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Jan 9

Large-Scale 3D Medical Image Pre-training with Geometric Context Priors

The scarcity of annotations poses a significant challenge in medical image analysis. Large-scale pre-training has emerged as a promising label-efficient solution, owing to the utilization of large-scale data, large models, and advanced pre-training techniques. However, its development in medical images remains underexplored. The primary challenge lies in harnessing large-scale unlabeled data and learning high-level semantics without annotations. We observe that 3D medical images exhibit consistent geometric context, i.e., consistent geometric relations between different organs, which leads to a promising way for learning consistent representations. Motivated by this, we introduce a simple-yet-effective Volume Contrast (VoCo) framework to leverage geometric context priors for self-supervision. Given an input volume, we extract base crops from different regions to construct positive and negative pairs for contrastive learning. Then we predict the contextual position of a random crop by contrasting its similarity to the base crops. In this way, VoCo encodes the inherent geometric context into model representations, facilitating high-level semantic learning without annotations. Specifically, we (1) introduce the largest medical pre-training dataset PreCT-160K; (2) investigate scaling laws and propose guidelines for tailoring different model sizes to various medical tasks; (3) build a benchmark encompassing 48 medical tasks. Extensive experiments highlight the superiority of VoCo. Codes at https://github.com/Luffy03/Large-Scale-Medical.

  • 3 authors
·
Oct 13, 2024

PatchDPO: Patch-level DPO for Finetuning-free Personalized Image Generation

Finetuning-free personalized image generation can synthesize customized images without test-time finetuning, attracting wide research interest owing to its high efficiency. Current finetuning-free methods simply adopt a single training stage with a simple image reconstruction task, and they typically generate low-quality images inconsistent with the reference images during test-time. To mitigate this problem, inspired by the recent DPO (i.e., direct preference optimization) technique, this work proposes an additional training stage to improve the pre-trained personalized generation models. However, traditional DPO only determines the overall superiority or inferiority of two samples, which is not suitable for personalized image generation because the generated images are commonly inconsistent with the reference images only in some local image patches. To tackle this problem, this work proposes PatchDPO that estimates the quality of image patches within each generated image and accordingly trains the model. To this end, PatchDPO first leverages the pre-trained vision model with a proposed self-supervised training method to estimate the patch quality. Next, PatchDPO adopts a weighted training approach to train the model with the estimated patch quality, which rewards the image patches with high quality while penalizing the image patches with low quality. Experiment results demonstrate that PatchDPO significantly improves the performance of multiple pre-trained personalized generation models, and achieves state-of-the-art performance on both single-object and multi-object personalized image generation. Our code is available at https://github.com/hqhQAQ/PatchDPO.

  • 7 authors
·
Dec 4, 2024

Gaussian2Scene: 3D Scene Representation Learning via Self-supervised Learning with 3D Gaussian Splatting

Self-supervised learning (SSL) for point cloud pre-training has become a cornerstone for many 3D vision tasks, enabling effective learning from large-scale unannotated data. At the scene level, existing SSL methods often incorporate volume rendering into the pre-training framework, using RGB-D images as reconstruction signals to facilitate cross-modal learning. This strategy promotes alignment between 2D and 3D modalities and enables the model to benefit from rich visual cues in the RGB-D inputs. However, these approaches are limited by their reliance on implicit scene representations and high memory demands. Furthermore, since their reconstruction objectives are applied only in 2D space, they often fail to capture underlying 3D geometric structures. To address these challenges, we propose Gaussian2Scene, a novel scene-level SSL framework that leverages the efficiency and explicit nature of 3D Gaussian Splatting (3DGS) for pre-training. The use of 3DGS not only alleviates the computational burden associated with volume rendering but also supports direct 3D scene reconstruction, thereby enhancing the geometric understanding of the backbone network. Our approach follows a progressive two-stage training strategy. In the first stage, a dual-branch masked autoencoder learns both 2D and 3D scene representations. In the second stage, we initialize training with reconstructed point clouds and further supervise learning using the geometric locations of Gaussian primitives and rendered RGB images. This process reinforces both geometric and cross-modal learning. We demonstrate the effectiveness of Gaussian2Scene across several downstream 3D object detection tasks, showing consistent improvements over existing pre-training methods.

  • 4 authors
·
Jun 10, 2025

WeakSTIL: Weak whole-slide image level stromal tumor infiltrating lymphocyte scores are all you need

We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of 0.45pm0.15 when compared to scores generated by an expert pathologist, and an AUC of 0.89pm0.05 when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.

  • 6 authors
·
Sep 13, 2021

Cross-Level Multi-Instance Distillation for Self-Supervised Fine-Grained Visual Categorization

High-quality annotation of fine-grained visual categories demands great expert knowledge, which is taxing and time consuming. Alternatively, learning fine-grained visual representation from enormous unlabeled images (e.g., species, brands) by self-supervised learning becomes a feasible solution. However, recent researches find that existing self-supervised learning methods are less qualified to represent fine-grained categories. The bottleneck lies in that the pre-text representation is built from every patch-wise embedding, while fine-grained categories are only determined by several key patches of an image. In this paper, we propose a Cross-level Multi-instance Distillation (CMD) framework to tackle the challenge. Our key idea is to consider the importance of each image patch in determining the fine-grained pre-text representation by multiple instance learning. To comprehensively learn the relation between informative patches and fine-grained semantics, the multi-instance knowledge distillation is implemented on both the region/image crop pairs from the teacher and student net, and the region-image crops inside the teacher / student net, which we term as intra-level multi-instance distillation and inter-level multi-instance distillation. Extensive experiments on CUB-200-2011, Stanford Cars and FGVC Aircraft show that the proposed method outperforms the contemporary method by upto 10.14% and existing state-of-the-art self-supervised learning approaches by upto 19.78% on both top-1 accuracy and Rank-1 retrieval metric.

  • 5 authors
·
Jan 16, 2024

Unsupervised Anomaly Detection in Medical Images with a Memory-augmented Multi-level Cross-attentional Masked Autoencoder

Unsupervised anomaly detection (UAD) aims to find anomalous images by optimising a detector using a training set that contains only normal images. UAD approaches can be based on reconstruction methods, self-supervised approaches, and Imagenet pre-trained models. Reconstruction methods, which detect anomalies from image reconstruction errors, are advantageous because they do not rely on the design of problem-specific pretext tasks needed by self-supervised approaches, and on the unreliable translation of models pre-trained from non-medical datasets. However, reconstruction methods may fail because they can have low reconstruction errors even for anomalous images. In this paper, we introduce a new reconstruction-based UAD approach that addresses this low-reconstruction error issue for anomalous images. Our UAD approach, the memory-augmented multi-level cross-attentional masked autoencoder (MemMC-MAE), is a transformer-based approach, consisting of a novel memory-augmented self-attention operator for the encoder and a new multi-level cross-attention operator for the decoder. MemMCMAE masks large parts of the input image during its reconstruction, reducing the risk that it will produce low reconstruction errors because anomalies are likely to be masked and cannot be reconstructed. However, when the anomaly is not masked, then the normal patterns stored in the encoder's memory combined with the decoder's multi-level cross attention will constrain the accurate reconstruction of the anomaly. We show that our method achieves SOTA anomaly detection and localisation on colonoscopy, pneumonia, and covid-19 chest x-ray datasets.

  • 10 authors
·
Mar 22, 2022