High-stakes applications require AI-generated models to be interpretable. Current algorithms for the synthesis of potentially interpretable models rely on objectives or regularization terms that represent interpretability only coarsely (e.g., model size) and are not designed for a specific user. Yet, interpretability is intrinsically subjective. In this paper, we propose an approach for the synthesis of models that are tailored to the user by enabling the user to steer the model synthesis process according to her or his preferences. We use a bi-objective evolutionary algorithm to synthesize models with trade-offs between accuracy and a user-specific notion of interpretability. The latter is estimated by a neural network that is trained concurrently to the evolution using the feedback of the user, which is collected using uncertainty-based active learning. To maximize usability, the user is only asked to tell, given two models at the time, which one is less complex. With experiments on two real-world datasets involving 61 participants, we find that our approach is capable of learning estimations of interpretability that can be very different for different users. Moreover, the users tend to prefer models found using the proposed approach over models found using non-personalized interpretability indices.

Model learning with personalized interpretability estimation (ML-PIE)

Abstract Background There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which constrain their deployment in biomedical settings. Methods This systematic review discusses DL models used to support inference in cancer biology with a particular emphasis on multi-omics analysis. It focuses on how existing models address the need for better dialogue with prior knowledge, biological plausibility and interpretability, fundamental properties in the biomedical domain. For this, we retrieved and analyzed 42 studies focusing on emerging architectural and methodological advances, the encoding of biological domain knowledge and the integration of explainability methods. Results We discuss the recent evolutionary arch of DL models in the direction of integrating prior biological relational and network knowledge to support better generalisation (e.g. pathways or Protein-Protein-Interaction networks) and interpretability. This represents a fundamental functional shift towards models which can integrate mechanistic and statistical inference aspects. We introduce a concept of bio-centric interpretability and according to its taxonomy, we discuss representational methodologies for the integration of domain prior knowledge in such models. Conclusions The paper provides a critical outlook into contemporary methods for explainability and interpretability used in DL for cancer. The analysis points in the direction of a convergence between encoding prior knowledge and improved interpretability. We introduce bio-centric interpretability which is an important step towards formalisation of biological interpretability of DL models and developing methods that are less problem- or application-specific. 

/pdf/a-systematic-review-of-biologically-informed-deep-learning-3815g8z9.pdf

A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data

As one of the most popular machine learning models today, graph neural networks (GNNs) have attracted intense interest recently, and so does their explainability. Users are increasingly interested in a better understanding of GNN models and their outcomes. Unfortunately, today's evaluation frameworks for GNN explainability often rely on few inadequate synthetic datasets, leading to conclusions of limited scope due to a lack of complexity in the problem instances. As GNN models are deployed to more mission-critical applications, we are in dire need for a common evaluation protocol of explainability methods of GNNs. In this paper, we propose, to our best knowledge, the first systematic evaluation framework for GNN explainability, considering explainability on three different"user needs". We propose a unique metric that combines the fidelity measures and classifies explanations based on their quality of being sufficient or necessary. We scope ourselves to node classification tasks and compare the most representative techniques in the field of input-level explainability for GNNs. For the inadequate but widely used synthetic benchmarks, surprisingly shallow techniques such as personalized PageRank have the best performance for a minimum computation time. But when the graph structure is more complex and nodes have meaningful features, gradient-based methods are the best according to our evaluation criteria. However, none dominates the others on all evaluation dimensions and there is always a trade-off. We further apply our evaluation protocol in a case study for frauds explanation on eBay transaction graphs to reflect the production environment.

GraphFramEx: Towards Systematic Evaluation of Explainability Methods for Graph Neural Networks

Analysis of PEM and AEM Electrolysis by Neural Network Pattern Recognition, Association Rule Mining and LIME

Abstract Background There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which constrain their deployment in biomedical settings. Methods This systematic review discusses DL models used to support inference in cancer biology with a particular emphasis on multi-omics analysis. It focuses on how existing models address the need for better dialogue with prior knowledge, biological plausibility and interpretability, fundamental properties in the biomedical domain. For this, we retrieved and analyzed 42 studies focusing on emerging architectural and methodological advances, the encoding of biological domain knowledge and the integration of explainability methods. Results We discuss the recent evolutionary arch of DL models in the direction of integrating prior biological relational and network knowledge to support better generalisation (e.g. pathways or Protein-Protein-Interaction networks) and interpretability. This represents a fundamental functional shift towards models which can integrate mechanistic and statistical inference aspects. We introduce a concept of bio-centric interpretability and according to its taxonomy, we discuss representational methodologies for the integration of domain prior knowledge in such models. Conclusions The paper provides a critical outlook into contemporary methods for explainability and interpretabiltiy used in DL for cancer. The analysis points in the direction of a convergence between encoding prior knowledge and improved interpretability. We introduce bio-centric interpretability which is an important step towards formalisation of biological interpretability of DL models and developing methods that are less problem- or application-specific. 

This working paper aims at providing a structured and accessible introduction to the topic of interpretable machine learning. We start with an overview of the research literature and we continue by analyzing selected methods to explain machine learning model outcomes. We apply these methods in two distinct case studies. The theory on machine learning interpretability is discussed together with the concepts of explanation, interpretation, and trust from philosophy and social sciences. We choose counterfactual explanations and Locally Interpretable Model-agnostic Explanations (LIME) as prominent examples of machine learning interpretability methods and we discuss their Python implementations in detail. We apply the chosen methods in two separate case studies; the first uses the Boston Housing dataset to classify census tracts in the Boston metropolitan area. The second case study is focused on the natural language processing and classification of Youtube comments. The results of the first case study show that the existing Python implementation of counterfactual explanations does not allow for controlling sparsity and feasibility of the explanations. Moreover, it does not properly handle datasets with categorical variables. The results of the second case study show that the understandability of LIME explanations depends, among others, on the structure of the text instance to be explained. Therefore, practitioners have to rely on domain knowledge to identify and share only the informative explanations. The above limitations have to be taken care of to ensure applicability of counterfactual explanations and LIME in real-world applications.

Explaining Interpretable Machine Learning: Theory, Methods and Applications

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Explaining Interpretable Machine Learning: Theory, Methods and Applications