arXiv subjects

Andreas Maier

Publications and source records attributed to Andreas Maier.

At least 253 records · Page 14Linked to original sources

arXiv2023

Multi-Scanner Canine Cutaneous Squamous Cell Carcinoma Histopathology Dataset

In histopathology, scanner-induced domain shifts are known to impede the performance of trained neural networks when tested on unseen data. Multi-domain pre-training or dedicated domain-generalization techniques can help to develop domain-agnostic algorithms. For this, multi-scanner datasets with a high variety of slide scanning systems are highly desirable. We present a publicly available multi-scanner dataset of canine cutaneous squamous cell carcinoma histopathology images, composed of 44 samples digitized with five slide scanners. This dataset provides local correspondences between images and thereby isolates the scanner-induced domain shift from other inherent, e.g. morphology-induced domain shifts. To highlight scanner differences, we present a detailed evaluation of color distributions, sharpness, and contrast of the individual scanner subsets. Additionally, to quantify the inherent scanner-induced domain shift, we train a tumor segmentation network on each scanner subset and evaluate the performance both in- and cross-domain. We achieve a class-averaged in-domain intersection over union coefficient of up to 0.86 and observe a cross-domain performance decrease of up to 0.38, which confirms the inherent domain shift of the presented dataset and its negative impact on the performance of deep neural networks.

eess.IV↗

arXiv2023

Retinal blood flow speed quantification at the capillary level using temporal autocorrelation fitting OCTA

Optical coherence tomography angiography (OCTA) can visualize vasculature structures, but provides limited information about the blood flow speeds. Here, we present a second generation variable interscan time analysis (VISTA) OCTA, which evaluates a quantitative surrogate marker for blood flow speed in vasculature. At the capillary level, spatially compiled OCTA and a simple temporal autocorrelation model, ρ(τ) = exp(-ατ), were used to evaluate a temporal autocorrelation decay constant, α, as the blood flow speed marker. A 600 kHz A-scan rate swept-source provides short interscan time OCTA and fine A-scan spacing acquisition, while maintaining multi mm2 field of views for human retinal imaging. We demonstrate the cardiac pulsatility and repeatability of α measured with VISTA. We show different α for different retinal capillary plexuses in healthy eyes and present representative VISTA OCTA of eyes with diabetic retinopathy.

eess.IV↗

arXiv2023

Risk Classification of Brain Metastases via Radiomics, Delta-Radiomics and Machine Learning

Stereotactic radiotherapy (SRT) is one of the most important treatment for patients with brain metastases (BM). Conventionally, following SRT patients are monitored by serial imaging and receive salvage treatments in case of significant tumor growth. We hypothesized that using radiomics and machine learning (ML), metastases at high risk for subsequent progression could be identified during follow-up prior to the onset of significant tumor growth, enabling personalized follow-up intervals and early selection for salvage treatment. All experiments are performed on a dataset from clinical routine of the Radiation Oncology department of the University Hospital Erlangen (UKER). The classification is realized via the maximum-relevance minimal-redundancy (MRMR) technique and support vector machines (SVM). The pipeline leads to a classification with a mean area under the curve (AUC) score of 0.83 in internal cross-validation and allows a division of the cohort into two subcohorts that differ significantly in their median time to progression (low-risk metastasis (LRM): 17.3 months, high-risk metastasis (HRM): 9.6 months, p < 0.01). The classification performance is especially enhanced by the analysis of medical images from different points in time (AUC 0.53 -> AUC 0.74). The results indicate that risk stratification of BM based on radiomics and machine learning during post-SRT follow-up is possible with good accuracy and should be further pursued to personalize and improve post-SRT follow-up.

cs.CV↗

arXiv2023

Word class representations spontaneously emerge in a deep neural network trained on next word prediction

How do humans learn language, and can the first language be learned at all? These fundamental questions are still hotly debated. In contemporary linguistics, there are two major schools of thought that give completely opposite answers. According to Chomsky's theory of universal grammar, language cannot be learned because children are not exposed to sufficient data in their linguistic environment. In contrast, usage-based models of language assume a profound relationship between language structure and language use. In particular, contextual mental processing and mental representations are assumed to have the cognitive capacity to capture the complexity of actual language use at all levels. The prime example is syntax, i.e., the rules by which words are assembled into larger units such as sentences. Typically, syntactic rules are expressed as sequences of word classes. However, it remains unclear whether word classes are innate, as implied by universal grammar, or whether they emerge during language acquisition, as suggested by usage-based approaches. Here, we address this issue from a machine learning and natural language processing perspective. In particular, we trained an artificial deep neural network on predicting the next word, provided sequences of consecutive words as input. Subsequently, we analyzed the emerging activation patterns in the hidden layers of the neural network. Strikingly, we find that the internal representations of nine-word input sequences cluster according to the word class of the tenth word to be predicted as output, even though the neural network did not receive any explicit information about syntactic rules or word classes during training. This surprising result suggests, that also in the human brain, abstract representational categories such as word classes may naturally emerge as a consequence of predictive coding and processing during language acquisition.

cs.CL↗

arXiv2023

Optimizing CT Scan Geometries With and Without Gradients

In computed tomography (CT), the projection geometry used for data acquisition needs to be known precisely to obtain a clear reconstructed image. Rigid patient motion is a cause for misalignment between measured data and employed geometry. Commonly, such motion is compensated by solving an optimization problem that, e.g., maximizes the quality of the reconstructed image with respect to the projection geometry. So far, gradient-free optimization algorithms have been utilized to find the solution for this problem. Here, we show that gradient-based optimization algorithms are a possible alternative and compare the performance to their gradient-free counterparts on a benchmark motion compensation problem. Gradient-based algorithms converge substantially faster while being comparable to gradient-free algorithms in terms of capture range and robustness to the number of free parameters. Hence, gradient-based optimization is a viable alternative for the given type of problems.

eess.IV↗

arXiv2023

Transient Hemodynamics Prediction Using an Efficient Octree-Based Deep Learning Model

Patient-specific hemodynamics assessment could support diagnosis and treatment of neurovascular diseases. Currently, conventional medical imaging modalities are not able to accurately acquire high-resolution hemodynamic information that would be required to assess complex neurovascular pathologies. Therefore, computational fluid dynamics (CFD) simulations can be applied to tomographic reconstructions to obtain clinically relevant information. However, three-dimensional (3D) CFD simulations require enormous computational resources and simulation-related expert knowledge that are usually not available in clinical environments. Recently, deep-learning-based methods have been proposed as CFD surrogates to improve computational efficiency. Nevertheless, the prediction of high-resolution transient CFD simulations for complex vascular geometries poses a challenge to conventional deep learning models. In this work, we present an architecture that is tailored to predict high-resolution (spatial and temporal) velocity fields for complex synthetic vascular geometries. For this, an octree-based spatial discretization is combined with an implicit neural function representation to efficiently handle the prediction of the 3D velocity field for each time step. The presented method is evaluated for the task of cerebral hemodynamics prediction before and during the injection of contrast agent in the internal carotid artery (ICA). Compared to CFD simulations, the velocity field can be estimated with a mean absolute error of 0.024 m/s, whereas the run time reduces from several hours on a high-performance cluster to a few seconds on a consumer graphical processing unit.

cs.LG↗

arXiv2023

AMD-HookNet for Glacier Front Segmentation

Knowledge on changes in glacier calving front positions is important for assessing the status of glaciers. Remote sensing imagery provides the ideal database for monitoring calving front positions, however, it is not feasible to perform this task manually for all calving glaciers globally due to time-constraints. Deep learning-based methods have shown great potential for glacier calving front delineation from optical and radar satellite imagery. The calving front is represented as a single thin line between the ocean and the glacier, which makes the task vulnerable to inaccurate predictions. The limited availability of annotated glacier imagery leads to a lack of data diversity (not all possible combinations of different weather conditions, terminus shapes, sensors, etc. are present in the data), which exacerbates the difficulty of accurate segmentation. In this paper, we propose Attention-Multi-hooking-Deep-supervision HookNet (AMD-HookNet), a novel glacier calving front segmentation framework for synthetic aperture radar (SAR) images. The proposed method aims to enhance the feature representation capability through multiple information interactions between low-resolution and high-resolution inputs based on a two-branch U-Net. The attention mechanism, integrated into the two branch U-Net, aims to interact between the corresponding coarse and fine-grained feature maps. This allows the network to automatically adjust feature relationships, resulting in accurate pixel-classification predictions. Extensive experiments and comparisons on the challenging glacier segmentation benchmark dataset CaFFe show that our AMD-HookNet achieves a mean distance error of 438 m to the ground truth outperforming the current state of the art by 42%, which validates its effectiveness.

cs.CV↗

arXiv2023

Automated Cardiac Resting Phase Detection Targeted on the Right Coronary Artery

Static cardiac imaging such as late gadolinium enhancement, mapping, or 3-D coronary angiography require prior information, e.g., the phase during a cardiac cycle with least motion, called resting phase (RP). The purpose of this work is to propose a fully automated framework that allows the detection of the right coronary artery (RCA) RP within CINE series. The proposed prototype system consists of three main steps. First, the localization of the regions of interest (ROI) is performed. Second, the cropped ROI series are taken for tracking motions over all time points. Third, the output motion values are used to classify RPs. In this work, we focused on the detection of the area with the outer edge of the cross-section of the RCA as our target. The proposed framework was evaluated on 102 clinically acquired dataset at 1.5T and 3T. The automatically classified RPs were compared with the reference RPs annotated manually by a expert for testing the robustness and feasibility of the framework. The predicted RCA RPs showed high agreement with the experts annotated RPs with 92.7% accuracy, 90.5% sensitivity and 95.0% specificity for the unseen study dataset. The mean absolute difference of the start and end RP was 13.6 $\pm$ 18.6 ms for the validation study dataset (n=102). In this work, automated RP detection has been introduced by the proposed framework and demonstrated feasibility, robustness, and applicability for static imaging acquisitions.

eess.IV↗

arXiv2023

Quantum-enhanced quantum Monte Carlo: an industrial view

In this work, we test a recently developed method to enhance classical auxiliary-field quantum Monte Carlo (AFQMC) calculations with quantum computers against examples from chemistry and material science, representatives of classes of industry-relevant systems. As molecular test cases, we calculate the energy curve of H4 and relative energies of ozone and singlet molecular oxygen with respect to triplet molecular oxygen, which are industrially relevant in organic oxidation reactions. We find that trial wave functions beyond single Slater determinants improve the performance of AFQMC and allow to generate energies close to chemical accuracy compared to full configuration interaction (FCI) or experimental results. As a representative for material science we study a quasi-1D Fermi-Hubbard model derived from CuBr2, a compound displaying electronic structure properties analogous to cuprates. We find that trial wave functions with both, significantly larger fidelities and lower energies over a Hartree-Fock solution, do not necessarily lead to better AFQMC results.

quant-ph↗

arXiv2023

Transfer Learning for Olfactory Object Detection

We investigate the effect of style and category similarity in multiple datasets used for object detection pretraining. We find that including an additional stage of object-detection pretraining can increase the detection performance considerably. While our experiments suggest that style similarities between pre-training and target datasets are less important than matching categories, further experiments are needed to verify this hypothesis.

cs.CV↗

arXiv2023

ODOR: The ICPR2022 ODeuropa Challenge on Olfactory Object Recognition

The Odeuropa Challenge on Olfactory Object Recognition aims to foster the development of object detection in the visual arts and to promote an olfactory perspective on digital heritage. Object detection in historical artworks is particularly challenging due to varying styles and artistic periods. Moreover, the task is complicated due to the particularity and historical variance of predefined target objects, which exhibit a large intra-class variance, and the long tail distribution of the dataset labels, with some objects having only very few training examples. These challenges should encourage participants to create innovative approaches using domain adaptation or few-shot learning. We provide a dataset of 2647 artworks annotated with 20 120 tightly fit bounding boxes that are split into a training and validation set (public). A test set containing 1140 artworks and 15 480 annotations is kept private for the challenge evaluation.

cs.CV↗

arXiv2023

Classification of Luminal Subtypes in Full Mammogram Images Using Transfer Learning

Automatic identification of patients with luminal and non-luminal subtypes during a routine mammography screening can support clinicians in streamlining breast cancer therapy planning. Recent machine learning techniques have shown promising results in molecular subtype classification in mammography; however, they are highly dependent on pixel-level annotations, handcrafted, and radiomic features. In this work, we provide initial insights into the luminal subtype classification in full mammogram images trained using only image-level labels. Transfer learning is applied from a breast abnormality classification task, to finetune a ResNet-18-based luminal versus non-luminal subtype classification task. We present and compare our results on the publicly available CMMD dataset and show that our approach significantly outperforms the baseline classifier by achieving a mean AUC score of 0.6688 and a mean F1 score of 0.6693 on the test dataset. The improvement over baseline is statistically significant, with a p-value of p<0.0001.

eess.IV↗

arXiv2023

Democratising Knowledge Representation with BioCypher

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to non-specialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://biocypher.org) frees up valuable developer time; we encourage further development and usage by the community.

q-bio.MN↗

arXiv2023

Learning Perspective Deformation in X-Ray Transmission Imaging

In cone-beam X-ray transmission imaging, perspective deformation causes difficulty in direct, accurate geometric assessments of anatomical structures. In this work, the perspective deformation correction problem is formulated and addressed in a framework using two complementary (180°) views. The complementary view setting provides a practical way to identify perspectively deformed structures by assessing the deviation between the two views. It also provides bounding information and reduces uncertainty for learning perspective deformation. Two representative networks Pix2pixGAN and TransU-Net for correcting perspective deformation are investigated. Experiments on numerical bead phantom data demonstrate the advantage of complementary views over orthogonal views or a single view. They show that Pix2pixGAN as a fully convolutional network achieves better performance in polar space than Cartesian space, while TransU-Net as a transformer-based hybrid network achieves comparable performance in Cartesian space to polar space. Further study demonstrates that the trained model has certain tolerance to geometric inaccuracy within calibration accuracy. The efficacy of the proposed framework on synthetic projection images from patients' chest and head data as well as real cadaver CBCT projection data and its robustness in the presence of bulky metal implants and surgical screws indicate the promising aspects of future real applications.

eess.IV↗

arXiv2022

Noise2Contrast: Multi-Contrast Fusion Enables Self-Supervised Tomographic Image Denoising

Self-supervised image denoising techniques emerged as convenient methods that allow training denoising models without requiring ground-truth noise-free data. Existing methods usually optimize loss metrics that are calculated from multiple noisy realizations of similar images, e.g., from neighboring tomographic slices. However, those approaches fail to utilize the multiple contrasts that are routinely acquired in medical imaging modalities like MRI or dual-energy CT. In this work, we propose the new self-supervised training scheme Noise2Contrast that combines information from multiple measured image contrasts to train a denoising model. We stack denoising with domain-transfer operators to utilize the independent noise realizations of different image contrasts to derive a self-supervised loss. The trained denoising operator achieves convincing quantitative and qualitative results, outperforming state-of-the-art self-supervised methods by 4.7-11.0%/4.8-7.3% (PSNR/SSIM) on brain MRI data and by 43.6-50.5%/57.1-77.1% (PSNR/SSIM) on dual-energy CT X-ray microscopy data with respect to the noisy baseline. Our experiments on different real measured data sets indicate that Noise2Contrast training generalizes to other multi-contrast imaging modalities.

eess.IV↗

arXiv2022

Gradient-Based Geometry Learning for Fan-Beam CT Reconstruction

Incorporating computed tomography (CT) reconstruction operators into differentiable pipelines has proven beneficial in many applications. Such approaches usually focus on the projection data and keep the acquisition geometry fixed. However, precise knowledge of the acquisition geometry is essential for high quality reconstruction results. In this paper, the differentiable formulation of fan-beam CT reconstruction is extended to the acquisition geometry. This allows to propagate gradient information from a loss function on the reconstructed image into the geometry parameters. As a proof-of-concept experiment, this idea is applied to rigid motion compensation. The cost function is parameterized by a trained neural network which regresses an image quality metric from the motion affected reconstruction alone. Using the proposed method, we are the first to optimize such an autofocus-inspired algorithm based on analytical gradients. The algorithm achieves a reduction in MSE by 35.5 % and an improvement in SSIM by 12.6 % over the motion affected reconstruction. Next to motion compensation, we see further use cases of our differentiable method for scanner calibration or hybrid techniques employing deep models.

eess.IV↗

arXiv2022

Mind the Gap: Scanner-induced domain shifts pose challenges for representation learning in histopathology

Computer-aided systems in histopathology are often challenged by various sources of domain shift that impact the performance of these algorithms considerably. We investigated the potential of using self-supervised pre-training to overcome scanner-induced domain shifts for the downstream task of tumor segmentation. For this, we present the Barlow Triplets to learn scanner-invariant representations from a multi-scanner dataset with local image correspondences. We show that self-supervised pre-training successfully aligned different scanner representations, which, interestingly only results in a limited benefit for our downstream task. We thereby provide insights into the influence of scanner characteristics for downstream applications and contribute to a better understanding of why established self-supervised methods have not yet shown the same success on histopathology data as they have for natural images.

eess.IV↗

arXiv2022

Metal-conscious Embedding for CBCT Projection Inpainting

The existence of metallic implants in projection images for cone-beam computed tomography (CBCT) introduces undesired artifacts which degrade the quality of reconstructed images. In order to reduce metal artifacts, projection inpainting is an essential step in many metal artifact reduction algorithms. In this work, a hybrid network combining the shift window (Swin) vision transformer (ViT) and a convolutional neural network is proposed as a baseline network for the inpainting task. To incorporate metal information for the Swin ViT-based encoder, metal-conscious self-embedding and neighborhood-embedding methods are investigated. Both methods have improved the performance of the baseline network. Furthermore, by choosing appropriate window size, the model with neighborhood-embedding could achieve the lowest mean absolute error of 0.079 in metal regions and the highest peak signal-to-noise ratio of 42.346 in CBCT projections. At the end, the efficiency of metal-conscious embedding on both simulated and real cadaver CBCT data has been demonstrated, where the inpainting capability of the baseline network has been enhanced.

cs.CV↗