Index
Improved Deep Learning Dose Prediction for Automated Head & Neck Radiotherapy Treatment Planning
Radiation therapy is one of the most important local cancer treatment modalities, enabling the non-invasive delivery of a spatially varying dose distribution within a patient’s body with high precision. Radiotherapy treatment planning aims to identify the optimal treatment plan that maximally spares surrounding normal tissue structures while delivering a high dose to the target volume. Deep Learning dose prediction is a novel technique that can automate the treatment planning process, improve standardization and reduce the treatment planning time to enable novel and improved therapies like same-day treatment and adaptive radiotherapy [1]. Deep learning dose prediction uses deep learning models like 3D U-Nets [2] to predict spatial dose distributions based on planning CT datasets, target volume, and organs at risk (OAR) segmentations [1, 3] (Figure 1). Subsequently, dose mimicking algorithms are used to translate these 3D dose predictions into deliverable treatment plans [1, 3–5]. An additional resource for dose prediction research is provided by the Open Knowledge-Based Planning Challenge (OpenKBP) [6], which offers a publicly available dataset and a standardized evaluation framework. The aim of this master thesis project is to improve an existing 3D
U-Net dose prediction model and evaluate its performance using a cohort of more than 450 Head & Neck cancer datasets from the Department of Radiation Oncology, University Hospital Erlangen.
The thesis will include the following points:
• Literature review on deep learning techniques for radiotherapy dose prediction and automated treatment planning.
• Data preprocessing for the private Head & Neck treatment plan dataset including conversion of DICOM (CT, RT DOSE, RT STRUCT) files into CSV files and label maps. Automatic cleaning and splitting of the datasets into subgroups according to plan parameters using custom Python scripts (Pydicom library).
• Training, Inference and Testing of a pre-existing 3D U-net (Figure 2) dose prediction model (Keras, PyTorch) on the cohort of 450 Head & Neck cancer datasets.
• Reframe of the pre-existing dose prediction model to enable multi-GPU training with PyTorch. Enable increased resolution of the predicted voxel grid using multi-GPU training, splitting into subvolumes and/or further strategies to decrease memory consumption (e.g., Automatic Mixed Precision). Optimization of training time and GPU usage by shifting pre-processing steps to before the training phase.
• Extension of the pre-existing dose prediction model by implementing an on-line augmentation pipeline tailored to the task of dose prediction. Hyperparameter optimization on the validation dataset.
• Optional: Exploration of additional deep learning architectures for radiotherapy dose prediction including novel techniques like diffusion models [7, 8] and transformer architectures [9, 10].
• Optional: Adaption of the developed dose prediction pipeline to lung tumors with a data set of 130 patient plans.
• Detailed evaluation of the deep learning dose prediction performance on the test dataset comparing automated treatment plans to manually created treatment plans. Comparison of the different deep learning approaches in regard to accuracy and inference time. Five training and inference repeats to enable statistical analysis.
If you are interested in the project, please send your request to: johann.brand@uk-erlangen.de
Having prior experience with building neural networks in Python, especially using frameworks such as PyTorch or TensorFlow, will greatly help to develop the project.
Link Prediction on Utility Networks Using Graph Neural Networks
Abstract:
Utility network is a commonly used term for a collection of physical infrastructure components such as pipes, valves, pumps, etc., pipes that supply utilities like heat, water, electricity, and gas throughout the city. Structurally, the network of interconnected components can be replicated digitally with the help of GIS measurements. An accurate digital representation is crucial to maintain data integrity and ensure operational reliability. However, when physical components are digitally represented, measurement inaccuracies are introduced, diminishing the reliability of the digital model and impeding the process of deriving meaningful information. These inaccuracies often appear as missing pipes or disconnected networks due to translational errors. This thesis aims to formulate and tackle this problem as a graph based link (edge) prediction task using Deep Learning (DL), through Graph Neural Networks (GNNs). We apply the theory and methodology of SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction) [1], to the domain of utility networks. SEAL extracts local enclosing subgraphs around a link to learn patterns and predicts the existence of links. Additionally, we compare the effect of using pre-trained node2vec embeddings to embeddings learned simultaneously with the GNN model while experimenting with two different graph structures – homogeneous and heterogeneous-bipartite representations. We applied the methodology to real-world heat and water networks from Denmark. Overall, the pre-trained node2vec embeddings consistently outperformed those simultaneously learned with the GNN model. The optimal choice for the graph structure varied between the heat and water networks. Our experimentation on the heat network shows that heterogeneous-bipartite representation yielded better results, with an AUC score of 98% on the test set. In the case of the water networks, both the heterogeneous bipartite and the homogeneous representations produced comparable results, with an AUC score of 95%.
References:
This thesis is part of the “UtilityTwin” project.
Emotion recognition Project
Parkinson’s Disease Assessment Using Gait Analysis
Aphasia Assessment Using Deep Learning
Investigation of appropriate measures for the automated preparation and processing of modifications in diagnostic data for commissioning in vehicle production
Investigation of appropriate measures for the automated preparation and processing of modifications in diagnostic data for commissioning in vehicle production.
Metal Artifact Reduction in Computed Tomography Using Deep Learning Method
Building Knowledge Graphs from Legal Texts: Enhancing Decision Support with Applications in Formula 1
Legal documents, such as the FIA rulebook, are complex and difficult to navigate. Understanding these texts is time-consuming and prone to error. This thesis proposes using Natural Language Processing (NLP) and Knowledge Graphs (KGs) to transform legal texts into queryable, visual formats that simplify decision-making. Formula 1 will serve as a case study.
Objectives:
• Develop a pipeline to convert legal texts into navigable knowledge graphs.
• Create a queryable system for understanding relationships, exceptions, and dependencies.
• Detect inconsistencies and ambiguities in legal texts.
• Generalize the framework to apply to multiple legal domains. Approach
• Theoretical: Study legal text syntax/semantics, NLP techniques (e.g., BERT, GPT), and KG principles for modeling legal complexities.
• Practical:
o Build the KG using tools like Neo4j and visualize relationships between entities.
o Use ML algorithms to flag ambiguities or conflicts.
o Develop a natural language query interface for user-friendly interaction.
Generating Styled Handwritten Images based on Latent Diffusion Models
Handwriting generation is an important direction in computer vision and natural language processing.Traditional models such as AE, VAE, and GAN have gradually developed, while diffusion models have attracted much attention due to their better generation quality and stability. At present, advanced methods include GANwriting, which extracts writing styles through style encoders and generates texts with matching styles and accurate content; VATr++ combines visual perception modules with Transformer architecture, and uses multi-level conditional control and hybrid attention mechanisms to achieve accurate imitation of complex handwriting styles; WordStylist combines semantic information and style features based on the latent diffusion model (LDM) to generate texts with accurate styles; DiffusionPen generates handwritten images by denoising in the latent space through content encoding and style encoding to ensure consistency of content and style; DiffCJK combines conditional diffusion models and language-specific knowledge to achieve high-quality generation with excellent local details and global structures based on the characteristics of Chinese, Japanese, and Korean characters. Although LDM performs well in generation quality and multi-language support, it still faces challenges such as insufficient efficiency, poor adaptability to few samples, and limited style diversity.
In this work, I want to generate Styled handwritten images based on LDM at the word level to further improve the generation efficiency, enhance the style generalization ability, and achieve more refined style control.
The implementation will be done in Python / Pytorch.
The thesis consists of the following milestones:
– Explore techniques to accelerate the diffusion process (e.g., fast sampling algorithms or segmented denoising strategies) to reduce generation time.
– Optimize the representation of the latent space to further reduce the computational complexity.
– Try using different mechanisms or enhanced learning methods to improve adaptability to extreme styles
– Further experiments and optimizations on the learning process and network architecture.
– Evaluate performance and compare with other new technologies