SD-MAD: Sign-Driven Few-shot Multi-Anomaly Detection in Medical Images

Medical anomaly detection (AD) is crucial for early clinical intervention, yet it faces challenges due to limited access to high-quality medical imaging data, caused by privacy concerns and data silos. Few-shot learning has emerged as a promising approach to alleviate these limitations by leveraging the large-scale prior knowledge embedded in vision-language models (VLMs). Recent advancements in few-shot medical AD have treated normal and abnormal cases as a one-class classification problem, often overlooking the distinction among multiple anomaly categories. Thus, in this paper, we propose a framework tailored for few-shot medical anomaly detection in the scenario where the identification of multiple anomaly categories is required. To capture the detailed radiological signs of medical anomaly categories, our framework incorporates diverse textual descriptions for each category generated by a Large-Language model, under the assumption that different anomalies in medical images may share common radiological signs in each category. Specifically, we introduce SD-MAD, a two-stage Sign-Driven few-shot Multi-Anomaly Detection framework: (i) Radiological signs are aligned with anomaly categories by amplifying inter-anomaly discrepancy; (ii) Aligned signs are selected further to mitigate the effect of the under-fitting and uncertain-sample issue caused by limited medical data, employing an automatic sign selection strategy at inference. Moreover, we propose three protocols to comprehensively quantify the performance of multi-anomaly detection. Extensive experiments illustrate the effectiveness of our method.

ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present \textbf{ChromFound}, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures

Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed to the limited availability, diversity, and heterogeneity of dynamic protein datasets. To address this gap, we propose to enhance existing prestigious static 3D protein structural databases, such as the Protein Data Bank (PDB), by integrating dynamic data and additional physical properties. Specifically, we introduce a large-scale dataset, Dynamic PDB, encompassing approximately 12.6K proteins, each subjected to all-atom molecular dynamics (MD) simulations lasting 1 microsecond to capture conformational changes. Furthermore, we provide a comprehensive suite of physical properties, including atomic velocities and forces, potential and kinetic energies of proteins, and the temperature of the simulation environment, recorded at 1 picosecond intervals throughout the simulations. For benchmarking purposes, we evaluate state-of-the-art methods on the proposed dataset for the task of trajectory prediction. To demonstrate the value of integrating richer physical properties in the study of protein dynamics and related model design, we base our approach on the SE(3) diffusion model and incorporate these physical properties into the trajectory prediction process. Preliminary results indicate that this straightforward extension of the SE(3) model yields improved accuracy, as measured by MAE and RMSD, when the proposed physical properties are taken into consideration.