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  1. Abstract Motivation

    Expanding our knowledge of small molecules beyond what is known in nature or designed in wet laboratories promises to significantly advance cheminformatics, drug discovery, biotechnology and material science. In silico molecular design remains challenging, primarily due to the complexity of the chemical space and the non-trivial relationship between chemical structures and biological properties. Deep generative models that learn directly from data are intriguing, but they have yet to demonstrate interpretability in the learned representation, so we can learn more about the relationship between the chemical and biological space. In this article, we advance research on disentangled representation learning for small molecule generation. We build on recent work by us and others on deep graph generative frameworks, which capture atomic interactions via a graph-based representation of a small molecule. The methodological novelty is how we leverage the concept of disentanglement in the graph variational autoencoder framework both to generate biologically relevant small molecules and to enhance model interpretability.

    Results

    Extensive qualitative and quantitative experimental evaluation in comparison with state-of-the-art models demonstrate the superiority of our disentanglement framework. We believe this work is an important step to address key challenges in small molecule generation with deep generative frameworks.

    Availability and implementation

    Training and generated data are made available at https://ieee-dataport.org/documents/dataset-disentangled-representation-learning-interpretable-molecule-generation. All code is made available at https://anonymous.4open.science/r/D-MolVAE-2799/.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
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  2. Free, publicly-accessible full text available September 28, 2024
  3. Improving the performance and explanations of ML algorithms is a priority for adoption by humans in the real world. In critical domains such as healthcare, such technology has significant potential to reduce the burden on humans and considerably reduce manual assessments by providing quality assistance at scale. In today‚Äôs data-driven world, artificial intelligence (AI) systems are still experiencing issues with bias, explainability, and human-like reasoning and interpretability. Causal AI is the technique that can reason and make human-like choices making it possible to go beyond narrow Machine learning-based techniques and can be integrated into human decision-making. It also offers intrinsic explainability, new domain adaptability, bias free predictions, and works with datasets of all sizes. In this tutorial of type lecture style, we detail how a richer representation of causality in AI systems using a knowledge graph (KG) based approach is needed for intervention and counterfactual reasoning (Figure 1), how do we get to model-based and domain explainability, how causal representations helps in web and health care. 
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