Interpretability refers to the degree to which a human can understand and make sense of the decisions or predictions made by a machine learning model. As machine learning models become more complex, particularly with the rise of deep learning, there is an increasing need for interpretability to ensure transparency, accountability, and trust in the deployment of these models, especially in critical applications. Interpretability is essential not only for model developers and data scientists but also for end-users, regulators, and stakeholders who need to understand, trust, and validate the decisions made by machine learning models in real-world applications. Efforts to improve interpretability contribute to the responsible and ethical deployment of machine learning technologies.

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Towards Learning Disentangled Representations for Time Series

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Promising progress has been made toward learning efficient time series representations in recent years, but the learned representations often lack interpretability and do not encode semantic meanings by the complex interactions of many latent factors. Learning representations that disentangle these latent factors can bring semantic-rich representations of time series and further enhance interpretability. However, directly adopting the sequential models, such as Long Short-Term Memory Variational AutoEncoder (LSTM-VAE), would encounter a Kullback?Leibler (KL) vanishing problem: the LSTM decoder often generates sequential data without efficiently using latent representations, and the latent spaces sometimes could even be independent of the observation space. And traditional disentanglement methods may intensify the trend of KL vanishing along with the disentanglement process, because they tend to penalize the mutual information between the latent space and the observations. In this paper, we propose Disentangle Time-Series, a novel disentanglement enhancement framework for time series data. Our framework achieves multi-level disentanglement by covering both individual latent factors and group semantic segments. We propose augmenting the original VAE objective by decomposing the evidence lower-bound and extracting evidence linking factorial representations to disentanglement. Additionally, we introduce a mutual information maximization term between the observation space to the latent space to alleviate the KL vanishing problem while preserving the disentanglement property. Experimental results on five real-world IoT datasets demonstrate that the representations learned by DTS achieve superior performance in various tasks with better interpretability.

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DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays

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MotivationMapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods with limited training data. Moreover, past approaches have implemented enhancer discovery as a binary classification problem without accurate boundary detection, producing low-resolution annotations with superfluous regions and reducing the statistical power for downstream analyses (e.g. causal variant mapping and functional validations). Here, we addressed these challenges via a two-step model called Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays (DECODE). First, we employed direct enhancer-activity readouts from novel functional characterization assays, such as STARR-seq, to train a deep neural network for accurate cell-type-specific enhancer prediction. Second, to improve the annotation resolution, we implemented a weakly supervised object detection framework for enhancer localization with precise boundary detection (to a 10 bp resolution) using Gradient-weighted Class Activation Mapping.ResultsOur DECODE binary classifier outperformed a state-of-the-art enhancer prediction method by 24% in transgenic mouse validation. Furthermore, the object detection framework can condense enhancer annotations to only 13% of their original size, and these compact annotations have significantly higher conservation scores and genome-wide association study variant enrichments than the original predictions. Overall, DECODE is an effective tool for enhancer classification and precise localization.

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