2021-11-18 • Constant input spikes
Contents
2021-11-18 • Constant input spikes¶
But vary tradeoff between number of inputs and each input’s spike rate.
Prelude¶
from voltage_to_wiring_sim.notebook_init import *
Preloading: numpy, numba, matplotlib.pyplot, seaborn.
Importing from submodules … ✔
Imported `np`, `mpl`, `plt`, `sns`, `pd`
Imported codebase (`voltage_to_wiring_sim`) as `v`
Imported `*` from `v.support.units`
Setup autoreload
v.print_reproducibility_info()
This cell was last run by lpxtf3 on DUIP74576 on Thu 18 Nov 2021, at 18:48 (UTC+0000).
Last git commit (Thu 18 Nov 2021, 17:05).
Uncommited changes to 3 files.
Calculate¶
from voltage_to_wiring_sim.experiments.N_to_1_IE import Params, simulate_and_test_connections, eval_performance
base_params = Params()
v.pprint(base_params)
Params
------
sim_duration = 600
timestep = 0.0001
τ_syn = 0.007
neuron_params = {'C': 1e-10, 'a': 30.0, 'b': -2e-09, 'c': -0.05, ...}
imaging_spike_SNR = 20
window_duration = 0.1
num_spike_trains = 30
p_inhibitory = 0.2
p_connected = 0.7
spike_rate = 20
Δg_syn_exc = 4E-10
Δg_syn_inh = 1.6E-09
v_syn_exc = 0
v_syn_inh = -0.065
rng_seed = 0
@v.cache_to_disk(directory="2021-11-18__constant_input_spikes")
def sim_test_eval(params: Params):
sim_data, _, test_summaries = simulate_and_test_connections(params)
evalu_p_0_05, _, AUC, AUC_exc, AUC_inh = eval_performance(sim_data, test_summaries)
output_spike_rate = sim_data.izh_output.spike_times.size / params.sim_duration
return (output_spike_rate,
evalu_p_0_05.TPR_exc, evalu_p_0_05.TPR_inh, evalu_p_0_05.FPR,
AUC, AUC_exc, AUC_inh)
from dataclasses import replace
from itertools import product
spike_rates = np.array([0.1, 1, 10, 20]); # of one input spike train, in Hz
def get_N(spike_rate):
return round(30 * 20 / spike_rate)
Ns = np.vectorize(get_N)(spike_rates)
array([6000, 600, 60, 30])
seeds = [0];
# seeds = [0, 1, 2];
# seeds = [0, 1, 2, 3, 4, 5];
# seeds = np.arange(20);
f = sim_test_eval
args = [replace(base_params,
spike_rate=rate,
num_spike_trains=get_N(rate),
rng_seed=seed,
)
for (rate, seed) in product(spike_rates, seeds)];
%%time
results = v.run_in_parallel(f, args);
---------------------------------------------------------------------------
_RemoteTraceback Traceback (most recent call last)
_RemoteTraceback:
"""
Traceback (most recent call last):
File "C:\miniforge3\lib\site-packages\joblib\externals\loky\process_executor.py", line 431, in _process_worker
r = call_item()
File "C:\miniforge3\lib\site-packages\joblib\externals\loky\process_executor.py", line 285, in __call__
return self.fn(*self.args, **self.kwargs)
File "C:\miniforge3\lib\site-packages\joblib\_parallel_backends.py", line 595, in __call__
return self.func(*args, **kwargs)
File "C:\miniforge3\lib\site-packages\joblib\parallel.py", line 262, in __call__
return [func(*args, **kwargs)
File "C:\miniforge3\lib\site-packages\joblib\parallel.py", line 262, in <listcomp>
return [func(*args, **kwargs)
File "C:\miniforge3\lib\site-packages\joblib\memory.py", line 591, in __call__
return self._cached_call(args, kwargs)[0]
File "C:\miniforge3\lib\site-packages\joblib\memory.py", line 534, in _cached_call
out, metadata = self.call(*args, **kwargs)
File "C:\miniforge3\lib\site-packages\joblib\memory.py", line 761, in call
output = self.func(*args, **kwargs)
File "C:\Users\lpxtf3\AppData\Local\Temp/ipykernel_57212/1966810356.py", line 4, in sim_test_eval
File "c:\users\lpxtf3\onedrive\phd\voltage-to-wiring-sim\codebase\voltage_to_wiring_sim\experiments\N_to_1_IE.py", line 155, in simulate_and_test_connections
sim_data = simulate(p)
File "c:\users\lpxtf3\onedrive\phd\voltage-to-wiring-sim\codebase\voltage_to_wiring_sim\experiments\N_to_1_IE.py", line 94, in simulate
g_syn = calc_synaptic_conductance(
File "c:\users\lpxtf3\onedrive\phd\voltage-to-wiring-sim\codebase\voltage_to_wiring_sim\sim\synapses.py", line 24, in calc_synaptic_conductance
g_syn = np.empty(num_timesteps) * nS
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 45.8 MiB for an array with shape (6000000,) and data type float64
"""
The above exception was the direct cause of the following exception:
MemoryError Traceback (most recent call last)
<timed exec> in <module>
c:\users\lpxtf3\onedrive\phd\voltage-to-wiring-sim\codebase\voltage_to_wiring_sim\support\high_performance.py in run_in_parallel(f, args)
62 def run_in_parallel(f, args):
63 """ Output printing is not done in notebook, but in jupyter terminal """
---> 64 return runner(joblib.delayed(f)(arg) for arg in args)
C:\miniforge3\lib\site-packages\joblib\parallel.py in __call__(self, iterable)
1052
1053 with self._backend.retrieval_context():
-> 1054 self.retrieve()
1055 # Make sure that we get a last message telling us we are done
1056 elapsed_time = time.time() - self._start_time
C:\miniforge3\lib\site-packages\joblib\parallel.py in retrieve(self)
931 try:
932 if getattr(self._backend, 'supports_timeout', False):
--> 933 self._output.extend(job.get(timeout=self.timeout))
934 else:
935 self._output.extend(job.get())
C:\miniforge3\lib\site-packages\joblib\_parallel_backends.py in wrap_future_result(future, timeout)
540 AsyncResults.get from multiprocessing."""
541 try:
--> 542 return future.result(timeout=timeout)
543 except CfTimeoutError as e:
544 raise TimeoutError from e
C:\miniforge3\lib\concurrent\futures\_base.py in result(self, timeout)
443 raise CancelledError()
444 elif self._state == FINISHED:
--> 445 return self.__get_result()
446 else:
447 raise TimeoutError()
C:\miniforge3\lib\concurrent\futures\_base.py in __get_result(self)
388 if self._exception:
389 try:
--> 390 raise self._exception
391 finally:
392 # Break a reference cycle with the exception in self._exception
MemoryError: Unable to allocate 45.8 MiB for an array with shape (6000000,) and data type float64
num_samples = 600 * 1000 * 10
num_arrays = 6000
byte_per_sample = 64 / 8
mem_needed_for_gsyns = num_samples * num_arrays * byte_per_sample / 1E9 # GB
288
M = np.reshape(results, (len(spike_rates), len(seeds), -1))
(output_spike_rate,
TPR_exc, TPR_inh, FPR,
AUC, AUC_exc, AUC_inh) = (M[:,:,i] for i in range(M.shape[-1]))
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_57212/3201251934.py in <module>
----> 1 M = np.reshape(results, (len(spike_rates), len(seeds), -1))
2
3 (output_spike_rate,
4 TPR_exc, TPR_inh, FPR,
5 AUC, AUC_exc, AUC_inh) = (M[:,:,i] for i in range(M.shape[-1]))
NameError: name 'results' is not defined
Plot¶
def plot_dots_and_mean(data, ax, x, c="0.2", label=None, ms=6, lw=5):
ax.plot(x, data, "o", alpha=0.3, c=c, ms=ms)
ax.plot(x, np.mean(data, axis=-1), "-", c=c, label=label, lw=lw)
smaller = dict(ms=4, lw=3);
def make_inv_ratio_ax():
fig, ax = plt.subplots()
ax.set_xscale('log')
ax.set_xticks(spike_rates)
ax.set_xticklabels(f"{r:g}" for r in spike_rates)
ax.set_xlabel("Spike rate per input (Hz)$")
# https://matplotlib.org/stable/gallery/subplots_axes_and_figures/secondary_axis.html
def one_over(x):
x = np.array(x).astype(float)
near_zero = np.isclose(x, 0)
x[near_zero] = np.inf
x[~near_zero] = 1 / x[~near_zero]
return x
sax = ax.secondary_xaxis("top", functions=(one_over, one_over))
sax.set_xticks(Ns)
sax.set_xticks([], minor=True)
sax.set_xticklabels(f"{r:.3g}" for r in Ns)
sax.set_xlabel("Number of inputs$", labelpad=8)
return fig, ax
plot = partial(plot_dots_and_mean, x=spike_rates);
fig, ax = make_inv_ratio_ax()
plot(output_spike_rate, ax)
ax.set_ylabel("Output spike rate (Hz)");
fig, ax = make_inv_ratio_ax()
plot(AUC_exc, ax, c=v.color_exc, label="Excitatory conn.")
plot(AUC_inh, ax, c=v.color_inh, label="Inhibitory conn.", **smaller)
ax.set_ylabel("Area under ROC curve")
ax.legend();
fig, ax = make_inv_ratio_ax()
plot(TPR_exc, ax, c=v.color_exc, label="Excitatory conn.")
plot(TPR_inh, ax, c=v.color_inh, label="Inhibitory conn.", **smaller)
plot(FPR, ax, c=v.color_unconn, label="Non-connections")
ax.set_ylabel("Fraction detected as connection")
ax.legend();
Inspect signals¶
sim_and_test = v.cache_to_disk(simulate_and_test_connections);
Reproducibility¶
v.print_reproducibility_info(verbose=True)
This cell was last run by lpxtf3 on DUIP74576
on Thu 18 Nov 2021, at 16:55 (UTC+0000).
Last git commit (Fri 12 Nov 2021, 00:23).
Uncommited changes to:
M ReadMe.md
M codebase/voltage_to_wiring_sim/__init__.py
M codebase/voltage_to_wiring_sim/experiments/N_to_1.py
M codebase/voltage_to_wiring_sim/support/__init__.py
AM codebase/voltage_to_wiring_sim/support/high_performance.py
M codebase/voltage_to_wiring_sim/support/misc.py
M notebooks/2021-01-02__full_network_sim_tryout.ipynb
M notebooks/2021-11-11__vary_both_inh_strength_and_proportion.ipynb
M website/thesis/references.bib
Platform:
Windows-10
CPython 3.9.6 (C:\miniforge3\python.exe)
Intel(R) Xeon(R) W-2123 CPU @ 3.60GHz
Dependencies of voltage_to_wiring_sim and their installed versions:
numpy 1.21.1
matplotlib 3.4.2
numba 0.53.1
joblib 1.0.1
seaborn 0.11.1
scipy 1.7.0
preload 2.2
nptyping 1.4.2
Full conda list:
# packages in environment at C:\miniforge3:
#
# Name Version Build Channel
argon2-cffi 20.1.0 py39hb82d6ee_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 21.2.0 pyhd8ed1ab_0 conda-forge
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backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
black 21.9b0 pyhd8ed1ab_1 conda-forge
bleach 3.3.1 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py39hb82d6ee_1001 conda-forge
ca-certificates 2021.10.8 h5b45459_0 conda-forge
certifi 2021.10.8 py39hcbf5309_1 conda-forge
cffi 1.14.6 py39h0878f49_0 conda-forge
chardet 4.0.0 py39hcbf5309_1 conda-forge
charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge
click 7.1.2 pypi_0 pypi
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colorful 0.5.4 pypi_0 pypi
conda 4.10.3 py39hcbf5309_2 conda-forge
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