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Mihail Zdravkov mzdravkov

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@mzdravkov
mzdravkov / build_sequences2.py
Created December 22, 2023 11:42
build_sequences_no_interpolation
def build_sequences(time_series, valid_periods, categories, train_size, test_size):
"""
Creates all possible test sequences with size <test_size> which have
a training sequence of <train_size> in front.
"""
X = []
y = []
final_categories = []
for ts, range, category in zip(time_series, valid_periods, categories):
valid_ts = cut_valid(ts, range)
@mzdravkov
mzdravkov / fourier_time_series_forecasting.py
Created December 16, 2023 20:23
Time series forecasting with fourier transformations
def build_sequences(time_series, valid_periods, categories, train_size, test_size):
"""
Creates all possible test sequences with size <test_size> which have
a training sequence of <train_size> in front.
"""
X = []
y = []
final_categories = []
for ts, range, category in zip(time_series, valid_periods, categories):
valid_ts = cut_valid(ts, range)
@mzdravkov
mzdravkov / build_sequences.py
Created December 10, 2023 22:23
Build time series sequences
def build_sequences(time_series, valid_periods, categories, train_size, test_size):
"""
Creates all possible test sequences with size <test_size> which have
a training sequence of <train_size> in front.
"""
X = []
y = []
final_categories = []
for ts, range, category in zip(time_series, valid_periods, categories):
valid_ts = cut_valid(ts, range)
@mzdravkov
mzdravkov / mobilenet_model.py
Created November 15, 2023 18:27
from keras.constraints import max_norm
def get_res_blocks(definitions, input, l2_factor=0.0001, kernel_constraint_norm=2.0):
hiddenx = tf.keras.layers.Dense(definitions[0],
activation='relu',
kernel_regularizer=tf.keras.regularizers.l2(l2_factor),
kernel_constraint=max_norm(kernel_constraint_norm),
bias_initializer=he_init)(input)
hiddeny = tf.keras.layers.Dense(definitions[0],
# activation='relu',
@mzdravkov
mzdravkov / Dataset.csv
Created April 17, 2023 21:42
Dataset.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 8 should actually have 43 columns, instead of 6. in line 7.
ID,GENDER,AGE,RACE/ETHNICITY,Diagnosis,MD,Assignment,EMR,LOS,RAR,A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,AB,AC,AD,# Psychotropic Medications,# Administrations,Therapeutic Guidances
1,F,49,W,"MDD, Recurrent, Unspecified",L,G,C,70,0,2,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,3,6,EG
2,F,21,W,"MDD, Recurrent, Unspecified",A,G,C,309,0,0,0,0,1,0,0,0,0,0,13,0,0,0,0,0,0,0,0,0,0,0,0,0,0,13,0,0,0,0,0,3,27,CT
3,M,28,L,"MDD, Single Episode, Severe With Psychotic Features",I,G,C,376,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,5,0,26,0,0,0,8,0,0,0,15,0,4,0,0,6,64,CT
4,F,63,L,Depressive Disorder NOS,L,G,C,115,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,0,0,0,0,0,5,0,0,0,0,0,5,0,0,0,0,3,14,CT
5,M,34,L,"MDD, Single Episode, Severe With Psychotic Features",G,S,C,120,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0,1,0,0,0,0,0,0,0,0,5,0,0,0,0,0,3,11,EG
6,F,24,L,"MDD, Single Episode,Severe Without Psychotic Features",T,S,C,120,0,0,5,0,0,0,0,0,0,0,0,0,2,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,5,0,0,4,13,EG
7,M,42,W,"MDD, Single Episode, Unspecified",
@mzdravkov
mzdravkov / biostatistics_project.r
Last active April 18, 2023 09:48
biostatistics_project.r
Dataset <- read.csv("Dataset.csv", stringsAsFactors=TRUE, header=TRUE)
Dataset <- Dataset[Dataset$Assignment != "",]
View(Dataset)
drugs <- data.frame(
Name = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z", "AA", "AB", "AC", "AD"),
Color = c("Red", "Red", "Green", "Yellow", "Red", "Yellow", "Red", "Red", "Red", "Red", "Green", "Red", "Red", "Red", "Green", "Red", "Red", "Green", "Yellow", "Red", "Red", "Yellow", "Yellow", "Red", "Yellow", "Red", "Yellow", "Red", "Red", "Green")
)
@mzdravkov
mzdravkov / dominant.awk
Created April 13, 2023 21:21
function allele_in_parent(allele, parent_alleles) {
return allele == parent_alleles[1] || allele == parent_alleles[2];
}
/^#/ { print $0; }
/^[^#]/ {
split($12, cfields, ":");
split(cfields[1], child, "/");
if (child[1] != 0 || child[2] != 0) print $0;
}
@mzdravkov
mzdravkov / recessive.awk
Created April 13, 2023 21:21
function allele_in_parent(allele, parent_alleles) {
return allele == parent_alleles[1] || allele == parent_alleles[2];
}
/^#/ { print $0; }
/^[^#]/ {
split($10, mfields, ":");
split(mfields[1], mother, "/");
split($11, ffields, ":");
split(ffields[1], father, "/");
@mzdravkov
mzdravkov / genomics_disease_annotation_pipeline.sh
Last active April 13, 2023 21:55
A pipeline for aligning, variant calling and annotating genomes for diagnosing rare genetic diseases.
# recessive.awk can be found here: https://gist.github.com/mzdravkov/443868e111263f8521268434436434e4
# dominant.awk can be found here: https://gist.github.com/mzdravkov/85409f4d0e7d5234f350a9a814a283bf
if [[ $# -lt 2 ]]; then
echo "./pipeline.sh CASE_NUMBER recessive/dominant"
exit;
fi
test_case=$1
pattern=$2
@mzdravkov
mzdravkov / unparsable.psl
Created December 11, 2022 19:32
Line 17 (match 829) seems to be the one that causes Bio.SearchIO.BlatIO to be unable to parse the file.
psLayout version 3
match mis- rep. N's Q gap Q gap T gap T gap strand Q Q Q Q T T T T block blockSizes qStarts tStarts
match match count bases count bases name size start end name size start end count
---------------------------------------------------------------------------------------------------------------------------------------------------------------
1034 214 0 0 6 -127 23 316 + XP_049281413.1 1152 31 1152 XP_035914594.1 1593 29 1593 26 47,95,21,95,77,35,3,27,44,76,35,31,45,41,24,42,105,57,58,38,33,71,24,48,22,54, 31,84,181,202,297,302,337,340,375,419,495,530,561,606,647,671,713,818,875,861,899,932,1003,1027,1075,1098, 29,81,176,231,355,379,462,470,497,613,699,739,775,825,876,905,952,1191,1258,1263,1306,1349,1430,1459,1515,1539,
841 148 0 0 5 -93 19 268 + XP_049281413.1 1152 181 1077 XP_035914594.1 1593 219 1476 23 18,53,74,27,25,76,35,28,24,41,35,31,87,25,23,48,39,46,76,38,52,71,17, 181,199,266,340,375,400,476,511,544,568,609,644,675,6