arXiv subjects

Florentin Bieder

Publications and source records attributed to Florentin Bieder.

27 records · Page 2Linked to original sources

arXiv2024

Binary Noise for Binary Tasks: Masked Bernoulli Diffusion for Unsupervised Anomaly Detection

The high performance of denoising diffusion models for image generation has paved the way for their application in unsupervised medical anomaly detection. As diffusion-based methods require a lot of GPU memory and have long sampling times, we present a novel and fast unsupervised anomaly detection approach based on latent Bernoulli diffusion models. We first apply an autoencoder to compress the input images into a binary latent representation. Next, a diffusion model that follows a Bernoulli noise schedule is employed to this latent space and trained to restore binary latent representations from perturbed ones. The binary nature of this diffusion model allows us to identify entries in the latent space that have a high probability of flipping their binary code during the denoising process, which indicates out-of-distribution data. We propose a masking algorithm based on these probabilities, which improves the anomaly detection scores. We achieve state-of-the-art performance compared to other diffusion-based unsupervised anomaly detection algorithms while significantly reducing sampling time and memory consumption. The code is available at https://github.com/JuliaWolleb/Anomaly_berdiff.

cs.CV↗

arXiv2023

Point Cloud Diffusion Models for Automatic Implant Generation

Advances in 3D printing of biocompatible materials make patient-specific implants increasingly popular. The design of these implants is, however, still a tedious and largely manual process. Existing approaches to automate implant generation are mainly based on 3D U-Net architectures on downsampled or patch-wise data, which can result in a loss of detail or contextual information. Following the recent success of Diffusion Probabilistic Models, we propose a novel approach for implant generation based on a combination of 3D point cloud diffusion models and voxelization networks. Due to the stochastic sampling process in our diffusion model, we can propose an ensemble of different implants per defect, from which the physicians can choose the most suitable one. We evaluate our method on the SkullBreak and SkullFix datasets, generating high-quality implants and achieving competitive evaluation scores.

eess.IV↗

arXiv2023

Diffusion Models for Contrast Harmonization of Magnetic Resonance Images

Magnetic resonance (MR) images from multiple sources often show differences in image contrast related to acquisition settings or the used scanner type. For long-term studies, longitudinal comparability is essential but can be impaired by these contrast differences, leading to biased results when using automated evaluation tools. This study presents a diffusion model-based approach for contrast harmonization. We use a data set consisting of scans of 18 Multiple Sclerosis patients and 22 healthy controls. Each subject was scanned in two MR scanners of different magnetic field strengths (1.5 T and 3 T), resulting in a paired data set that shows scanner-inherent differences. We map images from the source contrast to the target contrast for both directions, from 3 T to 1.5 T and from 1.5 T to 3 T. As we only want to change the contrast, not the anatomical information, our method uses the original image to guide the image-to-image translation process by adding structural information. The aim is that the mapped scans display increased comparability with scans of the target contrast for downstream tasks. We evaluate this method for the task of segmentation of cerebrospinal fluid, grey matter and white matter. Our method achieves good and consistent results for both directions of the mapping.

eess.IV↗

arXiv2023

Position Regression for Unsupervised Anomaly Detection

In recent years, anomaly detection has become an essential field in medical image analysis. Most current anomaly detection methods for medical images are based on image reconstruction. In this work, we propose a novel anomaly detection approach based on coordinate regression. Our method estimates the position of patches within a volume, and is trained only on data of healthy subjects. During inference, we can detect and localize anomalies by considering the error of the position estimate of a given patch. We apply our method to 3D CT volumes and evaluate it on patients with intracranial haemorrhages and cranial fractures. The results show that our method performs well in detecting these anomalies. Furthermore, we show that our method requires less memory than comparable approaches that involve image reconstruction. This is highly relevant for processing large 3D volumes, for instance, CT or MRI scans.

cs.CV↗

arXiv2022

Diffusion Models for Medical Anomaly Detection

In medical applications, weakly supervised anomaly detection methods are of great interest, as only image-level annotations are required for training. Current anomaly detection methods mainly rely on generative adversarial networks or autoencoder models. Those models are often complicated to train or have difficulties to preserve fine details in the image. We present a novel weakly supervised anomaly detection method based on denoising diffusion implicit models. We combine the deterministic iterative noising and denoising scheme with classifier guidance for image-to-image translation between diseased and healthy subjects. Our method generates very detailed anomaly maps without the need for a complex training procedure. We evaluate our method on the BRATS2020 dataset for brain tumor detection and the CheXpert dataset for detecting pleural effusions.

eess.IV↗

arXiv2022

Learn to Ignore: Domain Adaptation for Multi-Site MRI Analysis

The limited availability of large image datasets, mainly due to data privacy and differences in acquisition protocols or hardware, is a significant issue in the development of accurate and generalizable machine learning methods in medicine. This is especially the case for Magnetic Resonance (MR) images, where different MR scanners introduce a bias that limits the performance of a machine learning model. We present a novel method that learns to ignore the scanner-related features present in MR images, by introducing specific additional constraints on the latent space. We focus on a real-world classification scenario, where only a small dataset provides images of all classes. Our method \textit{Learn to Ignore (L2I)} outperforms state-of-the-art domain adaptation methods on a multi-site MR dataset for a classification task between multiple sclerosis patients and healthy controls.

cs.CV↗

arXiv2022

The Swiss Army Knife for Image-to-Image Translation: Multi-Task Diffusion Models

Recently, diffusion models were applied to a wide range of image analysis tasks. We build on a method for image-to-image translation using denoising diffusion implicit models and include a regression problem and a segmentation problem for guiding the image generation to the desired output. The main advantage of our approach is that the guidance during the denoising process is done by an external gradient. Consequently, the diffusion model does not need to be retrained for the different tasks on the same dataset. We apply our method to simulate the aging process on facial photos using a regression task, as well as on a brain magnetic resonance (MR) imaging dataset for the simulation of brain tumor growth. Furthermore, we use a segmentation model to inpaint tumors at the desired location in healthy slices of brain MR images. We achieve convincing results for all problems.

cs.CV↗

arXiv2021

Diffusion Models for Implicit Image Segmentation Ensembles

Diffusion models have shown impressive performance for generative modelling of images. In this paper, we present a novel semantic segmentation method based on diffusion models. By modifying the training and sampling scheme, we show that diffusion models can perform lesion segmentation of medical images. To generate an image specific segmentation, we train the model on the ground truth segmentation, and use the image as a prior during training and in every step during the sampling process. With the given stochastic sampling process, we can generate a distribution of segmentation masks. This property allows us to compute pixel-wise uncertainty maps of the segmentation, and allows an implicit ensemble of segmentations that increases the segmentation performance. We evaluate our method on the BRATS2020 dataset for brain tumor segmentation. Compared to state-of-the-art segmentation models, our approach yields good segmentation results and, additionally, detailed uncertainty maps.

cs.CV↗

arXiv2021

Comparison of Methods Generalizing Max- and Average-Pooling

Max- and average-pooling are the most popular pooling methods for downsampling in convolutional neural networks. In this paper, we compare different pooling methods that generalize both max- and average-pooling. Furthermore, we propose another method based on a smooth approximation of the maximum function and put it into context with related methods. For the comparison, we use a VGG16 image classification network and train it on a large dataset of natural high-resolution images (Google Open Images v5). The results show that none of the more sophisticated methods perform significantly better in this classification task than standard max- or average-pooling.

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