Bernhard Y. Renard

Maximilian Kleissl, Lukas Drews, Benedict B. Heyder et al.

Training sophisticated machine learning (ML) models requires large datasets that are difficult or expensive to collect for many applications. If prior knowledge about system dynamics is available, mechanistic representations can be used to supplement real-world data. We present SimbaML (Simulation-Based ML), an open-source tool that unifies realistic synthetic dataset generation from ordinary differential equation-based models and the direct analysis and inclusion in ML pipelines. SimbaML conveniently enables investigating transfer learning from synthetic to real-world data, data augmentation, identifying needs for data collection, and benchmarking physics-informed ML approaches. SimbaML is available from https://pypi.org/project/simba-ml/.

Isabel Kurth, Paulo Yanez Sarmiento, Bernhard Y. Renard

Explaining deep neural network predictions on genome sequences enables biological insight and hypothesis generation-often of greater interest than predictive performance alone. While explanations of convolutional neural networks (CNNs) have been shown to capture relevant patterns in genome sequences, it is unclear whether this transfers to more expressive Transformer-based genome language models (gLMs). To answer this question, we adapt AttnLRP, an extension of layer-wise relevance propagation to the attention mechanism, and apply it to the state-of-the-art gLM DNABERT-2. Thereby, we propose strategies to transfer explanations from token and nucleotide level. We evaluate the adaption of AttnLRP on genomic datasets using multiple metrics. Further, we provide an extensive comparison between the explanations of DNABERT-2 and a baseline CNN. Our results demonstrate that AttnLRP yields reliable explanations corresponding to known biological patterns. Hence, like CNNs, gLMs can also help derive biological insights. This work contributes to the explainability of gLMs and addresses the comparability of relevance attributions across different architectures.

Fábio M. Miranda, Niklas Köhnecke, Bernhard Y. Renard

HiClass is an open-source Python library for local hierarchical classification entirely compatible with scikit-learn. It contains implementations of the most common design patterns for hierarchical machine learning models found in the literature, that is, the local classifiers per node, per parent node and per level. Additionally, the package contains implementations of hierarchical metrics, which are more appropriate for evaluating classification performance on hierarchical data. The documentation includes installation and usage instructions, examples within tutorials and interactive notebooks, and a complete description of the API. HiClass is released under the simplified BSD license, encouraging its use in both academic and commercial environments. Source code and documentation are available at https://github.com/scikit-learn-contrib/hiclass.

Pascal Iversen, Simon Witzke, Katharina Baum et al.

Explainability and uncertainty quantification are key to trustable artificial intelligence. However, the reasoning behind uncertainty estimates is generally left unexplained. Identifying the drivers of uncertainty complements explanations of point predictions in recognizing model limitations and enhancing transparent decision-making. So far, explanations of uncertainties have been rarely studied. The few exceptions rely on Bayesian neural networks or technically intricate approaches, such as auxiliary generative models, thereby hindering their broad adoption. We propose a straightforward approach to explain predictive aleatoric uncertainties. We estimate uncertainty in regression as predictive variance by adapting a neural network with a Gaussian output distribution. Subsequently, we apply out-of-the-box explainers to the model's variance output. This approach can explain uncertainty influences more reliably than complex published approaches, which we demonstrate in a synthetic setting with a known data-generating process. We substantiate our findings with a nuanced, quantitative benchmark including synthetic and real, tabular and image datasets. For this, we adapt metrics from conventional XAI research to uncertainty explanations. Overall, the proposed method explains uncertainty estimates with little modifications to the model architecture and outperforms more intricate methods in most settings.

Paulo Yanez Sarmiento, Simon Witzke, Nadja Klein et al.

Explainability is a key component in many applications involving deep neural networks (DNNs). However, current explanation methods for DNNs commonly leave it to the human observer to distinguish relevant explanations from spurious noise. This is not feasible anymore when going from easily human-accessible data such as images to more complex data such as genome sequences. To facilitate the accessibility of DNN outputs from such complex data and to increase explainability, we present a modification of the widely used explanation method layer-wise relevance propagation. Our approach enforces sparsity directly by pruning the relevance propagation for the different layers. Thereby, we achieve sparser relevance attributions for the input features as well as for the intermediate layers. As the relevance propagation is input-specific, we aim to prune the relevance propagation rather than the underlying model architecture. This allows to prune different neurons for different inputs and hence, might be more appropriate to the local nature of explanation methods. To demonstrate the efficacy of our method, we evaluate it on two types of data: images and genome sequences. We show that our modification indeed leads to noise reduction and concentrates relevance on the most important features compared to the baseline.

Hartwig Anzt, Felix Bach, Stephan Druskat et al.

Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.