2023-04-11 • Nto1 AdEx sims: conntest method comparison¶

Data generated in 2023-02-24__multisim-winline.jl

using CSV

using DataFrames

df = CSV.read("../data/Nto1_AdEx.csv", DataFrame)

90×13 DataFrame

65 rows omitted

Row	N	Nᵤ	δ_nS	duration	seed	method	TPRₑ	TPRᵢ	TPR	FPR	AUC	AUCₑ	AUCᵢ
	Int64	Int64	Float64	Float64	Int64	String15	Float64	Float64	Float64	Float64	Float64	Float64	Float64
1	5	100	5.0	600.0	1	STA_corr_2pass	1.0	1.0	1.0	0.08	0.96	0.96	0.96
2	5	100	5.0	600.0	1	STA_height	1.0	1.0	1.0	0.04	0.985	0.985	0.985
3	5	100	5.0	600.0	1	fit_upstroke	1.0	1.0	1.0	0.05	1.0	1.0	1.0
4	5	100	5.0	600.0	2	fit_upstroke	1.0	1.0	1.0	0.05	1.0	1.0	1.0
5	5	100	5.0	600.0	2	STA_corr_2pass	1.0	1.0	1.0	0.06	0.995	0.995	0.995
6	5	100	5.0	600.0	2	STA_height	1.0	1.0	1.0	0.05	0.97	0.97	0.97
7	5	100	5.0	600.0	3	fit_upstroke	1.0	1.0	1.0	0.05	1.0	1.0	1.0
8	5	100	5.0	600.0	3	STA_corr_2pass	1.0	1.0	1.0	0.05	0.985	0.985	0.985
9	5	100	5.0	600.0	3	STA_height	1.0	1.0	1.0	0.06	0.99	0.99	0.99
10	5	100	5.0	600.0	4	STA_corr_2pass	1.0	1.0	1.0	0.06	0.99	0.99	0.99
11	5	100	5.0	600.0	4	fit_upstroke	1.0	1.0	1.0	0.05	1.0	1.0	1.0
12	5	100	5.0	600.0	4	STA_height	1.0	1.0	1.0	0.06	0.98	0.98	0.98
13	5	100	5.0	600.0	5	fit_upstroke	1.0	1.0	1.0	0.05	1.0	1.0	1.0
&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;	&vellip;
79	6500	100	0.02	600.0	2	fit_upstroke	0.100577	0.238462	0.128154	0.05	0.497183	0.461942	0.638146
80	6500	100	0.02	600.0	2	STA_height	0.0155769	0.0338462	0.0192308	0.05	0.260312	0.252032	0.293431
81	6500	100	0.02	600.0	2	STA_corr_2pass	0.0157692	0.00153846	0.0129231	0.05	0.0909446	0.105377	0.0332154
82	6500	100	0.02	600.0	3	STA_height	0.0225	0.0553846	0.0290769	0.06	0.246565	0.237464	0.282965
83	6500	100	0.02	600.0	3	STA_corr_2pass	0.00480769	0.00230769	0.00430769	0.04	0.0894808	0.101411	0.0417615
84	6500	100	0.02	600.0	3	fit_upstroke	0.0511538	0.141538	0.0692308	0.05	0.459509	0.425523	0.595454
85	6500	100	0.02	600.0	4	fit_upstroke	0.110769	0.224615	0.133538	0.05	0.452885	0.422706	0.5736
86	6500	100	0.02	600.0	4	STA_height	0.0278846	0.06	0.0343077	0.05	0.245365	0.235721	0.283938
87	6500	100	0.02	600.0	4	STA_corr_2pass	0.00307692	0.000769231	0.00261538	0.07	0.0818215	0.0937317	0.0341808
88	6500	100	0.02	600.0	5	STA_height	0.02	0.0438462	0.0247692	0.05	0.242268	0.236267	0.266273
89	6500	100	0.02	600.0	5	STA_corr_2pass	0.00923077	0.00230769	0.00784615	0.04	0.108368	0.120388	0.0602846
90	6500	100	0.02	600.0	5	fit_upstroke	0.110192	0.206923	0.129538	0.05	0.478345	0.448963	0.595869

df[df.N .== 6500, :]

15×13 DataFrame

Row	N	Nᵤ	δ_nS	duration	seed	method	TPRₑ	TPRᵢ	TPR	FPR	AUC	AUCₑ	AUCᵢ
	Int64	Int64	Float64	Float64	Int64	String15	Float64	Float64	Float64	Float64	Float64	Float64	Float64
1	6500	100	0.02	600.0	1	STA_corr_2pass	0.00346154	0.000769231	0.00292308	0.06	0.0851831	0.0970885	0.0375615
2	6500	100	0.02	600.0	1	fit_upstroke	0.121346	0.25	0.147077	0.05	0.489955	0.458617	0.615308
3	6500	100	0.02	600.0	1	STA_height	0.0159615	0.0430769	0.0213846	0.05	0.251928	0.24099	0.295677
4	6500	100	0.02	600.0	2	fit_upstroke	0.100577	0.238462	0.128154	0.05	0.497183	0.461942	0.638146
5	6500	100	0.02	600.0	2	STA_height	0.0155769	0.0338462	0.0192308	0.05	0.260312	0.252032	0.293431
6	6500	100	0.02	600.0	2	STA_corr_2pass	0.0157692	0.00153846	0.0129231	0.05	0.0909446	0.105377	0.0332154
7	6500	100	0.02	600.0	3	STA_height	0.0225	0.0553846	0.0290769	0.06	0.246565	0.237464	0.282965
8	6500	100	0.02	600.0	3	STA_corr_2pass	0.00480769	0.00230769	0.00430769	0.04	0.0894808	0.101411	0.0417615
9	6500	100	0.02	600.0	3	fit_upstroke	0.0511538	0.141538	0.0692308	0.05	0.459509	0.425523	0.595454
10	6500	100	0.02	600.0	4	fit_upstroke	0.110769	0.224615	0.133538	0.05	0.452885	0.422706	0.5736
11	6500	100	0.02	600.0	4	STA_height	0.0278846	0.06	0.0343077	0.05	0.245365	0.235721	0.283938
12	6500	100	0.02	600.0	4	STA_corr_2pass	0.00307692	0.000769231	0.00261538	0.07	0.0818215	0.0937317	0.0341808
13	6500	100	0.02	600.0	5	STA_height	0.02	0.0438462	0.0247692	0.05	0.242268	0.236267	0.266273
14	6500	100	0.02	600.0	5	STA_corr_2pass	0.00923077	0.00230769	0.00784615	0.04	0.108368	0.120388	0.0602846
15	6500	100	0.02	600.0	5	fit_upstroke	0.110192	0.206923	0.129538	0.05	0.478345	0.448963	0.595869

df2 = groupby(df, [:method, :N])

GroupedDataFrame with 18 groups based on keys: method, N

First Group (5 rows): method = "STA_corr_2pass", N = 5

Row	N	Nᵤ	δ_nS	duration	seed	method	TPRₑ	TPRᵢ	TPR	FPR	AUC	AUCₑ	AUCᵢ
	Int64	Int64	Float64	Float64	Int64	String15	Float64	Float64	Float64	Float64	Float64	Float64	Float64
1	5	100	5.0	600.0	1	STA_corr_2pass	1.0	1.0	1.0	0.08	0.96	0.96	0.96
2	5	100	5.0	600.0	2	STA_corr_2pass	1.0	1.0	1.0	0.06	0.995	0.995	0.995
3	5	100	5.0	600.0	3	STA_corr_2pass	1.0	1.0	1.0	0.05	0.985	0.985	0.985
4	5	100	5.0	600.0	4	STA_corr_2pass	1.0	1.0	1.0	0.06	0.99	0.99	0.99
5	5	100	5.0	600.0	5	STA_corr_2pass	1.0	1.0	1.0	0.06	0.97	0.97	0.97

&vellip;

Last Group (5 rows): method = "STA_height", N = 6500

Row	N	Nᵤ	δ_nS	duration	seed	method	TPRₑ	TPRᵢ	TPR	FPR	AUC	AUCₑ	AUCᵢ
	Int64	Int64	Float64	Float64	Int64	String15	Float64	Float64	Float64	Float64	Float64	Float64	Float64
1	6500	100	0.02	600.0	1	STA_height	0.0159615	0.0430769	0.0213846	0.05	0.251928	0.24099	0.295677
2	6500	100	0.02	600.0	2	STA_height	0.0155769	0.0338462	0.0192308	0.05	0.260312	0.252032	0.293431
3	6500	100	0.02	600.0	3	STA_height	0.0225	0.0553846	0.0290769	0.06	0.246565	0.237464	0.282965
4	6500	100	0.02	600.0	4	STA_height	0.0278846	0.06	0.0343077	0.05	0.245365	0.235721	0.283938
5	6500	100	0.02	600.0	5	STA_height	0.02	0.0438462	0.0247692	0.05	0.242268	0.236267	0.266273

using Statistics

dfm = sort!(combine(df2, Between(:TPRₑ, :AUCᵢ) .=> mean), :N)

18×9 DataFrame

Row	method	N	TPRₑ_mean	TPRᵢ_mean	TPR_mean	FPR_mean	AUC_mean	AUCₑ_mean	AUCᵢ_mean
	String15	Int64	Float64	Float64	Float64	Float64	Float64	Float64	Float64
1	STA_corr_2pass	5	1.0	1.0	1.0	0.062	0.98	0.98	0.98
2	STA_height	5	1.0	1.0	1.0	0.052	0.983	0.983	0.983
3	fit_upstroke	5	1.0	1.0	1.0	0.05	1.0	1.0	1.0
4	STA_corr_2pass	20	1.0	1.0	1.0	0.06	0.985	0.985	0.985
5	STA_height	20	0.9	1.0	0.92	0.05	0.89905	0.879312	0.978
6	fit_upstroke	20	1.0	1.0	1.0	0.05	1.0	1.0	1.0
7	fit_upstroke	100	1.0	1.0	1.0	0.05	0.99996	0.99995	1.0
8	STA_height	100	0.74	0.86	0.764	0.04	0.75201	0.72835	0.84665
9	STA_corr_2pass	100	1.0	1.0	1.0	0.05	0.986	0.986	0.986
10	fit_upstroke	400	0.966875	1.0	0.9735	0.05	0.993595	0.992044	0.9998
11	STA_height	400	0.505625	0.625	0.5295	0.05	0.547612	0.530375	0.616563
12	STA_corr_2pass	400	0.93625	0.9925	0.9475	0.06	0.96611	0.964381	0.973025
13	STA_corr_2pass	1600	0.00015625	0.0	0.000125	0.058	0.00722563	0.00899531	0.000146875
14	fit_upstroke	1600	0.461094	0.831875	0.53525	0.05	0.814803	0.780755	0.950994
15	STA_height	1600	0.204062	0.4125	0.24575	0.054	0.405968	0.392338	0.460484
16	STA_corr_2pass	6500	0.00726923	0.00153846	0.00612308	0.052	0.0911595	0.103599	0.0414008
17	fit_upstroke	6500	0.0988077	0.212308	0.121508	0.05	0.475575	0.44355	0.603675
18	STA_height	6500	0.0203846	0.0472308	0.0257538	0.052	0.249287	0.240495	0.284457

using WithFeedback

@withfb import PyPlot     # mpl wrapper
@withfb using Sciplotlib  # pyplot wrapper
@withfb using PhDPlots    # local plotting funcs

import PyPlot … ✔ (4.8 s)
using Sciplotlib … ✔ (4.7 s)
using PhDPlots … ✔

Plots¶

function plotrates(m)

    df3 = df[df.method .== m, :]
    df3m = dfm[dfm.method .== m, :]

    # jitter(x) = x .* (0.95 .+ 0.1.*rand(length(x)))
    jitter(x) = x

    fig, ax = plt.subplots()
    clip_on = false
    plt.semilogx(jitter(df3.N), df3.TPR, ".", ms = 8; clip_on)
    plt.semilogx(jitter(df3m.N), df3m.TPR_mean, "C0-"; clip_on)
    plt.semilogx(jitter(df3.N), df3.FPR, ".", ms = 3; clip_on)

    Ns = unique(df.N)

    plt.xticks(Ns, Ns)
    plt.minorticks_off()

    plt.ylabel("Detection rate")
    plt.xlabel("Number of inputs (N)")
    plt.title(m)
end

plotrates("STA_corr_2pass")
plotrates("STA_height")
plotrates("fit_upstroke")
;

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_12_0.png

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_12_1.png

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_12_2.png

What’s up with that N=100, zero detections point¶

This has been fixed by now

Which seed is it?

df[df.N .== 100 .&& df.seed .== 1, :]

3×13 DataFrame

Row	N	Nᵤ	δ_nS	duration	seed	method	TPRₑ	TPRᵢ	TPR	FPR	AUC	AUCₑ	AUCᵢ
	Int64	Int64	Float64	Float64	Int64	String15	Float64	Float64	Float64	Float64	Float64	Float64	Float64
1	100	100	0.75	600.0	1	fit_upstroke	0.0125	0.2	0.05	0.05	0.5	0.4605	0.658
2	100	100	0.75	600.0	1	STA_height	0.0	0.0	0.0	0.0	0.34	0.325	0.4
3	100	100	0.75	600.0	1	STA_corr_2pass	0.0	0.0	0.0	0.0	0.5	0.5	0.5

First let’s inspect the simulation

include("2023-03-14__[setup]_Nto1_sim_AdEx.jl");

using Distributed … ✔
using Revise … ✔ (2.0 s)
using SpikeWorks … ✔ (2.4 s)
using SpikeWorks.Units … ✔ (1.0 s)
using ConnectionTests … ✔ (0.2 s)
using DataFrames … ✔
using MemDiskCache … ✔ (2.0 s)

sd = sims(; N=100, seed=1, duration=10minutes, δ_nS=0.75);

Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/run_sim/_  N=100  δ_nS=0.75  duration=600.0  seed=1  _.jld2] … ✔ (4.7 s)

plotsig(voltsig(sd) / mV, [0,500], ms, hylabel = "Simulated membrane voltage (mV)");

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_20_0.png

We need to fix the spike peaks for aesthetics. But otherwise seems fine.

spikerate(sd) / Hz

8.856666667832444

Maybe sth went wrong during calc and wrong data was saved. Otoh, both the STA methods and the upstroke fit (which uses the sim directly) have bad perf..

Ok but first, is this very different from another seed?

sd2 = sims(; N=100, seed=2, duration=10minutes, δ_nS=0.75);

Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/run_sim/_  N=100  δ_nS=0.75  duration=600.0  seed=2  _.jld2] … ✔ (0.5 s)

plotsig(voltsig(sd2) / mV, [0,500], ms, hylabel = "Simulated membrane voltage (mV)", ylim=[-80, 0]);

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_26_0.png

So no, looks similar.

Let’s then look at some STAs.

kw = (; N=100, duration=10minutes, δ_nS=0.75, Nᵤ=100, batch_size, part=1);

# reals, shufs = STA_sets(; kw..., seed=1);

# ylim = [-59, -56]
# plotSTA(reals[1]; ylim);

Seems proper

# reals2, shufs2 = STA_sets(; kw..., seed=2);
# plotSTA(reals2[1]; ylim, color=C1);

Not too different.

# plotSTA(shufs[1][1]; ylim);
# plotSTA(shufs2[1][1]; ylim);

So only difference is a lower avg Vm.

mean(voltsig(sd)) / mV

-57.73967079215508

mean(voltsig(sd2)) / mV

-58.51984240174548

Or maybe, let’s delete the cached data and recalculate, see if it stays the same.

Nope, it stayed the same.

Huh!

Solution¶

(Hit me offline)

N = 100, Nᵤ = 100, and the seed used to generate both is the same.

So, add Nᵤ to the seed, e.g.

First, let’s plot em

plot_dots_and_means(
    df, ycol;
    xcol = :N,
    xlabel = (xcol == :N ? "Number of inputs (N)" : string(xcol)),
    hylabel = string(ycol),
    color = C0,
    ax = nothing,
    kw...
) = begin
    clip_on = false
    isnothing(ax) && (fig, ax = plt.subplots())
    ax.set_xscale("log")
    x = df[:, xcol]
    y = df[:, ycol]
    plot(x, y, "."; clip_on, ms=8, alpha=0.6, color, ax)
    xu = unique(x)
    ax.set_xticks(xu, xu)
    ax.set_xlim(xu[1]/1.4, xu[end]*1.4)
    ax.minorticks_off()
    set(ax; xlabel, hylabel, kw...)
    dfm = combine(groupby(df, xcol), ycol => mean => ycol)
    ym = dfm[:, ycol]
    plot(xu, ym, "-"; clip_on, color, ax)
end

plot_AUC(df, method) = begin
    fig, ax = plt.subplots()
    ax.axhline(0.5, c="gray", lw=1, ls="--")
    plot_dots_and_means(
        df[df.method .== method, :],
        :AUC,
        title = method,
        ylim = [0, 1];
        ax
    )
end

methods = unique(df.method)
for m in methods
    plot_AUC(df, m)
end

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_50_0.png

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_50_1.png

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_50_2.png

kw = (; N=6500, duration=10minutes, δ_nS=0.02, Nᵤ=100, seed=1, method="STA_corr_2pass");

conntest = conntest_tables(; kw...);

using ConnTestEval

sweep = sweep_threshold(conntest);

plot_ROC(sweep) = begin
    fig, ax = plt.subplots()
    ax.set_aspect("equal")
    plot(
        sweep.FPR,
        sweep.TPR;
        ax,
        xlabel = "FPR",
        ylabel = ("TPR", :loc=>"top"),
        xlim = [0, 1],
        ylim = [0, 1],
    )    
end
ax = plot_ROC(sweep);

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_55_0.png

For the last point on the graph:

print_confusion_matrix(sweep[end])

              Predicted
           exc   inh   unc
      exc 1349  3851     0
Real  inh 1139   161     0
      unc   58    42     0

So the problem is that we only count a detection as correct if it’s the right type: exc or inh. Hence why, even with a threshold as low as possible, we do not detect all real connections.

Two-pass STA template for high N¶

Finally, what’s the template look like for the high N 2 pass case.

I suspect it’s zeros: not enough (or no) connections detected in the first pass, with a high threshold.

kw = (; N=1600, duration=10minutes, δ_nS=0.08, Nᵤ=100, seed=1, method="STA_height");

table = conntest_tables(; kw...)
maximum(table.t)

0.99

So there is indeed not one connection with t-value 1. So no excitatory STAs for the template.

We must change the method. Auto-choose a threshold at which we do have at least some detections.

We can do the full sweep: and then start from high thresholds, and pick the first where we cross a detrate; or we have a fixed integer number of exc detections.

Aha wait no ofc, we don’t have the groundtruth.

So rather we’ll, maybe, go in a loop and lower the thr? You need to know the range then.. that’s np, just sorted unique. ok

ts = sort!(unique(table.t), rev = true)
for θ in ts
    predtype = ConnTestEval.predicted_types(table.t, θ)
    N = count(predtype .== :exc)
    @show (θ, N)
    N > 5 && break
end

(θ, N) = (0.99, 0)
(θ, N) = (0.98, 305)

Something like that.

Now to insert it in the code.

Wait, it’s still so low after that change. Ok then so how many do we have and what’s template like (now that we should have at least some).

include("2023-03-14__[setup]_Nto1_sim_AdEx.jl");

using Distributed … ✔
using Revise … ✔
using SpikeWorks … ✔
using SpikeWorks.Units … ✔
using ConnectionTests … ✔
using DataFrames … ✔
using MemDiskCache … ✔

batch_size

simkw = (; N=1600, duration=10minutes, δ_nS=0.08, Nᵤ=100, seed=1);
m = TwoPassCorrTest();

template = get_template(m, simkw, batch_size);

Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/calc_all_STAs/_  N=1600  Nᵤ=100  δ_nS=0.08  duration=600.0  seed=1  batch_size=300  part=1  _.jld2] … ✔ (0.4 s)
First pass … Testing connection 1 / 300 … ✔
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✔ (0.2 s)

Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/calc_all_STAs/_  N=1600  Nᵤ=100  δ_nS=0.08  duration=600.0  seed=1  batch_size=300  part=2  _.jld2] … ✔ (0.8 s)
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✔
Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/calc_all_STAs/_  N=1600  Nᵤ=100  δ_nS=0.08  duration=600.0  seed=1  batch_size=300  part=3  _.jld2] … ✔ (0.7 s)
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✔ (0.1 s)
Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/calc_all_STAs/_  N=1600  Nᵤ=100  δ_nS=0.08  duration=600.0  seed=1  batch_size=300  part=4  _.jld2] … ✔ (0.6 s)
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✔
Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/calc_all_STAs/_  N=1600  Nᵤ=100  δ_nS=0.08  duration=600.0  seed=1  batch_size=300  part=5  _.jld2] … ✔ (0.7 s)
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Loading [/root/.julia/MemDiskCache.jl/2023-03-14__Nto1_AdEx/calc_all_STAs/_  N=1600  Nᵤ=100  δ_nS=0.08  duration=600.0  seed=1  batch_size=300  part=6  _.jld2] … ✔ (0.4 s)
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plotSTA(template);

../_images/2023-04-11__Nto1_AdEx_conntest_methods_comparison_72_0.png

Aha, here’s the problem. We do have an STA. But it’s negative. It’s classified as positive cause the heuristic for that – ‘net area above start’ – is.. Ah yes, that is positive, so classified as positive.

One ad-hoc solution would be to use a shorter stretch of time for this ‘area-above start’. I.e. first 20 ms. (Here, first 5 or 10 would be even better; but imagine a spike transmission delay).

Voltage-to-Wiring Sim

2023-04-11 • Nto1 AdEx sims: conntest method comparison

Contents

2023-04-11 • Nto1 AdEx sims: conntest method comparison¶

Plots¶

What’s up with that N=100, zero detections point¶

Solution¶

Why is AUC < 0.5¶

Two-pass STA template for high N¶