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Tree-based machine learning performed in-memory with memristive analog CAM.

ABSTRACT: Tree-based machine learning techniques, such as Decision Trees and Random Forests, are top performers in several domains as they do well with limited training datasets and offer improved interpretability compared to Deep Neural Networks (DNN). However, these models are difficult to optimize for fast inference at scale without accuracy loss in von Neumann architectures due to non-uniform memory access patterns. Recently, we proposed a novel analog content addressable memory (CAM) based on emerging memristor devices for fast look-up table operations. Here, we propose for the first time to use the analog CAM as an in-memory computational primitive to accelerate tree-based model inference. We demonstrate an efficient mapping algorithm leveraging the new analog CAM capabilities such that each root to leaf path of a Decision Tree is programmed into a row. This new in-memory compute concept for enables few-cycle model inference, dramatically increasing 10³ × the throughput over conventional approaches.

SUBMITTER: Pedretti G

PROVIDER: S-EPMC8490381 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.

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Tree-based machine learning performed in-memory with memristive analog CAM.

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