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Species determination using AI machine-learning algorithms: Hebeloma as a case study.

ABSTRACT: The genus Hebeloma is renowned as difficult when it comes to species determination. Historically, many dichotomous keys have been published and used with varying success rate. Over the last 20 years the authors have built a database of Hebeloma collections containing not only metadata but also parametrized morphological descriptions, where for about a third of the cases micromorphological characters have been analysed and are included, as well as DNA sequences for almost every collection. The database now has about 9000 collections including nearly every type collection worldwide and represents over 120 different taxa. Almost every collection has been analysed and identified to species using a combination of the available molecular and morphological data in addition to locality and habitat information. Based on these data an Artificial Intelligence (AI) machine-learning species identifier has been developed that takes as input locality data and a small number of the morphological parameters. Using a random test set of more than 600 collections from the database, not utilized within the set of collections used to train the identifier, the species identifier was able to identify 77% correctly with its highest probabilistic match, 96% within its three most likely determinations and over 99% of collections within its five most likely determinations.

SUBMITTER: Bartlett P

PROVIDER: S-EPMC9245212 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Background:Epilepsy is a disorder that can manifest as abnormalities in neurological or physical function. Stress cardiomyopathy is closely associated with neurological stimulation. However, the mechanisms underlying the interrelationship between epilepsy and stress cardiomyopathy are unclear. This paper aims to explore the genetic features and potential molecular mechanisms shared in epilepsy and stress cardiomyopathy. Methods:By analyzing the epilepsy dataset and stress cardiomyopathy dataset separately, the intersection of the two disease co-expressed differential genes is obtained, the co-expressed differential genes reveal the biological functions, the network is constructed, and the core modules are identified to reveal the interaction mechanism, the co-expressed genes with diagnostic validity are screened by machine learning algorithms, and the co-expressed genes are validated in parallel on the epilepsy single-cell data and the stress cardiomyopathy rat model. Results: Epilepsy causes stress cardiomyopathy, and its key pathways are Complement and coagulation cascades, HIF-1 signaling pathway, its key co-expressed genes include SPOCK2, CTSZ, HLA-DMB, ALDOA, SFRP1, ERBB3.The key immune cell subpopulations localized by single-cell data are the T_cells subgroup, Microglia subgroup, Macrophage subgroup, Astrocyte subgroup, and Oligodendrocytes subgroup. Conclusion: We believe epilepsy causing stress cardiomyopathy results from a multi-gene, multi-pathway combination. We identified the core co-expressed genes (SPOCK2, CTSZ, HLA-DMB, ALDOA, SFRP1, ERBB3) and the pathways that function in them (Complement and coagulation cascades, HIF-1 signaling pathway,JAK-STAT signaling pathway), and finally localized their key cellular subgroups(T_cells subgroup, Microglia subgroup, Macrophage subgroup, Astrocyte subgroup,and Oligodendrocytes subgroup). Also, combining cell subpopulations with hypercoagulability as well as sympathetic excitation further narrowed the cell subpopulations of related functions.

Project description:Dry days at varied scale are an important topic in climate discussions. Prolonged dry days define a dry period. Dry days with a specific rainfall threshold may visualize a climate scenario of a locality. The variation of monthly dry days from station to station could be correlated with several climatic factors. This study suggests a novel approach for predicting monthly dry days (MDD) of six target stations using different machine learning (ML) algorithms in Bangladesh. Several rainfall thresholds were used to prepare the datasets of monthly dry days (MDD) and monthly wet days (MWD). A group of ML algorithms, like Bagged Trees (BT), Exponential Gaussian Process Regression (EGPR), Matern Gaussian Process Regression (MGPR), Linear Support Vector Machine (LSVM), Fine Trees (FT) and Linear Regression (LR) were evaluated on building a competitive prediction model of MDD. In validation of the study, EGPR-based models were able to better capture the monthly dry days (MDD) over Bangladesh compared to those by MGPR, LSVM, BT, LR and FT-based models. When MDD were the predictors for all six target stations, EGPR produced highest mean R2 of 0.91 (min. 0.89 and max. 0.92) with a least mean RMSE of 2.14 (min. 1.78 and max. 2.69) compared to other models. An explicit evaluation of the ML algorithms using one-year lead time approach demonstrated that BT and EGPR were the most result-oriented algorithms (R2 = 0.78 for both models). However, having a least RMSE, EGPR was chosen as the best model in one year lead time. The dataset of monthly dry-wet days was the best predictor in the lead-time approach. In addition, sensitivity analysis demonstrated sensitivity of each station on the prediction of MDD of target stations. Monte Carlo simulation was introduced to assess the robustness of the developed models. EGPR model declared its robustness up to certain limit of randomness on the testing data. The output of this study can be referred to the agricultural sector to mitigate the impacts of dry spells on agriculture.

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Species determination using AI machine-learning algorithms: Hebeloma as a case study.

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