Ensemble inspired Probabilistic Neural Network

Developing lightweight ensemble neural networks for probabilistic modeling.

Probabilistic models allow for uncertainty aware predictions. This is relevant for safety critical applications but also enables the use of active learning or Bayesian optimization. Within our research, we develop Bayesian optimization based methods for biological sequence design. This includes DNA, RNA but also protein sequences. The relation between sequence and functionality (i.e. expression levels) can be represented naturally by sequence-to-function neural networks, with ensemble neural networks being a natural method for generating probabilistic predictions. Large ensembles allow for straight forward implementation and well calibrated uncertainty representation but can lead to substantial computational overhead. To this end, we envisioned the creation of approximate ensembles by implementing the ensembling only at the later stages of the network. A special focus then applies to the quality of uncertainty calibration. The goal of this project is to implement and advance the development of these approximate ensembles with a special focus on sequence-to-function neural networks. The project is also applicable as a group project.

Background in electrical engineering, computer science, bioinformatics, (computational) biology, or related fields Proficiency in Python Proficiency with deep learning frameworks (PyTorch) Interest in interdisciplinary research combining computational methods with biological applications

NAND Hybrid Riboswitch Design by Deep Batch Bayesian Optimization: https://www.biorxiv.org/content/10.1101/2025.03.28.645907v1

Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles: https://arxiv.org/abs/1612.01474

Additional Information

Supervisor
Contact at Department
Prof. Dr. Heinz Koeppl
Erik Kubaczka
Availability Spring, Summer 2026
Capacity 5 Students
Credits 18 ECTS
Remote Option no