Gastroenterology
PolypSense3D: AMulti-Source Benchmark Dataset for Depth-Aware Polyp Size Measurement in Endoscopy
Accurate polyp sizing during endoscopy is crucial for cancer risk assessment but is hindered by subjective methods and inadequate datasets lacking integrated 2D appearance, 3D structure, and real-world size information. We introduce PolypSense3D, the first multi-source benchmark dataset specifically targeting depth-aware polyp size measurement. It uniquely integrates over 43,000 frames from virtual simulations, physical phantoms, and clinical sequences, providing synchronized RGB, dense/sparse depth, segmentation masks, camera parameters, and millimeter-scale size labels derived via a novel forceps-assisted in-vivo annotation technique. To establish its value, we benchmark state-of-the-art segmentation and depth estimation models. Results quantify significant domain gaps between simulated/phantom and clinical data and reveal substantial error propagation from perception stages to final size estimation, with the best fully automated pipelines achieving an average Mean Absolute Error (MAE) of 0.95 mm on the clinical data subset. Publicly released under CCBY-SA 4.0 with code and evaluation protocols, PolypSense3D offers a standardized platform to accelerate research in robust, clinically relevant quantitative endoscopic vision.
G2M: AGeneralized Gaussian Mirror Method to boost feature selection power
Recent advances in false discovery rate (FDR)-controlled feature selection methods have improved reliability by effectively limiting false positives, making them wellsuited for complex applications. A popular FDR-controlled framework called data splitting uses the "mirror statistics" to select features. However, we find that the unit variance assumption on mirror statistics could potentially limit the feature selection power. To address this, we generalize the mirror statistics in the Gaussian mirror framework and introduce a new approach called "generalized Gaussian mirror" (G2M), which adaptively learns the variance and forms new test statistics. We demonstrate both theoretically and empirically that the proposed test statistics achieve higher power than those of Gaussian mirror and data splitting. Comparisons with other FDR-controlled frameworks on synthetic, semi-synthetic, and real datasets highlight the superior performance of the G2M method in achieving higher power while maintaining FDR control. These findings suggest the potential for the G2M method for practical applications in real-world problems. Code is available at: https://github.com/skyve2012/G2M.
ClinicalLab: Aligning Agents for Multi-Departmental Clinical Diagnostics in the Real World
Large language models (LLMs) have achieved significant performance progress in various natural language processing applications. However, LLMs still struggle to meet the strict requirements for accuracy and reliability in the medical field and face many challenges in clinical applications. Existing clinical diagnostic evaluation benchmarks for evaluating medical agents powered by LLMs have severe limitations. Firstly, most existing medical evaluation benchmarks face the risk of data leakage or contamination.
Can We Infer Confidential Properties of Training Data from LLMs?
Large language models (LLMs) are increasingly fine-tuned on domain-specific datasets to support applications in fields such as healthcare, finance, and law. These fine-tuning datasets often have sensitive and confidential dataset-level properties -- such as patient demographics or disease prevalence--that are not intended to be revealed. While prior work has studied property inference attacks on discriminative models (e.g., image classification models) and generative models (e.g., GANs for image data), it remains unclear if such attacks transfer to LLMs. In this work, we introduce PropInfer, a benchmark task for evaluating property inference in LLMs under two fine-tuning paradigms: question-answering and chat-completion. Built on the ChatDoctor dataset, our benchmark includes a range of property types and task configurations. We further propose two tailored attacks: a prompt-based generation attack and a shadow-model attack leveraging word frequency signals.
PanTS: The Pancreatic Tumor Segmentation Dataset
PanTS is a large-scale, multi-institutional dataset curated to advance research in pancreatic CT analysis. It contains 36,390 CT scans from 145 medical centers, with expert-validated, voxel-wise annotations of over 993,000 anatomical structures, covering pancreatic tumors, pancreas head, body, and tail, and 24 surrounding anatomical structures such as vascular/skeletal structures and abdominal/thoracic organs. Each scan includes metadata such as patient age, sex, diagnosis, contrast phase, in-plane spacing, slice thickness, etc. AI models trained on PanTS achieve significantly better performance in pancreatic tumor detection, localization, and segmentation than those trained on existing public datasets. Our analysis indicates that these gains are directly attributable to the 16 larger-scale tumor annotations and indirectly supported by the 24 additional surrounding anatomical structures. As the largest and most comprehensive resource of its kind, PanTS offers a new benchmark for developing and evaluating AI models in pancreatic CT analysis.
NFL-BA: Near-Field Light Bundle Adjustment for SLAM in Dynamic Lighting
Simultaneous Localization and Mapping (SLAM) systems typically assume static, distant illumination; however, many real-world scenarios, such as endoscopy, subterranean robotics, and search & rescue in collapsed environments, require agents to operate with a co-located light and camera in the absence of external lighting. In such cases, dynamic near-field lighting introduces strong, view-dependent shading that significantly degrades SLAM performance. We introduce Near-Field Lighting Bundle Adjustment Loss (NFL-BA) which explicitly models near-field lighting as a part of Bundle Adjustment loss and enables better performance for scenes captured with dynamic lighting. NFL-BA can be integrated into neural rendering-based SLAM systems with implicit or explicit scene representations. Our evaluations mainly focus on endoscopy procedure where SLAM can enable autonomous navigation, guidance to unsurveyed regions, blindspot detections, and 3D visualizations, which can significantly improve patient outcomes and endoscopy experience for both physicians and patients. Replacing Photometric Bundle Adjustment loss of SLAM systems with NFL-BA leads to significant improvement in camera tracking, 37% for MonoGS and 14% for EndoGSLAM, and leads to state-of-the-art camera tracking and mapping performance on the C3VD colonoscopy dataset. Further evaluation on indoor scenes captured with phone camera with flashlight turned on, also demonstrate significant improvement in SLAM performance due to NFL-BA.
Donor-Aware scRNA-seq Benchmarks for IBD Classification
Donor-level disease classification from single-cell RNA sequencing (scRNA-seq) requires strict donor-aware cross-validation: naive pipelines that split cells randomly conflate training and test donors, inflating reported performance through pseudoreplication. We present a donor-aware benchmark evaluating three feature representations across two independent IBD cohorts: centered log-ratio (CLR) transformed cell-type composition, GatedStructuralCFN dependency embeddings, and scVI variational autoencoder latent embeddings. The cohorts are the SCP259 ulcerative colitis atlas (UC vs. Healthy, n=30 donors, 51 cell types) and the Kong 2023 Crohn's disease atlas (CD vs. Healthy, n=71 donors, 55-68 cell types across three intestinal regions). Compartment-stratified CLR composition achieves AUROC 0.956 +/- 0.061 on SCP259; GatedStructuralCFN on the same features achieves 0.978 +/- 0.050. In the Kong cohort, CFN achieves its best performance in the colon region (0.960 +/- 0.055 after feature filtering), exceeding linear CLR (0.900 +/- 0.100), while terminal ileum classification is dominated by linear models (CatBoost CLR 0.967 +/- 0.075 vs. CFN 0.811 +/- 0.164). Cross-dataset transfer (CD->UC, four shared cell types) achieves AUC 0.833 with XGBoost CLR; the reverse direction performs at chance. CFN edge stability analysis shows that compartment-wise composition eliminates spurious unit-sum-induced instability present in global composition (Jaccard 0.026 vs. top-20 recurrence 1.0). CFN shows a consistent numerical advantage over linear models in the colon region of CD (AUROC 0.960 vs. 0.900), though no inter-method comparison reached statistical significance at n<=34 donors per region. Compartment-aware feature construction is critical for both classification performance and structural interpretability. Code: https://github.com/Jonathan-321/sfn-scrna-study