arXiv subjects

Andreas Maier

Publications and source records attributed to Andreas Maier.

At least 181 records · Page 10Linked to original sources

arXiv2024

Enhancing Cross-Modality Synthesis: Subvolume Merging for MRI-to-CT Conversion

Providing more precise tissue attenuation information, synthetic computed tomography (sCT) generated from magnetic resonance imaging (MRI) contributes to improved radiation therapy treatment planning. In our study, we employ the advanced SwinUNETR framework for synthesizing CT from MRI images. Additionally, we introduce a three-dimensional subvolume merging technique in the prediction process. By selecting an optimal overlap percentage for adjacent subvolumes, stitching artifacts are effectively mitigated, leading to a decrease in the mean absolute error (MAE) between sCT and the labels from 52.65 HU to 47.75 HU. Furthermore, implementing a weight function with a gamma value of 0.9 results in the lowest MAE within the same overlap area. By setting the overlap percentage between 50% and 70%, we achieve a balance between image quality and computational efficiency.

eess.IV↗

arXiv2024

Generalist Segmentation Algorithm for Photoreceptors Analysis in Adaptive Optics Imaging

Analyzing the cone photoreceptor pattern in images obtained from the living human retina using quantitative methods can be crucial for the early detection and management of various eye conditions. Confocal adaptive optics scanning light ophthalmoscope (AOSLO) imaging enables visualization of the cones from reflections of waveguiding cone photoreceptors. While there have been significant improvements in automated algorithms for segmenting cones in confocal AOSLO images, the process of labelling data remains labor-intensive and manual. This paper introduces a method based on deep learning (DL) for detecting and segmenting cones in AOSLO images. The models were trained on a semi-automatically labelled dataset of 20 AOSLO batches of images of 18 participants for 0$^{\circ}$, 1$^{\circ}$, and 2$^{\circ}$ from the foveal center. F1 scores were 0.968, 0.958, and 0.954 for 0$^{\circ}$, 1$^{\circ}$, and 2$^{\circ}$, respectively, which is better than previously reported DL approaches. Our method minimizes the need for labelled data by only necessitating a fraction of labelled cones, which is especially beneficial in the field of ophthalmology, where labelled data can often be limited.

eess.IV↗

arXiv2024

Fine-Tuning a Local LLaMA-3 Large Language Model for Automated Privacy-Preserving Physician Letter Generation in Radiation Oncology

Generating physician letters is a time-consuming task in daily clinical practice. This study investigates local fine-tuning of large language models (LLMs), specifically LLaMA models, for physician letter generation in a privacy-preserving manner within the field of radiation oncology. Our findings demonstrate that base LLaMA models, without fine-tuning, are inadequate for effectively generating physician letters. The QLoRA algorithm provides an efficient method for local intra-institutional fine-tuning of LLMs with limited computational resources (i.e., a single 48 GB GPU workstation within the hospital). The fine-tuned LLM successfully learns radiation oncology-specific information and generates physician letters in an institution-specific style. ROUGE scores of the generated summary reports highlight the superiority of the 8B LLaMA-3 model over the 13B LLaMA-2 model. Further multidimensional physician evaluations of 10 cases reveal that, although the fine-tuned LLaMA-3 model has limited capacity to generate content beyond the provided input data, it successfully generates salutations, diagnoses and treatment histories, recommendations for further treatment, and planned schedules. Overall, clinical benefit was rated highly by the clinical experts (average score of 3.44 on a 4-point scale). With careful physician review and correction, automated LLM-based physician letter generation has significant practical value.

cs.AI↗

arXiv2024

Recurrence Resonance -- Noise-Enhanced Dynamics in Recurrent Neural Networks

In specific motifs of three recurrently connected neurons with probabilistic response, the spontaneous information flux, defined as the mutual information between subsequent states, has been shown to increase by adding ongoing white noise of some optimal strength to each of the neurons \cite{krauss2019recurrence}. However, the precise conditions for and mechanisms of this phenomenon called 'recurrence resonance' (RR) remain largely unexplored. Using Boltzmann machines of different sizes and with various types of weight matrices, we show that RR can generally occur when a system has multiple dynamical attractors, but is trapped in one or a few of them. In probabilistic networks, the phenomenon is bound to a suitable observation time scale, as the system could autonomously access its entire attractor landscape even without the help of external noise, given enough time. Yet, even in large systems, where time scales for observing RR in the full network become too long, the resonance can still be detected in small subsets of neurons. Finally, we show that short noise pulses can be used to transfer recurrent neural networks, both probabilistic and deterministic, between their dynamical attractors. Our results are relevant to the fields of reservoir computing and neuroscience, where controlled noise may turn out a key factor for efficient information processing leading to more robust and adaptable systems.

q-bio.NC↗

arXiv2024

Deep Learning for Cancer Prognosis Prediction Using Portrait Photos by StyleGAN Embedding

Survival prediction for cancer patients is critical for optimal treatment selection and patient management. Current patient survival prediction methods typically extract survival information from patients' clinical record data or biological and imaging data. In practice, experienced clinicians can have a preliminary assessment of patients' health status based on patients' observable physical appearances, which are mainly facial features. However, such assessment is highly subjective. In this work, the efficacy of objectively capturing and using prognostic information contained in conventional portrait photographs using deep learning for survival predication purposes is investigated for the first time. A pre-trained StyleGAN2 model is fine-tuned on a custom dataset of our cancer patients' photos to empower its generator with generative ability suitable for patients' photos. The StyleGAN2 is then used to embed the photographs to its highly expressive latent space. Utilizing the state-of-the-art survival analysis models and based on StyleGAN's latent space photo embeddings, this approach achieved a C-index of 0.677, which is notably higher than chance and evidencing the prognostic value embedded in simple 2D facial images. In addition, thanks to StyleGAN's interpretable latent space, our survival prediction model can be validated for relying on essential facial features, eliminating any biases from extraneous information like clothing or background. Moreover, a health attribute is obtained from regression coefficients, which has important potential value for patient care.

eess.IV↗

arXiv2024

Towards QCD at Five Loops

We report on recent progress on five-loop calculations in perturbative QCD. We discuss the computation of the perturbative quark condensate, decoupling in QCD, and the precision determination of charm and bottom quark masses. For the latter, we give some first results from a gauge-invariant subset of five-loop diagrams.

hep-ph↗

arXiv2024

Qiskit-Torch-Module: Fast Prototyping of Quantum Neural Networks

Quantum computer simulation software is an integral tool for the research efforts in the quantum computing community. An important aspect is the efficiency of respective frameworks, especially for training variational quantum algorithms. Focusing on the widely used Qiskit software environment, we develop the qiskit-torch-module. It improves runtime performance by two orders of magnitude over comparable libraries, while facilitating low-overhead integration with existing codebases. Moreover, the framework provides advanced tools for integrating quantum neural networks with PyTorch. The pipeline is tailored for single-machine compute systems, which constitute a widely employed setup in day-to-day research efforts.

quant-ph↗

arXiv2024

Novel Artistic Scene-Centric Datasets for Effective Transfer Learning in Fragrant Spaces

Olfaction, often overlooked in cultural heritage studies, holds profound significance in shaping human experiences and identities. Examining historical depictions of olfactory scenes can offer valuable insights into the role of smells in history. We show that a transfer-learning approach using weakly labeled training data can remarkably improve the classification of fragrant spaces and, more generally, artistic scene depictions. We fine-tune Places365-pre-trained models by querying two cultural heritage data sources and using the search terms as supervision signal. The models are evaluated on two manually corrected test splits. This work lays a foundation for further exploration of fragrant spaces recognition and artistic scene classification. All images and labels are released as the ArtPlaces dataset at https://zenodo.org/doi/10.5281/zenodo.11584328.

cs.CV↗

arXiv2024

Synthetic Electroretinogram Signal Generation Using Conditional Generative Adversarial Network for Enhancing Classification of Autism Spectrum Disorder

The electroretinogram (ERG) is a clinical test that records the retina's electrical response to light. The ERG is a promising way to study different neurodevelopmental and neurodegenerative disorders, including autism spectrum disorder (ASD) - a neurodevelopmental condition that impacts language, communication, and reciprocal social interactions. However, in heterogeneous populations, such as ASD, where the ability to collect large datasets is limited, the application of artificial intelligence (AI) is complicated. Synthetic ERG signals generated from real ERG recordings carry similar information as natural ERGs and, therefore, could be used as an extension for natural data to increase datasets so that AI applications can be fully utilized. As proof of principle, this study presents a Generative Adversarial Network capable of generating synthetic ERG signals of children with ASD and typically developing control individuals. We applied a Time Series Transformer and Visual Transformer with Continuous Wavelet Transform to enhance classification results on the extended synthetic signals dataset. This approach may support classification models in related psychiatric conditions where the ERG may help classify disorders.

cs.LG↗

arXiv2024

Smell and Emotion: Recognising emotions in smell-related artworks

Emotions and smell are underrepresented in digital art history. In this exploratory work, we show that recognising emotions from smell-related artworks is technically feasible but has room for improvement. Using style transfer and hyperparameter optimization we achieve a minor performance boost and open up the field for future extensions.

cs.CV↗

arXiv2024

Speaker- and Text-Independent Estimation of Articulatory Movements and Phoneme Alignments from Speech

This paper introduces a novel combination of two tasks, previously treated separately: acoustic-to-articulatory speech inversion (AAI) and phoneme-to-articulatory (PTA) motion estimation. We refer to this joint task as acoustic phoneme-to-articulatory speech inversion (APTAI) and explore two different approaches, both working speaker- and text-independently during inference. We use a multi-task learning setup, with the end-to-end goal of taking raw speech as input and estimating the corresponding articulatory movements, phoneme sequence, and phoneme alignment. While both proposed approaches share these same requirements, they differ in their way of achieving phoneme-related predictions: one is based on frame classification, the other on a two-staged training procedure and forced alignment. We reach competitive performance of 0.73 mean correlation for the AAI task and achieve up to approximately 87% frame overlap compared to a state-of-the-art text-dependent phoneme force aligner.

cs.SD↗

arXiv2024

Data-driven Modeling in Metrology -- A Short Introduction, Current Developments and Future Perspectives

Mathematical models are vital to the field of metrology, playing a key role in the derivation of measurement results and the calculation of uncertainties from measurement data, informed by an understanding of the measurement process. These models generally represent the correlation between the quantity being measured and all other pertinent quantities. Such relationships are used to construct measurement systems that can interpret measurement data to generate conclusions and predictions about the measurement system itself. Classic models are typically analytical, built on fundamental physical principles. However, the rise of digital technology, expansive sensor networks, and high-performance computing hardware have led to a growing shift towards data-driven methodologies. This trend is especially prominent when dealing with large, intricate networked sensor systems in situations where there is limited expert understanding of the frequently changing real-world contexts. Here, we demonstrate the variety of opportunities that data-driven modeling presents, and how they have been already implemented in various real-world applications.

cs.LG↗

arXiv2024

Review of Zero-Shot and Few-Shot AI Algorithms in The Medical Domain

In this paper, different techniques of few-shot, zero-shot, and regular object detection have been investigated. The need for few-shot learning and zero-shot learning techniques is crucial and arises from the limitations and challenges in traditional machine learning, deep learning, and computer vision methods where they require large amounts of data, plus the poor generalization of those traditional methods. Those techniques can give us prominent results by using only a few training sets reducing the required amounts of data and improving the generalization. This survey will highlight the recent papers of the last three years that introduce the usage of few-shot learning and zero-shot learning techniques in addressing the challenges mentioned earlier. In this paper we reviewed the Zero-shot, few-shot and regular object detection methods and categorized them in an understandable manner. Based on the comparison made within each category. It been found that the approaches are quite impressive. This integrated review of diverse papers on few-shot, zero-shot, and regular object detection reveals a shared focus on advancing the field through novel frameworks and techniques. A noteworthy observation is the scarcity of detailed discussions regarding the difficulties encountered during the development phase. Contributions include the introduction of innovative models, such as ZSD-YOLO and GTNet, often showcasing improvements with various metrics such as mean average precision (mAP),Recall@100 (RE@100), the area under the receiver operating characteristic curve (AUROC) and precision. These findings underscore a collective move towards leveraging vision-language models for versatile applications, with potential areas for future research including a more thorough exploration of limitations and domain-specific adaptations.

cs.CV↗

arXiv2024

Towards Intelligent Speech Assistants in Operating Rooms: A Multimodal Model for Surgical Workflow Analysis

To develop intelligent speech assistants and integrate them seamlessly with intra-operative decision-support frameworks, accurate and efficient surgical phase recognition is a prerequisite. In this study, we propose a multimodal framework based on Gated Multimodal Units (GMU) and Multi-Stage Temporal Convolutional Networks (MS-TCN) to recognize surgical phases of port-catheter placement operations. Our method merges speech and image models and uses them separately in different surgical phases. Based on the evaluation of 28 operations, we report a frame-wise accuracy of 92.65 $\pm$ 3.52% and an F1-score of 92.30 $\pm$ 3.82%. Our results show approximately 10% improvement in both metrics over previous work and validate the effectiveness of integrating multimodal data for the surgical phase recognition task. We further investigate the contribution of individual data channels by comparing mono-modal models with multimodal models.

eess.AS↗

arXiv2024

On the Influence of Smoothness Constraints in Computed Tomography Motion Compensation

Computed tomography (CT) relies on precise patient immobilization during image acquisition. Nevertheless, motion artifacts in the reconstructed images can persist. Motion compensation methods aim to correct such artifacts post-acquisition, often incorporating temporal smoothness constraints on the estimated motion patterns. This study analyzes the influence of a spline-based motion model within an existing rigid motion compensation algorithm for cone-beam CT on the recoverable motion frequencies. Results demonstrate that the choice of motion model crucially influences recoverable frequencies. The optimization-based motion compensation algorithm is able to accurately fit the spline nodes for frequencies almost up to the node-dependent theoretical limit according to the Nyquist-Shannon theorem. Notably, a higher node count does not compromise reconstruction performance for slow motion patterns, but can extend the range of recoverable high frequencies for the investigated algorithm. Eventually, the optimal motion model is dependent on the imaged anatomy, clinical use case, and scanning protocol and should be tailored carefully to the expected motion frequency spectrum to ensure accurate motion compensation.

eess.IV↗

arXiv2024

SNOBERT: A Benchmark for clinical notes entity linking in the SNOMED CT clinical terminology

The extraction and analysis of insights from medical data, primarily stored in free-text formats by healthcare workers, presents significant challenges due to its unstructured nature. Medical coding, a crucial process in healthcare, remains minimally automated due to the complexity of medical ontologies and restricted access to medical texts for training Natural Language Processing models. In this paper, we proposed a method, "SNOBERT," of linking text spans in clinical notes to specific concepts in the SNOMED CT using BERT-based models. The method consists of two stages: candidate selection and candidate matching. The models were trained on one of the largest publicly available dataset of labeled clinical notes. SNOBERT outperforms other classical methods based on deep learning, as confirmed by the results of a challenge in which it was applied.

cs.CL↗

arXiv2024

Application of Gated Recurrent Units for CT Trajectory Optimization

Recent advances in computed tomography (CT) imaging, especially with dual-robot systems, have introduced new challenges for scan trajectory optimization. This paper presents a novel approach using Gated Recurrent Units (GRUs) to optimize CT scan trajectories. Our approach exploits the flexibility of robotic CT systems to select projections that enhance image quality by improving resolution and contrast while reducing scan time. We focus on cone-beam CT and employ several projection-based metrics, including absorption, pixel intensities, contrast-to-noise ratio, and data completeness. The GRU network aims to minimize data redundancy and maximize completeness with a limited number of projections. We validate our method using simulated data of a test specimen, focusing on a specific voxel of interest. The results show that the GRU-optimized scan trajectories can outperform traditional circular CT trajectories in terms of image quality metrics. For the used specimen, SSIM improves from 0.38 to 0.49 and CNR increases from 6.97 to 9.08. This finding suggests that the application of GRU in CT scan trajectory optimization can lead to more efficient, cost-effective, and high-quality imaging solutions.

cs.CV↗

arXiv2024

Analyzing Narrative Processing in Large Language Models (LLMs): Using GPT4 to test BERT

The ability to transmit and receive complex information via language is unique to humans and is the basis of traditions, culture and versatile social interactions. Through the disruptive introduction of transformer based large language models (LLMs) humans are not the only entity to "understand" and produce language any more. In the present study, we have performed the first steps to use LLMs as a model to understand fundamental mechanisms of language processing in neural networks, in order to make predictions and generate hypotheses on how the human brain does language processing. Thus, we have used ChatGPT to generate seven different stylistic variations of ten different narratives (Aesop's fables). We used these stories as input for the open source LLM BERT and have analyzed the activation patterns of the hidden units of BERT using multi-dimensional scaling and cluster analysis. We found that the activation vectors of the hidden units cluster according to stylistic variations in earlier layers of BERT (1) than narrative content (4-5). Despite the fact that BERT consists of 12 identical building blocks that are stacked and trained on large text corpora, the different layers perform different tasks. This is a very useful model of the human brain, where self-similar structures, i.e. different areas of the cerebral cortex, can have different functions and are therefore well suited to processing language in a very efficient way. The proposed approach has the potential to open the black box of LLMs on the one hand, and might be a further step to unravel the neural processes underlying human language processing and cognition in general.

cs.CL↗