the potential of LLM systems to reduce the burden of manual chart review through automated extraction and increase consistency in data capture, accelerating clinical research.

cs.AI↗