Harnessing Deep Learning to Analyze Cryptic Morphological Variability of Marchantia polymorpha

Characterizing phenotypes is a fundamental aspect of biological sciences, although it can be challenging due to various factors. For instance, the liverwort Marchantia polymorpha is a model system for plant biology and exhibits morphological variability, making it difficult to identify and quantify distinct phenotypic features using objective measures. To address this issue, we utilized a deep-learning-based image classifier that can handle plant images directly without manual extraction of phenotypic features and analyzed pictures of M. polymorpha. This dioicous plant species exhibits morphological differences between male and female wild accessions at an early stage of gemmaling growth, although it remains elusive whether the differences are attributable to sex chromosomes. To isolate the effects of sex chromosomes from autosomal polymorphisms, we established a male and female set of recombinant inbred lines (RILs) from a set of male and female wild accessions. We then trained deep learning models to classify the sexes of the RILs and the wild accessions. Our results showed that the trained classifiers accurately classified male and female gemmalings of wild accessions in the first week of growth, confirming the intuition of researchers in a reproducible and objective manner. In contrast, the RILs were less distinguishable, indicating that the differences between the parental wild accessions arose from autosomal variations. Furthermore, we validated our trained models by an 'eXplainable AI' technique that highlights image regions relevant to the classification. Our findings demonstrate that the classifier-based approach provides a powerful tool for analyzing plant species that lack standardized phenotyping metrics.

Learning where to look for COVID-19 growth: Multivariate analysis of COVID-19 cases over time using explainable convolution-LSTM

Determinant factors which contribute to the prediction should take into account multivariate analysis for capturing coarse-to-fine contextual information. From the preliminary descriptive analysis, it shows that environmental factor such as UV (ultraviolet) is one of the essential factors that should be considered to observe the COVID-19 epidemic drivers. Moreover, there are education, government, morphological, health, economic, and behavioral factors contributing to the growth of COVID-19. Besides descriptive analysis, in this research, multivariate analysis is considered to provide comprehensive explanations about factors contributing to pandemic dynamics. To achieve rich explanations, visual attribution of explainable Convolution-LSTM is utilized to see high contributing factors responsible for the growth of daily COVID-19 cases. Our model consists of 1 D CNN in the first layer to capture local relationships among variables followed by LSTM layers to capture local dependencies over time. It produces the lowest prediction errors compared to the other existing models. This permits us to employ gradient-based visual attribution for generating saliency maps for each time dimension and variable. These are then used for explaining which variables throughout which period of the interval is contributing for a given time-series prediction, likewise as explaining that during that time intervals were the joint contribution of most vital variables for that prediction. The explanations are useful for stakeholders to make decisions during and post pandemics. The explainable Convolution-LSTMcode is available here: https://github.com/cbasemaster/time-series-attribution.