@prefix beam: <https://github.com/imallona/beam/owl/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

beam:accuracy a obo:STATO_0000415,
        owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Classification accuracy" ;
    rdfs:comment """Fraction of correctly classified instances. Defined as the number of
matches between predicted and true labels, divided by the total number
of instances.""" ;
    rdfs:seeAlso <https://github.com/huggingface/evaluate/tree/main/metrics/accuracy> ;
    owl:sameAs obo:STATO_0000415 .

beam:ari a obo:STATO_0000593,
        owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Adjusted Rand Index (Hubert-Arabie)" ;
    rdfs:comment """Corrected-for-chance similarity between two partitions of the same set of
elements. Defined as the Rand Index adjusted by its expected value under a
random model of partition pairs. Equals 1 for identical partitions and 0 for
random partitions; can be negative for worse-than-random agreement.""" ;
    owl:sameAs obo:STATO_0000593 .

beam:asw_batch a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Batch ASW (silhouette over batches)" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a batch-removal score. Measures degree to which batches mix within a cell type, from the batch silhouette width inverted so well-mixed batches score high. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:asw_label a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Cell-type ASW (silhouette over labels)" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a biological-conservation score. Measures how compactly and separately the cell-type labels form clusters in the integrated embedding, from the silhouette width rescaled to the unit interval. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:calibration_slope a obo:STATO_0000687,
        owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Calibration slope" ;
    rdfs:comment "Slope of a logistic recalibration model that regresses the observed binary outcome on the linear predictor (the log-odds) of a risk model. A value of 1 means the predicted risks are correctly scaled. A slope below 1 means the predictions are too extreme, the usual signature of an overfit model; a slope above 1 means they are too moderate. The slope is therefore a target_value metric: neither the highest nor the lowest value is best, the ideal is exactly 1. It is one of the standard calibration summaries for clinical risk-prediction models alongside the calibration intercept and the calibration plot." ;
    owl:sameAs obo:STATO_0000687 .

beam:cell_cycle_conservation a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Cell-cycle conservation" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a biological-conservation score. Measures conservation of the cell-cycle signal, from the variance explained by S and G2M cell-cycle scores before versus after integration. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:clisi a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Cell-type LISI (cLISI)" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a biological-conservation score. Measures cell-type label purity, from the inverse Simpson index of cell-type labels in local neighbourhoods, rescaled so pure neighbourhoods score high. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:co2 a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Carbon dioxide emissions per distance" ;
    rdfs:comment """Carbon dioxide emitted per kilometre travelled, in grams. A measured
quantity, lower is better, with a true zero for zero-emission modes such as
walking or cycling. Used as a domain-neutral performance metric in the
transportation example. Because several modes emit exactly zero, the card
recommends a rank normalization, which stays defined when a column carries
hard zeros, rather than a log rescale.""" ;
    rdfs:seeAlso obo:UO_0000021 .

beam:correlation a obo:STATO_0000201,
        owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Spatial-variability rank correlation" ;
    rdfs:comment "Spatial transcriptomics metric from the OpenProblems spatially variable genes task. Correlation between a method's ranking of spatially variable genes and a reference ranking; higher means closer agreement with the reference." ;
    rdfs:seeAlso <https://github.com/huggingface/evaluate/tree/main/metrics/spearmanr> ;
    owl:sameAs obo:STATO_0000201 .

beam:cost a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Monetary cost per distance" ;
    rdfs:comment """Monetary cost of travel per kilometre, in a generic currency unit. A measured
quantity, lower is better. One of the three metrics in the transportation
example, which exercises the registry and the MCDA pipeline outside
bioinformatics.""" .

beam:f1_score a obo:STATO_0000628,
        owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "F1 score" ;
    rdfs:comment """Harmonic mean of precision and recall. Used for binary classification or
per-class evaluation in multiclass settings. Equals 1 only when both
precision and recall are 1.""" ;
    rdfs:seeAlso <https://github.com/huggingface/evaluate/tree/main/metrics/f1> ;
    owl:sameAs obo:STATO_0000628 .

beam:graph_connectivity a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Graph connectivity" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a batch-removal score. Measures fraction of cells of a given label that remain in a single connected component of the integrated knn graph, averaged over labels. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:hvg_overlap a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Highly variable gene overlap" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a biological-conservation score. Measures mean per-batch overlap of the highly variable genes computed before versus after integration. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:ilisi a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Integration LISI (iLISI)" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a batch-removal score. Measures batch mixing, from the inverse Simpson index of batch labels in local neighbourhoods, rescaled to the unit interval. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:isolated_label_asw a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Isolated-label ASW" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a biological-conservation score. Measures silhouette width restricted to the most batch-isolated cell labels, measuring how well rare or isolated types separate. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:isolated_label_f1 a obo:STATO_0000628,
        owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Isolated-label F1" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a biological-conservation score. Measures best F1 of clustering the isolated labels against the rest over a clustering resolution sweep. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 ;
    owl:sameAs obo:STATO_0000628 .

beam:kbet a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "kBET (k-nearest-neighbour batch effect test)" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a batch-removal score. Measures local batch mixing, from the acceptance rate of the knn batch-effect test relative to the global batch composition. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0002631 .

beam:mase a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Mean Absolute Scaled Error" ;
    rdfs:comment """Mean absolute forecast error scaled by the in-sample mean absolute error of
the seasonal naive method on the same series. A value below 1 means the
forecast beats the in-sample seasonal naive baseline; a value above 1 means
it does not. Because the scaling uses the series' own history, MASE is
scale-free and comparable across series of different magnitudes, and it is
defined even when actual values are zero.""" ;
    rdfs:seeAlso <https://github.com/huggingface/evaluate/tree/main/metrics/mase> .

beam:nclust_deviation a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Cluster-count deviation from the truth" ;
    rdfs:comment "Deviation of the estimated number of clusters from the true number of clusters, as used in the Duo 2018 clustering benchmark (the nclust.vs.true column). It is the absolute difference between the number of clusters a method reports and the number of clusters in the reference partition. A value of 0 means the method recovered the correct cluster count; larger values mean it over- or under-clustered. This metric is sparsely populated in Duo 2018: 101 of the 168 method by data set cells are missing, because several methods do not report a fixed cluster count for every data set, so callers should expect many NaN entries and account for partial coverage when aggregating." .

beam:nmi a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Normalized mutual information" ;
    rdfs:comment """Mutual information between two partitions, normalized to [0, 1] using one
of several conventions (arithmetic mean of entropies, geometric mean, or
max). Equals 1 for identical partitions and 0 for independent partitions.
Unlike ARI, NMI is not chance-corrected.""" .

beam:pcr a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Principal component regression comparison" ;
    rdfs:comment "Single-cell data-integration metric from the scIB benchmark, a batch-removal score. Measures change in the variance attributable to batch, regressed on principal components, before versus after integration. scIB rescales it to the unit interval where higher is better." ;
    rdfs:seeAlso obo:OBI_0200104 .

beam:peak_memory a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Peak resident set size" ;
    rdfs:comment """Maximum resident set size of the process executing a method, in bytes.
Measured by the operating system or a monitoring tool wrapping the
process.""" ;
    rdfs:seeAlso obo:UO_0000233 .

beam:runtime a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Wall-clock runtime" ;
    rdfs:comment """Wall-clock seconds elapsed during the execution of a method on a given
input. A measured metric: the value comes from a timer surrounding the
method invocation, not from a comparison of outputs.""" ;
    rdfs:seeAlso obo:UO_0000010 .

beam:shannon_entropy_diff a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Shannon entropy difference of cluster sizes" ;
    rdfs:comment "Difference in the normalized Shannon entropy of the cluster size distribution between an estimated partition and the true partition. The normalized Shannon entropy of a partition measures how evenly elements are spread across clusters, scaled to [0, 1] by the log of the number of clusters so that a perfectly balanced partition reaches 1 and a fully concentrated one reaches 0. This metric is the absolute difference between the estimated partition's normalized entropy and the true partition's normalized entropy, as used in the Duo 2018 clustering benchmark (the s.norm.vs.true column). A value of 0 means the estimated clustering matches the truth in how evenly it distributes elements across clusters; larger values mean the estimated cluster size profile departs further from the truth." .

beam:silhouette a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Silhouette coefficient" ;
    rdfs:comment """Mean silhouette coefficient over all clustered instances. For each
instance, s = (b - a) / max(a, b), where a is the mean distance to
other instances in the same cluster and b is the mean distance to
instances in the nearest other cluster. Ranges over [-1, 1].""" .

beam:smape a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Symmetric Mean Absolute Percentage Error" ;
    rdfs:comment """Symmetric mean absolute percentage error between a point forecast and the
realized future values, in percent. Using the M4 competition definition,
each horizon step contributes 2 * |F - A| / (|F| + |A|), averaged over the
horizon and expressed as a percentage. The symmetric denominator bounds the
value in [0, 200], unlike the classic MAPE which is unbounded and undefined
when an actual value is zero.""" ;
    rdfs:seeAlso <https://github.com/huggingface/evaluate/tree/main/metrics/smape> .

beam:speed a owl:NamedIndividual,
        beam:Metric ;
    rdfs:label "Travel speed" ;
    rdfs:comment """Average travel speed in kilometres per hour. A measured quantity: the value
is distance covered divided by time taken, not a comparison of outputs. The
transportation example uses it, along with cost and co2, to run the registry
and the MCDA pipeline on a problem that has nothing to do with bioinformatics.""" ;
    rdfs:seeAlso obo:UO_0010008 .

beam:Metric a owl:Class ;
    rdfs:label "beam metric" .