Frederic Runge

Jörg K. H. Franke, Frederic Runge, Frank Hutter

Our world is ambiguous and this is reflected in the data we use to train our algorithms. This is particularly true when we try to model natural processes where collected data is affected by noisy measurements and differences in measurement techniques. Sometimes, the process itself is ambiguous, such as in the case of RNA folding, where the same nucleotide sequence can fold into different structures. This suggests that a predictive model should have similar probabilistic characteristics to match the data it models. Therefore, we propose a hierarchical latent distribution to enhance one of the most successful deep learning models, the Transformer, to accommodate ambiguities and data distributions. We show the benefits of our approach (1) on a synthetic task that captures the ability to learn a hidden data distribution, (2) with state-of-the-art results in RNA folding that reveal advantages on highly ambiguous data, and (3) demonstrating its generative capabilities on property-based molecule design by implicitly learning the underlying distributions and outperforming existing work.

Jörg K. H. Franke, Frederic Runge, Frank Hutter

The field of RNA secondary structure prediction has made significant progress with the adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep learning model using axial attention and recycling in the latent space. We gain performance improvements by designing the architecture for modeling the adjacency matrix directly in the latent space and by scaling the size of the model. Our approach achieves state-of-the-art performance on the popular TS0 benchmark dataset and even outperforms methods that use external information. Further, we show experimentally that the RNAformer can learn a biophysical model of the RNA folding process.

Frederic Runge, Jörg K. H. Franke, Frank Hutter

Experimental screening and selection pipelines for the discovery of novel riboswitches are expensive, time-consuming, and inefficient. Using computational methods to reduce the number of candidates for the screen could drastically decrease these costs. However, existing computational approaches do not fully satisfy all requirements for the design of such initial screening libraries. In this work, we present a new method, libLEARNA, capable of providing RNA focus libraries of diverse variable-length qualified candidates. Our novel structure-based design approach considers global properties as well as desired sequence and structure features. We demonstrate the benefits of our method by designing theophylline riboswitch libraries, following a previously published protocol, and yielding 30% more unique high-quality candidates.

Frederic Runge, Jörg K. H. Franke, Daniel Fertmann et al.

Accurate RNA secondary structure prediction is vital for understanding cellular regulation and disease mechanisms. Deep learning (DL) methods have surpassed traditional algorithms by predicting complex features like pseudoknots and multi-interacting base pairs. However, traditional distance measures can hardly deal with such tertiary interactions and the currently used evaluation measures (F1 score, MCC) have limitations. We propose the Weisfeiler-Lehman graph kernel (WL) as an alternative metric. Embracing graph-based metrics like WL enables fair and accurate evaluation of RNA structure prediction algorithms. Further, WL provides informative guidance, as demonstrated in an RNA design experiment.

Frederic Runge, Danny Stoll, Stefan Falkner et al.

Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and translation. Since an RNA's function depends on its structural properties, the RNA Design problem is to find an RNA sequence which satisfies given structural constraints. Here, we propose a new algorithm for the RNA Design problem, dubbed LEARNA. LEARNA uses deep reinforcement learning to train a policy network to sequentially design an entire RNA sequence given a specified target structure. By meta-learning across 65000 different RNA Design tasks for one hour on 20 CPU cores, our extension Meta-LEARNA constructs an RNA Design policy that can be applied out of the box to solve novel RNA Design tasks. Methodologically, for what we believe to be the first time, we jointly optimize over a rich space of architectures for the policy network, the hyperparameters of the training procedure and the formulation of the decision process. Comprehensive empirical results on two widely-used RNA Design benchmarks, as well as a third one that we introduce, show that our approach achieves new state-of-the-art performance on the former while also being orders of magnitudes faster in reaching the previous state-of-the-art performance. In an ablation study, we analyze the importance of our method's different components.