Skip to content

[1/6] Add inhibitory_nts, excluded_nts, lambda_max, syn_weight_measure as kwargs#5

Open
alexanderbates wants to merge 1 commit intoDrugowitschLab:mainfrom
alexanderbates:pr1-params-and-signed-fix
Open

[1/6] Add inhibitory_nts, excluded_nts, lambda_max, syn_weight_measure as kwargs#5
alexanderbates wants to merge 1 commit intoDrugowitschLab:mainfrom
alexanderbates:pr1-params-and-signed-fix

Conversation

@alexanderbates
Copy link
Copy Markdown

Surface inhibitory_nts, excluded_nts, lambda_max, syn_weight_measure as kwargs

Replaces the hardcoded NEG_NEUROTRANSMITTERS module constant with two
explicit constructor arguments so that the library no longer pre-empts
the user's neurotransmitter sign assignment:

  • inhibitory_nts: pre-neuron top_nt values to negate when signed=True
    (required when signed=True; raises ValueError otherwise).
  • excluded_nts: pre-neuron top_nt values to drop entirely from W,
    independent of signed=True/False. Useful for transmitter classes
    whose net sign at a given target depends on the receptor mix and so
    cannot be assigned a single sign safely.

Adds lambda_max as a constructor argument (default 0.99 for backwards
compatibility). _normalize_W now always rescales to lambda_max exactly
rather than only capping when the natural eigenvalue exceeds it, so the
parameter is a true control knob over leading-mode amplification rather
than just a stability ceiling. The amplification of the leading mode in
(I - W_rescaled)^-1 is 1 / (1 - lambda_max), so 0.99 gives ~100x and
0.5 gives ~2x.

Surfaces syn_weight_measure ('count' or 'norm') as a constructor
argument and changes the default from 'norm' to 'count'. Fixes a
pre-existing bug in _create_sparse_W: the signed=True path negated the
'count' column unconditionally, but the matrix was populated from the
column named by syn_weight_measure (default 'norm'), so the signed flag
silently produced the same matrix as signed=False. The negation now
applies to the column actually consumed. An inline comment notes that
flipping signs on 'norm' breaks the column-sums-to-1 interpretation, so
'count' is the more natural choice in signed mode.

Sign preservation: _build_influence_dataframe now keeps the real part
of the steady-state vector in signed mode rather than always taking the
magnitude, so net-inhibited targets carry a negative score.

Validates lambda_max in (0, 1) and syn_weight_measure in {'count',
'norm'}. When signed=True or excluded_nts is set, the SQLite meta
table must include a 'top_nt' column or _create_sparse_W raises.

…as kwargs

Replaces the hardcoded NEG_NEUROTRANSMITTERS module constant with two
explicit constructor arguments so that the library no longer pre-empts
the user's neurotransmitter sign assignment:

- inhibitory_nts: pre-neuron top_nt values to negate when signed=True
  (required when signed=True; raises ValueError otherwise).
- excluded_nts: pre-neuron top_nt values to drop entirely from W,
  independent of signed=True/False. Useful for transmitter classes
  whose net sign at a given target depends on the receptor mix and so
  cannot be assigned a single sign safely.

Adds lambda_max as a constructor argument (default 0.99 for backwards
compatibility). _normalize_W now always rescales to lambda_max exactly
rather than only capping when the natural eigenvalue exceeds it, so the
parameter is a true control knob over leading-mode amplification rather
than just a stability ceiling. The amplification of the leading mode in
(I - W_rescaled)^-1 is 1 / (1 - lambda_max), so 0.99 gives ~100x and
0.5 gives ~2x.

Surfaces syn_weight_measure ('count' or 'norm') as a constructor
argument and changes the default from 'norm' to 'count'. Fixes a
pre-existing bug in _create_sparse_W: the signed=True path negated the
'count' column unconditionally, but the matrix was populated from the
column named by syn_weight_measure (default 'norm'), so the signed flag
silently produced the same matrix as signed=False. The negation now
applies to the column actually consumed. An inline comment notes that
flipping signs on 'norm' breaks the column-sums-to-1 interpretation, so
'count' is the more natural choice in signed mode.

Sign preservation: _build_influence_dataframe now keeps the real part
of the steady-state vector in signed mode rather than always taking the
magnitude, so net-inhibited targets carry a negative score.

Validates lambda_max in (0, 1) and syn_weight_measure in {'count',
'norm'}. When signed=True or excluded_nts is set, the SQLite meta
table must include a 'top_nt' column or _create_sparse_W raises.

lambda_max is the target largest real eigenvalue of the rescaled
W after normalisation; W is scaled in place by
lambda_max / lambda_max(W) so that lambda_max of the rescaled W
Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I would write instead: lambda_max / max(eigenvalue(W))

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants