add: eeg.R and psqt.tex
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% Authomatically generated by `dataAnalysis/chess.R`
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\documentclass{standalone}
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\usepackage[LSB, T1]{fontenc}
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\usepackage{chessboard}
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\usepackage{skak}
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\usepackage{tikz}
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\usepackage{amsmath}
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\usepackage{xcolor}
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\setboardfontencoding{LSB}
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\setchessboard{linewidth = 0.1em, showmover = false, smallboard}
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\begin{document}
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\begin{tikzpicture}
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\coordinate (pawn) at (0, 0);
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\coordinate (knight) at (5, 0);
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\coordinate (bishop) at (10, 0);
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\coordinate (rook) at (0, -5.2);
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\coordinate (queen) at (5, -5.2);
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\coordinate (king) at (10, -5.2);
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\node (bishop) at (bishop) {\chessboard[color=col73,colorbackfield=a8,color=col72,colorbackfield=a7,color=col71,colorbackfield=a6,color=col80,colorbackfield=a5,color=col70,colorbackfield=a4,color=col76,colorbackfield=a3,color=col67,colorbackfield=a2,color=col66,colorbackfield=a1,color=col70,colorbackfield=b8,color=col70,colorbackfield=b7,color=col69,colorbackfield=b6,color=col74,colorbackfield=b5,color=col69,colorbackfield=b4,color=col72,colorbackfield=b3,color=col66,colorbackfield=b2,color=col68,colorbackfield=b1,color=col71,colorbackfield=c8,color=col66,colorbackfield=c7,color=col66,colorbackfield=c6,color=col78,colorbackfield=c5,color=col66,colorbackfield=c4,color=col68,colorbackfield=c3,color=col66,colorbackfield=c2,color=col67,colorbackfield=c1,color=col68,colorbackfield=d8,color=col68,colorbackfield=d7,color=col67,colorbackfield=d6,color=col70,colorbackfield=d5,color=col67,colorbackfield=d4,color=col69,colorbackfield=d3,color=col66,colorbackfield=d2,color=col67,colorbackfield=d1,color=col68,colorbackfield=e8,color=col68,colorbackfield=e7,color=col67,colorbackfield=e6,color=col71,colorbackfield=e5,color=col67,colorbackfield=e4,color=col70,colorbackfield=e3,color=col66,colorbackfield=e2,color=col65,colorbackfield=e1,color=col73,colorbackfield=f8,color=col70,colorbackfield=f7,color=col68,colorbackfield=f6,color=col82,colorbackfield=f5,color=col66,colorbackfield=f4,color=col75,colorbackfield=f3,color=col67,colorbackfield=f2,color=col65,colorbackfield=f1,color=col71,colorbackfield=g8,color=col70,colorbackfield=g7,color=col69,colorbackfield=g6,color=col73,colorbackfield=g5,color=col70,colorbackfield=g4,color=col70,colorbackfield=g3,color=col66,colorbackfield=g2,color=col79,colorbackfield=g1,color=col73,colorbackfield=h8,color=col72,colorbackfield=h7,color=col70,colorbackfield=h6,color=col79,colorbackfield=h5,color=col70,colorbackfield=h4,color=col75,colorbackfield=h3,color=col67,colorbackfield=h2,color=col64,colorbackfield=h1]};
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\node (rook) at (rook) {\chessboard[color=col104,colorbackfield=a8,color=col95,colorbackfield=a7,color=col105,colorbackfield=a6,color=col103,colorbackfield=a5,color=col97,colorbackfield=a4,color=col81,colorbackfield=a3,color=col84,colorbackfield=a2,color=col89,colorbackfield=a1,color=col95,colorbackfield=b8,color=col90,colorbackfield=b7,color=col97,colorbackfield=b6,color=col97,colorbackfield=b5,color=col92,colorbackfield=b4,color=col77,colorbackfield=b3,color=col81,colorbackfield=b2,color=col84,colorbackfield=b1,color=col105,colorbackfield=c8,color=col96,colorbackfield=c7,color=col106,colorbackfield=c6,color=col104,colorbackfield=c5,color=col98,colorbackfield=c4,color=col82,colorbackfield=c3,color=col85,colorbackfield=c2,color=col90,colorbackfield=c1,color=col89,colorbackfield=d8,color=col86,colorbackfield=d7,color=col91,colorbackfield=d6,color=col91,colorbackfield=d5,color=col87,colorbackfield=d4,color=col74,colorbackfield=d3,color=col79,colorbackfield=d2,color=col80,colorbackfield=d1,color=col93,colorbackfield=e8,color=col88,colorbackfield=e7,color=col95,colorbackfield=e6,color=col94,colorbackfield=e5,color=col90,colorbackfield=e4,color=col75,colorbackfield=e3,color=col80,colorbackfield=e2,color=col83,colorbackfield=e1,color=col100,colorbackfield=f8,color=col93,colorbackfield=f7,color=col102,colorbackfield=f6,color=col100,colorbackfield=f5,color=col95,colorbackfield=f4,color=col79,colorbackfield=f3,color=col83,colorbackfield=f2,color=col88,colorbackfield=f1,color=col97,colorbackfield=g8,color=col92,colorbackfield=g7,color=col99,colorbackfield=g6,color=col98,colorbackfield=g5,color=col93,colorbackfield=g4,color=col79,colorbackfield=g3,color=col83,colorbackfield=g2,color=col84,colorbackfield=g1,color=col106,colorbackfield=h8,color=col96,colorbackfield=h7,color=col108,colorbackfield=h6,color=col105,colorbackfield=h5,color=col99,colorbackfield=h4,color=col82,colorbackfield=h3,color=col85,colorbackfield=h2,color=col91,colorbackfield=h1]};
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\node (queen) at (queen) {\chessboard[color=col126,colorbackfield=a8,color=col125,colorbackfield=a7,color=col124,colorbackfield=a6,color=col122,colorbackfield=a5,color=col117,colorbackfield=a4,color=col110,colorbackfield=a3,color=col108,colorbackfield=a2,color=col99,colorbackfield=a1,color=col125,colorbackfield=b8,color=col125,colorbackfield=b7,color=col124,colorbackfield=b6,color=col123,colorbackfield=b5,color=col118,colorbackfield=b4,color=col111,colorbackfield=b3,color=col110,colorbackfield=b2,color=col101,colorbackfield=b1,color=col124,colorbackfield=c8,color=col126,colorbackfield=c7,color=col126,colorbackfield=c6,color=col125,colorbackfield=c5,color=col122,colorbackfield=c4,color=col117,colorbackfield=c3,color=col115,colorbackfield=c2,color=col105,colorbackfield=c1,color=col109,colorbackfield=d8,color=col118,colorbackfield=d7,color=col120,colorbackfield=d6,color=col120,colorbackfield=d5,color=col122,colorbackfield=d4,color=col124,colorbackfield=d3,color=col122,colorbackfield=d2,color=col111,colorbackfield=d1,color=col124,colorbackfield=e8,color=col128,colorbackfield=e7,color=col128,colorbackfield=e6,color=col127,colorbackfield=e5,color=col126,colorbackfield=e4,color=col122,colorbackfield=e3,color=col120,colorbackfield=e2,color=col109,colorbackfield=e1,color=col125,colorbackfield=f8,color=col126,colorbackfield=f7,color=col126,colorbackfield=f6,color=col124,colorbackfield=f5,color=col120,colorbackfield=f4,color=col114,colorbackfield=f3,color=col113,colorbackfield=f2,color=col103,colorbackfield=f1,color=col127,colorbackfield=g8,color=col125,colorbackfield=g7,color=col124,colorbackfield=g6,color=col122,colorbackfield=g5,color=col115,colorbackfield=g4,color=col106,colorbackfield=g3,color=col105,colorbackfield=g2,color=col97,colorbackfield=g1,color=col127,colorbackfield=h8,color=col123,colorbackfield=h7,color=col122,colorbackfield=h6,color=col120,colorbackfield=h5,color=col112,colorbackfield=h4,color=col102,colorbackfield=h3,color=col101,colorbackfield=h2,color=col94,colorbackfield=h1]};
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\node (king) at (king) {\chessboard[color=col55,colorbackfield=a8,color=col56,colorbackfield=a7,color=col56,colorbackfield=a6,color=col56,colorbackfield=a5,color=col56,colorbackfield=a4,color=col55,colorbackfield=a3,color=col58,colorbackfield=a2,color=col65,colorbackfield=a1,color=col57,colorbackfield=b8,color=col59,colorbackfield=b7,color=col59,colorbackfield=b6,color=col58,colorbackfield=b5,color=col58,colorbackfield=b4,color=col57,colorbackfield=b3,color=col60,colorbackfield=b2,color=col69,colorbackfield=b1,color=col58,colorbackfield=c8,color=col58,colorbackfield=c7,color=col58,colorbackfield=c6,color=col58,colorbackfield=c5,color=col58,colorbackfield=c4,color=col58,colorbackfield=c3,color=col60,colorbackfield=c2,color=col65,colorbackfield=c1,color=col57,colorbackfield=d8,color=col58,colorbackfield=d7,color=col58,colorbackfield=d6,color=col57,colorbackfield=d5,color=col57,colorbackfield=d4,color=col57,colorbackfield=d3,color=col59,colorbackfield=d2,color=col64,colorbackfield=d1,color=col57,colorbackfield=e8,color=col58,colorbackfield=e7,color=col58,colorbackfield=e6,color=col58,colorbackfield=e5,color=col58,colorbackfield=e4,color=col58,colorbackfield=e3,color=col60,colorbackfield=e2,color=col64,colorbackfield=e1,color=col62,colorbackfield=f8,color=col62,colorbackfield=f7,color=col62,colorbackfield=f6,color=col61,colorbackfield=f5,color=col61,colorbackfield=f4,color=col61,colorbackfield=f3,color=col63,colorbackfield=f2,color=col67,colorbackfield=f1,color=col61,colorbackfield=g8,color=col62,colorbackfield=g7,color=col62,colorbackfield=g6,color=col62,colorbackfield=g5,color=col62,colorbackfield=g4,color=col61,colorbackfield=g3,color=col63,colorbackfield=g2,color=col70,colorbackfield=g1,color=col60,colorbackfield=h8,color=col61,colorbackfield=h7,color=col61,colorbackfield=h6,color=col60,colorbackfield=h5,color=col60,colorbackfield=h4,color=col60,colorbackfield=h3,color=col61,colorbackfield=h2,color=col64,colorbackfield=h1]};
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\node[anchor = north, yshift = -0.4em] at (pawn.north) {Pawn};
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\node[anchor = north, yshift = -0.4em] at (knight.north) {Knight};
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\node[anchor = north, yshift = -0.4em] at (bishop.north) {Bishop};
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\node[anchor = north, yshift = -0.4em] at (rook.north) {Rook};
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\node[anchor = north, yshift = -0.4em] at (queen.north) {Queen};
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\node[anchor = north, yshift = -0.4em] at (king.north) {King};
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\end{tikzpicture}
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\end{document}
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@ -0,0 +1,93 @@
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options(keep.source = TRUE, keep.source.pkgs = TRUE)
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library(tensorPredictors)
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# Load as 3D predictors `X` and flat response `y`
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c(X, F, y) %<-% local({
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# Load from file
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ds <- readRDS("eeg_data.rds")
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# Dimension values
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n <- nrow(ds) # sample size (nr. of people)
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p <- 64L # nr. of predictors (count of sensorce)
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t <- 256L # nr. of time points (measurements)
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# Extract dimension names
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nNames <- ds$PersonID
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tNames <- as.character(seq(t))
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pNames <- unlist(strsplit(colnames(ds)[2 + t * seq(p)], "_"))[c(TRUE, FALSE)]
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# Split into predictors (with proper dims and names) and response
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X <- array(as.matrix(ds[, -(1:2)]),
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dim = c(person = n, time = t, sensor = p),
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dimnames = list(person = nNames, time = tNames, sensor = pNames)
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)
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y <- ds$Case_Control
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list(X, array(y, c(n, 1L, 1L)), y)
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})
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# fit a tensor normal model to the data sample axis 1 indexes persons)
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fit.gmlm <- gmlm_tensor_normal(X, F, sample.axis = 1L)
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# Performa a LOO prediction
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y.hat <- sapply(seq_len(dim(X)[1L]), function(i) {
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# Fit with i'th observation removes
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fit <- gmlm_tensor_normal(X[-i, , ], F[-i, , , drop = FALSE], sample.axis = 1L)
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# Reduce the entire data set
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r <- as.vector(mlm(X, fit$betas, modes = 2:3, transpose = TRUE))
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# Fit a logit model on reduced data with i'th observation removed
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logit <- glm(y ~ r, family = binomial(link = "logit"),
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data = data.frame(y = y[-i], r = r[-i])
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)
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# predict i'th response given i'th reduced observation
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y.hat <- predict(logit, newdata = data.frame(r = r[i]), type = "response")
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# report progress
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cat(sprintf("%3d/%d\n", i, dim(X)[1L]))
|
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|
||||
y.hat
|
||||
})
|
||||
|
||||
### Classification performance measures
|
||||
# acc: Accuracy. P(Yhat = Y). Estimated as: (TP+TN)/(P+N).
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(acc <- mean(round(y.hat) == y)) # 0.7868852
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# err: Error rate. P(Yhat != Y). Estimated as: (FP+FN)/(P+N).
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(err <- mean(round(y.hat) != y)) # 0.2131148
|
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# fpr: False positive rate. P(Yhat = + | Y = -). aliases: Fallout.
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(fpr <- mean((round(y.hat) == 1)[y == 0])) # 0.4
|
||||
# tpr: True positive rate. P(Yhat = + | Y = +). aliases: Sensitivity, Recall.
|
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(tpr <- mean((round(y.hat) == 1)[y == 1])) # 0.8961039
|
||||
# fnr: False negative rate. P(Yhat = - | Y = +). aliases: Miss.
|
||||
(fnr <- mean((round(y.hat) == 0)[y == 1])) # 0.1038961
|
||||
# tnr: True negative rate. P(Yhat = - | Y = -).
|
||||
(tnr <- mean((round(y.hat) == 0)[y == 0])) # 0.6
|
||||
# auc: Area Under the Curve
|
||||
(auc <- pROC::roc(y, y.hat, quiet = TRUE)$auc) # 0.838961
|
||||
|
||||
|
||||
with(fit.gmlm, {
|
||||
par.reset <- par(mfrow = c(2, 1))
|
||||
plot(seq(0, 1, len = 256), betas[[1]], main = "Time", xlab = "Time [s]", ylab = expression(beta[1]))
|
||||
plot(betas[[2]], main = "Sensors", xlab = "Sensor Index", ylab = expression(beta[2]))
|
||||
par(par.reset)
|
||||
})
|
||||
|
||||
|
||||
# dimX <- c(4, 3, 5)
|
||||
# Omegas <- Map(function(p) {
|
||||
# O <- matrix(rnorm(p^2), p)
|
||||
# O %*% t(O)
|
||||
# }, dimX)
|
||||
|
||||
# # Numerically more stable version of `sum(log(mapply(det, Omegas)) / dimX)`
|
||||
# # which is itself equivalent to `log(det(Omega)) / prod(nrow(Omega))` where
|
||||
# # `Omega <- Reduce(kronecker, rev(Omegas))`.
|
||||
|
||||
# Omega <- Reduce(kronecker, rev(Omegas))
|
||||
# log(det(Omega)) / prod(nrow(Omega))
|
||||
|
||||
# (det.Omega <- sum(log(mapply(det, Omegas)) / dimX))
|
||||
# sum(mapply(function(Omega) {
|
||||
# sum(log(eigen(Omega, TRUE, TRUE)$values))
|
||||
# }, Omegas) / dimX)
|
||||
Loading…
Reference in New Issue