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Add topographical placement and connectivity #12

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Add topographical placement and connectivity #12

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a9efd9f
Normalize weights
dhasegan Jul 27, 2021
7ef0bb4
Add topographical placement and connectivity
dhasegan Aug 5, 2021
a773649
Merge branch 'master' into d/normalize
dhasegan Aug 5, 2021
2cdfbea
Merge branch 'd/normalize' into d/topographic
dhasegan Aug 5, 2021
d015097
Small changes
dhasegan Aug 5, 2021
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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -55,14 +55,14 @@ Evaluate the model before and after training:

Optional: Maybe evaluate in depth

for ((i=0;i<20;i+=2)); do
for ((i=1;i<2;i+=2)); do
echo "Evaluating at $i"
py neurosim/main.py eval $WDIR --resume_tidx=$i
done

Run all evaluation:

WDIR=results/20210713
WDIR=results/20210805
py neurosim/tools/evaluate.py frequency $WDIR --timestep 10000
py neurosim/tools/evaluate.py medians $WDIR
py neurosim/tools/evaluate.py rewards $WDIR
Expand Down
108 changes: 54 additions & 54 deletions config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@
"savemp4": 0,
"render": 0,
"observation_map": [
{"type": "rf_normal", "bins": 5, "mean": -0.00645789, "std": 0.06894682},
{"type": "rf_normal", "bins": 5, "mean": -0.03634136, "std": 0.53989509},
{"type": "rf_normal", "bins": 10, "mean": 0.00529333, "std": 0.09129902},
{"type": "rf_normal", "bins": 20, "mean": -0.00645789, "std": 1.0},
{"type": "rf_normal", "bins": 20, "mean": -0.03634136, "std": 0.53989509},
{"type": "rf_normal", "bins": 20, "mean": 0.00529333, "std": 0.09129902},
{"type": "rf_normal", "bins": 20, "mean": 0.04752025, "std": 0.82070579}
],
"episodes": 21,
Expand All @@ -24,9 +24,13 @@
"rewardsToKeep": 100,
"critic": {
"angv_bias": 0.2,
"total_gain": 5.0,
"max_reward": 2.0,
"posRewardBias": 2.0
"total_gain": 6.0,
"max_reward": 3.0,
"posRewardBias": 2.0,
"modulation": {
"type": "linear",
"steps": 25
}
},
"verbose": 0,
"stayStepLim": 0,
Expand All @@ -35,12 +39,13 @@
"ResumeSimFromFile": "...pkl"
},
"sim": {
"duration": 1000,
"duration": 2000,
"dt": 0.6,
"verbose": 0,
"recordStep": 1.0,
"recordStim": 0,
"recordWeightStepSize": 1000,
"normalizeStepSize": 2333,
"RLFakeUpRule": 0,
"RLFakeDownRule": 0,
"RLFakeStayRule": 0,
Expand Down Expand Up @@ -114,15 +119,43 @@
"I": 0.0
},
"allpops": {
"ES": 40,
"ES": 80,

"EA": 40,
"IA": 10,
"IAL": 10,

"EM": 40,
"IM": 10,
"IML": 10
"EM": 60,
"IM": 15,
"IML": 15
},
"out_pop_sort_tag": "x",
"topographic": {
"stimModES": {
"xnormRange": [0.4, 0.6],
"ynormRange": [0.0, 0.1]
},
"ES": {
"ynormRange": [0.1, 0.3]
},
"EA": {
"ynormRange": [0.35, 0.45]
},
"IA": {
"ynormRange": [0.50, 0.55]
},
"IAL": {
"ynormRange": [0.55, 0.60]
},
"EM": {
"ynormRange": [0.70, 0.90]
},
"IM": {
"ynormRange": [0.90, 0.95]
},
"IML": {
"ynormRange": [0.95, 1.0]
}
},
"inputPop": "ES",
"STDPconns": {
Expand Down Expand Up @@ -161,18 +194,18 @@
"IA":{"GA2": 2.25,"p": 0.2},
"IAL":{"GA2": 5.5,"p": 0.1}},
"EM":{
"EM":{"AM2": 0.01,"NM2": 0.001, "conv": 1},
"IM":{"AM2": 1.95,"NM2":0.0195, "conv": 8},
"IML":{"AM2": 0.98,"NM2":0.098, "conv": 8},
"EA":{"AM2": 0.5,"NM2": 0.01,"conv": 6}},
"EM":{"AM2": 0.01,"NM2": 0.001, "p": "0.2*exp(-dist_xnorm*3)"},
"IM":{"AM2": 1.95,"NM2":0.0195, "p": "0.4*(1.0-exp(-dist_xnorm*3))"},
"IML":{"AM2": 0.98,"NM2":0.098, "p": "0.4*(1.0-exp(-dist_xnorm*3))"},
"EA":{"AM2": 0.5,"NM2": 0.01,"conv": 4}},
"IM":{
"EM":{"GA": 9.0,"p": 0.4},
"IM":{"GA": 4.5,"p": 0.1},
"IML":{"GA": 4.5,"p": 0.2}},
"EM":{"GA": 9.0,"p": "0.5*exp(-dist_xnorm*3)"},
"IM":{"GA": 4.5,"p": "0.2*(1.0-exp(-dist_xnorm*3))"},
"IML":{"GA": 4.5,"p": "0.05*(1.0-exp(-dist_xnorm*3))"}},
"IML":{
"EM":{"GA2": 2.5,"p": 0.4},
"IM":{"GA2": 2.25,"p": 0.2},
"IML":{"GA2": 5.5,"p": 0.1}}
"EM":{"GA2": 2.5,"p": "0.5*exp(-dist_xnorm*3)"},
"IM":{"GA2": 2.25,"p": "0.2*(1.0-exp(-dist_xnorm*3))"},
"IML":{"GA2": 5.5,"p": "0.05*(1.0-exp(-dist_xnorm*3))"}}
},
"weightVar": 0.5,
"delays": {
Expand Down Expand Up @@ -241,38 +274,5 @@
"softthresh": 0,
"verbose": 0
}
},
"noise": {
"EMLEFT": {
"AM": {"w":0, "rate":0},
"NM": {"w":0, "rate":0},
"GA": {"w":1.875, "rate": 100},
"AM2": {"w": 3.938, "rate": 200},
"NM2": {"w": 0, "rate": 0},
"GA2": {"w": 1.875, "rate": 100}},
"EMRIGHT": {"AM": {"w":0, "rate":0},
"NM": {"w":0, "rate":0},
"GA": {"w":1.875, "rate": 100},
"AM2": {"w": 3.938, "rate": 200},
"NM2": {"w": 0, "rate": 0},
"GA2": {"w": 1.875, "rate": 100}},
"EA": {"AM": {"w":0, "rate":0},
"NM": {"w":0, "rate":0},
"GA": {"w":1.875, "rate": 100},
"AM2": {"w": 3.938, "rate": 200},
"NM2": {"w": 0, "rate": 0},
"GA2": {"w": 1.875, "rate": 100}},
"IA": {"AM": {"w":1.875, "rate": 100},
"NM": {"w":0, "rate":0},
"GA": {"w":0, "rate":0},
"AM2": {"w": 4.125, "rate": 200},
"NM2": {"w": 0, "rate": 0},
"GA2": {"w": 1.875, "rate": 100}},
"IAL": {"AM": {"w":1.875, "rate": 100},
"NM": {"w":0, "rate":0},
"GA": {"w":0, "rate":0},
"AM2": {"w": 3.0, "rate": 200},
"NM2": {"w": 0, "rate": 0},
"GA2": {"w": 1.875, "rate": 100}}
}
}
5 changes: 3 additions & 2 deletions neurosim/critic.py
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Expand Up @@ -11,9 +11,10 @@ def _modulate_linear(mod_steps, reward, min_steps=1):
k_pos = len([st for st in mod_steps if st > EPS])
k_neg = len([st for st in mod_steps if st < -EPS])
if reward >= 0:
return reward * (M - k_pos) / M
new_reward = reward * (M - k_pos + 1) / (M+1)
else:
return reward * (M - k_neg) / M
new_reward = reward * (M - k_neg + 1) / (M+1)
return new_reward

class Critic:

Expand Down
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