Jörg K. H. Franke

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.

Jörg K. H. Franke, Michael Hefenbrock, Gregor Koehler et al.

Regularization is a critical component in deep learning. The most commonly used approach, weight decay, applies a constant penalty coefficient uniformly across all parameters. This may be overly restrictive for some parameters, while insufficient for others. To address this, we present Constrained Parameter Regularization (CPR) as an alternative to traditional weight decay. Unlike the uniform application of a single penalty, CPR enforces an upper bound on a statistical measure, such as the L2-norm, of individual parameter matrices. Consequently, learning becomes a constraint optimization problem, which we tackle using an adaptation of the augmented Lagrangian method. CPR introduces only a minor runtime overhead and only requires setting an upper bound. We propose simple yet efficient mechanisms for initializing this bound, making CPR rely on no hyperparameter or one, akin to weight decay. Our empirical studies on computer vision and language modeling tasks demonstrate CPR's effectiveness. The results show that CPR can outperform traditional weight decay and increase performance in pre-training and fine-tuning.

Simon Blauth, Tobias Bürger, Zacharias Häringer et al.

In this paper, we present the Fast Optimizer Benchmark (FOB), a tool designed for evaluating deep learning optimizers during their development. The benchmark supports tasks from multiple domains such as computer vision, natural language processing, and graph learning. The focus is on convenient usage, featuring human-readable YAML configurations, SLURM integration, and plotting utilities. FOB can be used together with existing hyperparameter optimization (HPO) tools as it handles training and resuming of runs. The modular design enables integration into custom pipelines, using it simply as a collection of tasks. We showcase an optimizer comparison as a usage example of our tool. FOB can be found on GitHub: https://github.com/automl/FOB.

Riccardo Grazzi, Julien Siems, Arber Zela et al.

Linear Recurrent Neural Networks (LRNNs) such as Mamba, RWKV, GLA, mLSTM, and DeltaNet have emerged as efficient alternatives to Transformers for long sequences. However, both Transformers and LRNNs struggle to perform state-tracking, which may impair performance in tasks such as code evaluation. In one forward pass, current architectures are unable to solve even parity, the simplest state-tracking task, which non-linear RNNs can handle effectively. Recently, Sarrof et al. (2024) demonstrated that the failure of LRNNs like Mamba to solve parity stems from restricting the value range of their diagonal state-transition matrices to $[0, 1]$ and that incorporating negative values can resolve this issue. We extend this result to non-diagonal LRNNs such as DeltaNet. We prove that finite precision LRNNs with state-transition matrices having only positive eigenvalues cannot solve parity, while non-triangular matrices are needed to count modulo $3$. Notably, we also prove that LRNNs can learn any regular language when their state-transition matrices are products of identity minus vector outer product matrices, each with eigenvalues in the range $[-1, 1]$. Our experiments confirm that extending the eigenvalue range of Mamba and DeltaNet to include negative values not only enables them to solve parity but consistently improves their performance on state-tracking tasks. We also show that state-tracking enabled LRNNs can be pretrained stably and efficiently at scale (1.3B parameters), achieving competitive performance on language modeling and showing promise on code and math tasks.

Tobias Strangmann, Lennart Purucker, Jörg K. H. Franke et al.

As the landscape of large language models expands, efficiently finetuning for specific tasks becomes increasingly crucial. At the same time, the landscape of parameter-efficient finetuning methods rapidly expands. Consequently, practitioners face a multitude of complex choices when searching for an optimal finetuning pipeline for large language models. To reduce the complexity for practitioners, we investigate transfer learning for finetuning large language models and aim to transfer knowledge about configurations from related finetuning tasks to a new task. In this work, we transfer learn finetuning by meta-learning performance and cost surrogate models for grey-box meta-optimization from a new meta-dataset. Counter-intuitively, we propose to rely only on transfer learning for new datasets. Thus, we do not use task-specific Bayesian optimization but prioritize knowledge transferred from related tasks over task-specific feedback. We evaluate our method on eight synthetic question-answer datasets and a meta-dataset consisting of 1,800 runs of finetuning Microsoft's Phi-3. Our transfer learning is superior to zero-shot, default finetuning, and meta-optimization baselines. Our results demonstrate the transferability of finetuning to adapt large language models more effectively.

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.

Jörg K. H. Franke, Urs Spiegelhalter, Marianna Nezhurina et al.

The successful training of deep neural networks requires addressing challenges such as overfitting, numerical instabilities leading to divergence, and increasing variance in the residual stream. A common solution is to apply regularization and normalization techniques that usually require tuning additional hyperparameters. An alternative is to force all parameters and representations to lie on a hypersphere. This removes the need for regularization and increases convergence speed, but comes with additional costs. In this work, we propose a more holistic, approximate normalization via simple scalar multiplications motivated by the tight concentration of the norms of high-dimensional random vectors. Additionally, instead of applying strict normalization for the parameters, we constrain their norms. These modifications remove the need for weight decay and learning rate warm-up as well, but do not increase the total number of normalization layers. Our experiments with transformer architectures show up to 40% faster convergence compared to GPT models with QK normalization, with only 3% additional runtime cost. When deriving scaling laws, we found that our method enables training with larger batch sizes while preserving the favorable scaling characteristics of classic GPT architectures.

Urs Spiegelhalter, Jörg K. H. Franke, Frank Hutter

Adapting language models to new tasks through continued pretraining faces a fundamental trade-off: models must learn new capabilities while avoiding catastrophic forgetting of existing knowledge. While prior work has studied synthetic data generation techniques, the optimal replay ratios for balancing task performance and knowledge retention under computational constraints remain poorly understood. We present a comprehensive empirical study investigating the interplay between replay ratio configuration and computational budget when adapting language models to new tasks. Using the bAbI reasoning tasks as our target objective, we apply synthetic data generation and systematically evaluate different total token budgets and replay ratio configurations. We analyze their effects on both task mastery and general knowledge retention. Our experiments reveal an optimal configuration that balances task-specific performance with general knowledge retention. Based on our findings, we provide empirically-grounded guidelines for selecting replay ratios based on computational budget, enabling practitioners to achieve strong task adaptation with significantly reduced training costs.

Danny Stoll, Jörg K. H. Franke, Diane Wagner et al.

After developer adjustments to a machine learning (ML) algorithm, how can the results of an old hyperparameter optimization (HPO) automatically be used to speedup a new HPO? This question poses a challenging problem, as developer adjustments can change which hyperparameter settings perform well, or even the hyperparameter search space itself. While many approaches exist that leverage knowledge obtained on previous tasks, so far, knowledge from previous development steps remains entirely untapped. In this work, we remedy this situation and propose a new research framework: hyperparameter transfer across adjustments (HT-AA). To lay a solid foundation for this research framework, we provide four simple HT-AA baseline algorithms and eight benchmarks changing various aspects of ML algorithms, their hyperparameter search spaces, and the neural architectures used. The best baseline, on average and depending on the budgets for the old and new HPO, reaches a given performance 1.2--2.6x faster than a prominent HPO algorithm without transfer. As HPO is a crucial step in ML development but requires extensive computational resources, this speedup would lead to faster development cycles, lower costs, and reduced environmental impacts. To make these benefits available to ML developers off-the-shelf and to facilitate future research on HT-AA, we provide python packages for our baselines and benchmarks.

Jörg K. H. Franke, Gregor Köhler, André Biedenkapp et al.

Despite significant progress in challenging problems across various domains, applying state-of-the-art deep reinforcement learning (RL) algorithms remains challenging due to their sensitivity to the choice of hyperparameters. This sensitivity can partly be attributed to the non-stationarity of the RL problem, potentially requiring different hyperparameter settings at various stages of the learning process. Additionally, in the RL setting, hyperparameter optimization (HPO) requires a large number of environment interactions, hindering the transfer of the successes in RL to real-world applications. In this work, we tackle the issues of sample-efficient and dynamic HPO in RL. We propose a population-based automated RL (AutoRL) framework to meta-optimize arbitrary off-policy RL algorithms. In this framework, we optimize the hyperparameters and also the neural architecture while simultaneously training the agent. By sharing the collected experience across the population, we substantially increase the sample efficiency of the meta-optimization. We demonstrate the capabilities of our sample-efficient AutoRL approach in a case study with the popular TD3 algorithm in the MuJoCo benchmark suite, where we reduce the number of environment interactions needed for meta-optimization by up to an order of magnitude compared to population-based training.

Jörg K. H. Franke, Gregor Köhler, Noor Awad et al.

Current Deep Reinforcement Learning algorithms still heavily rely on handcrafted neural network architectures. We propose a novel approach to automatically find strong topologies for continuous control tasks while only adding a minor overhead in terms of interactions in the environment. To achieve this, we combine Neuroevolution techniques with off-policy training and propose a novel architecture mutation operator. Experiments on five continuous control benchmarks show that the proposed Actor-Critic Neuroevolution algorithm often outperforms the strong Actor-Critic baseline and is capable of automatically finding topologies in a sample-efficient manner which would otherwise have to be found by expensive architecture search.