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[*] docs/source_sink: simplify metric explanation
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alyst committed Jan 12, 2024
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## [Network Metrics](@id network_metrics)

It's is important to have a way to check the relevance of *HierarchicalHotNet* predictions.
It is important to have a way to check the relevance of *HierarchicalHotNet* predictions.
For example, one can [randomize the input data](@ref permweights) and show that, at some edge weight
threshold ``t_*``, *HHotNet* predictions based on the real data, ``H(\mathcal{D}_{\mathrm{real}}, t_*)``,
demnostrate significantly more order than the ones based on randomized data,
``H(\mathcal{D}_{\mathrm{perm}}^i, t_*)``, ``i=1,2,\ldots,N_{\mathrm{perm}}``.
If the "order" could be expressed as some metric ``m(H)``, then we can easily define
demnostrate significantly more "order" than the ones based on randomized data,
``H(\mathcal{D}_{\mathrm{perm}}, t_*)``.
If the "order" could be expressed as some metric ``m(H)``, then we can define
the ``p``-value for the hypothesis that ``H(\mathcal{D}_{\mathrm{real}}, t)`` is significantly
more "ordered" than expected by chance:
```math
p_m(H(\mathcal{D}_{\mathrm{real}}, t)) = P\big(M_{\mathrm{perm}}(t) \geq m(H(\mathcal{D}_{\mathrm{real}}, t)) \big),
p_m(H(\mathcal{D}_{\mathrm{real}}, t)) = P\big(m(H(\mathcal{D}_{\mathrm{perm}}, t_*)) \geq m(H(\mathcal{D}_{\mathrm{real}}, t)) \big).
```
where ``M_{\mathrm{perm}}(t)`` is a random variable derived from the empirical distribution
of ``m(H(\mathcal{D}_{\mathrm{perm}}^i, t))``, ``i = 1, 2, \ldots, N_{\mathrm{perm}}``.
The definition above was given for the case of ``m(H)`` growing with the increase of ``H`` "order".
If the metric ``m`` decreases as the "order" of ``H`` grows, ``P(M \geq m(H))`` should be changed
``p_m`` could be approximated by generating a family *HHotNet* prediction based on randomized data,
``H(\mathcal{D}_{\mathrm{perm}}^i, t))``, ``i = 1, 2, \ldots, N_{\mathrm{perm}}``.
The definition above was given for the metric ``m(H)`` that increases as ``H`` becomes more "ordered".
If the metric ``m(H)`` decreases as the "order" of ``H`` grows, ``P(M \geq m(H))`` should be changed
to ``P(M \leq m(H))``.

In [_M.A. Reyna et al_ (2018)](https://academic.oup.com/bioinformatics/article/34/17/i972/5093236),
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