Comments (2)
Thanks for pointing it out. Can you provide a MCVE so that I can get started.
from msa.
import numpy as np
from msapy import msa
import matplotlib.pyplot as plt
import networkx as nx
from copy import deepcopy
import seaborn as sns
We need to simulate a system so these functions:
def event_maker(
n_units: int,
timesteps: int,
probability: float = 1,
rng: np.random.Generator = np.random.default_rng(seed=2023),
) -> np.ndarray:
if probability < 1:
input = rng.choice(
[0, 1], p=[1 - probability, probability], size=(n_units, timesteps)
)
input = input.astype(float)
else:
input = np.zeros((n_units, timesteps))
for node in range(n_units):
event_timepoints = rng.integers(0, timesteps, 1)
input[node, event_timepoints] += 1
return input
def identity(x):
return x
def simulate_dynamical_system_parallel(adjacency_matrix:np.ndarray,
input_matrix:np.ndarray,
coupling:float=1,
dt:float=0.001,
duration:int=10,
timeconstant:float=0.01,
function = identity,
)->np.ndarray:
N = input_matrix.shape[0]
T = np.arange(1, duration/dt + 1) # holds time steps
X = np.zeros((N, len(T)+1)) # holds variable x
dt = dt/timeconstant
for timepoint in range(len(T)):
for node in range(N):
if timepoint == 0:
X[node, timepoint] = input_matrix[node, timepoint]
else:
inputs = np.dot(coupling * adjacency_matrix[node, :], X[:, timepoint-1]) + input_matrix[node, timepoint]
X[node, timepoint] = (1 - dt) * X[node, timepoint-1] + dt * function(inputs)
return X
def lesion_simple_nodes(complements,
adjacency_matrix: np.ndarray,
index: int,
input: np.ndarray,
model = simulate_dynamical_system_parallel,
model_kwargs:dict={},
) -> np.ndarray:
lesioned_connectivity = deepcopy(adjacency_matrix)
for target in complements:
lesioned_connectivity[:, target] = 0.0
lesioned_connectivity[target, :] = 0.0
dynamics = model(adjacency_matrix = lesioned_connectivity,
input_matrix=input,
**model_kwargs)
lesioned_signal = dynamics[index]
return lesioned_signal
And then these parameters:
rng = np.random.default_rng(seed=2023)
chain = nx.to_numpy_array(nx.generators.path_graph(6,nx.DiGraph())).T
chain *= 0.9
timesteps = 100
example_input = event_maker(6,timesteps)
NOISE_STRENGTH = 0.05
DELTA = 0.01
TAU = 0.02
G = 0.74
DURATION = 1
model_params = {'dt':DELTA,'timeconstant':TAU,'coupling':G,'duration':DURATION}
After running the game you see the zeroth column went after 5 in pandas 1.5 and 2 but not 1.3.5.
lesion_params = {'adjacency_matrix': chain, 'input': example_input, 'model_kwargs': model_params}
ci_chain = msa.estimate_causal_influences(elements=list(range(len(chain))),
objective_function=lesion_simple_nodes,
objective_function_params=lesion_params,
n_permutations=128, n_cores=1)
from msa.
Related Issues (6)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from msa.