Please contact the co-supervisor if you are interested in a thesis.
Motivation:
Inferring and manipulating the metabolic network of single-cell organisms holds excellent promise for synthesizing novel chemical substances. Together with the Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB we want to contribute to methodologies of inferring the metabolic network (and proposing possible interventions) of organisms in a bioreactor. As a first step, we want to develop and solve toy problems close to real-world data.
Challenges: formalization of the problem setting together with domain experts, proposing an algorithm, efficient implementation
Prerequisites: ideally, some background in probability theory and combinatorial optimization, potentially deep learning
Co-Supervisor: Gerrit Großmann (with support of Jonathan Fabarius)
Related Work: Unsupervised Relational Inference Using Masked Reconstruction and Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquensAM1 and In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories.
Motivation:
Exploring the prediction of properties of neural networks (both deep and shallow) based on their weights is an intriguing new research direction filled with numerous unanswered questions. Our goal is to investigate which properties can be inferred from the weights of neural networks and to understand the characteristics of these weights. Key questions of interest include:
Challenges: The main challenges involve identifying a suitable research question and task class, training neural networks for the chosen task, and then developing a secondary neural network for weight space prediction. It also includes the empirical examination of various facets of these predictions.
Prerequisites: A strong foundation in deep learning and an interest in mechanistic interpretability.
Co-Supervisor: Gerrit Großmann
Related Work:
Motivation: Diffusion models have shown great promise in the generation of discrete structures like graphs and molecules, but many problems still remain (see our seminar’s paper list for more information.) We offer several topics in this area, for instance:
Challenges: derivation of the corresponding equations; efficient implementation
Prerequisites: background in probability theory and deep learning, PyTorch
Co-Supervisor: Gerrit Großmann
Related Work: See Deep Generative Diffusion Models Seminar website.
Motivation: Inferring the underlying (i.e., hidden) interaction structure of complex systems from time-series data presents a significant challenge. Recent advancements in deep learning techniques have demonstrated remarkable progress in identifying these interaction structures by jointly learning the structure and a prediction model based on the time-series data. In this research, the student aims to improve this process by replacing the conventional prediction model with a symbolic regression layer.
Deep symbolic regression leverages discrete optimization to derive mathematical equations that accurately represent the given observations. By integrating a symbolic regression layer into the deep learning model, the proposed approach seeks to uncover more interpretable and generalizable representations of the hidden interaction structures within complex systems. This enhanced method will not only increase the transparency of the learning process but also facilitate a deeper understanding of the underlying dynamics governing the system.
Challenges: exploring suitable methods of integrating symbolic regression in network inference methods; efficient implementation, evaluation
Prerequisites: background in probability theory and deep learning
Co-Supervisor: Gerrit Großmann
Related Work: See Unsupervised Relational Inference Using Masked Reconstruction and Deep symbolic regression for physics guided by units constraints: toward the automated discovery of physical laws
Motivation: Numerous graph types, such as molecular graphs, consist of recurring functional units. This thesis explores graph mining strategies to deduce either a sub-graph vocabulary or a graph transformation, aiming to enhance tasks related to molecular machine learning. This includes not only the interpretability and explainability of graph regression tasks but also seeks to improve the data efficiency of generative tasks.
Challenges: The thesis primarily challenges the development of efficient techniques (likely based on differentiable graph representation) for graph translations and sub-graph mining, and their integration into existing graph ML methodologies.
Prerequisites: background in GNNs and interest in molecular ML