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Copy file name to clipboardExpand all lines: src/metrics/downstream/config.vsh.yaml
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@@ -5,7 +5,7 @@ name: downstream
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info:
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metrics:
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- name: clustering_ari
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label: ARI
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label: clustering_ari
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summary: Adjusted rand index (ARI) measures the similarity between two clusters in real and simulated datasets.
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description: |
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Adjusted Rand Index used in spatial clustering to measure the similarity between two data clusterings, adjusted for chance.
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max: +Inf
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maximize: true
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- name: clustering_nmi
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label: NMI
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label: clustering_nmi
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summary: Normalized mutual information (NMI) measures of the mutual dependence between the real and simulated spatial clusters.
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description: |
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Normalized Mutual Information used in spatial clustering to measure the agreement between two different clusterings, scaled to [0, 1].
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max: 1
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maximize: true
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- name: svg_recall
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label: recall
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label: svg_recall
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summary: Recall measures the proportion of real SVG correctly identified in the simulated dataset.
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description: |
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Recall used in identifying spatial variable genes, measuring the true positive rate.
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max: 1
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maximize: true
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- name: svg_precision
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label: precision
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label: svg_precision
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summary: Precision measures the proportion of correctly identified items in simulated datasets.
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description: |
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Precision used in identifying spatial variable genes, measuring the accuracy of positive predictions.
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max: 1
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maximize: true
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- name: ctdeconvolute_rmse
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label: RMSE
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label: ctdeconvolute_rmse
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summary: Root Mean Square deviation is calculated between the true and predicted proportion of per cell type.
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description: |
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Root Mean Squared Error used in cell type deconvolution to measure the difference between observed and predicted values.
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max: +Inf
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maximize: false
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- name: ctdeconcolute_jsd
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label: JSD
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label: ctdeconcolute_jsd
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summary: Jensen-Shannon divergence (JSD) is calculated between the true and predicted proportion per cell type in all spots.
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description: |
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Jensen-Shannon Divergence used in cell type deconvolution to measure the similarity between two probability distributions.
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max: 1
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maximize: false
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- name: crosscor_mantel
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label: mantel_stat
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label: crosscor_mantel
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summary: Mantel statistic is the test statistic for the Mantel test, which is a correlation coefficient calculated between bivariate Moran’s I of real dataset and that of in simulation dataset.
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description: |
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Mantel statistic used in spatial cross-correlation to test the correlation between two distance matrices.
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max: 1
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maximize: true
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- name: crosscor_cosine
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label: cosine
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label: crosscor_cosine
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summary: Cosine similarity measures similarity between bivariate Moran’s I of real dataset and that of in simulation dataset.
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description: |
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Cosine similarity used in spatial cross-correlation to measure the cosine of the angle between two non-zero vectors.
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