README.md

multi_task_learning

summary

multi task learning model using tensorflow

the raw data is metrics on ecg reports.

the according label represents the diagnoses of doctors.

data demostration

the label is from 0 to 32. that's 33 classes.

the raw data has 12 columns first two columns are id.

the following 10 columns are:
'MDC_ECG_HEART_RATE'
'MDC_ECG_TIME_PD_PR'
'MDC_ECG_TIME_PD_QRS'
'MDC_ECG_TIME_PD_QT'
'MDC_ECG_TIME_PD_QTc'
'MDC_ECG_ANGLE_P_FRONT'
'MDC_ECG_ANGLE_QRS_FRONT'
'MDC_ECG_ANGLE_T_FRONT'
'RV5'
'SV1'

i shuffled the raw data to:
shuffled_metrics_in_report_label.csv
shuffled_metrics_in_report.csv

then i sliced the shuffled raw data into the data folder
the data folder includes train\dev\test data

development procedure log

about precision and recall

because this project is based on real medical data,
so the samples are labeled as imbalanced classes,
precision and recall estimation is best suit imbalanced sample at this time.
this paper gave a quick experiment on traditionally ROC and precision-recall,
and the conclusion shows that,
precision-recall is more informative when facing imbalanced data.
https://classeval.wordpress.com/simulation-analysis/roc-and-precision-recall-with-imbalanced-datasets/

shrink the classes

commit 500c0aa46f223ddf033f39b35b152be79006b326
Date: Tue May 29 19:58:49 2018 +0800

after 10000 epochs, only five classes has precision and recall rate that not tend to 0

base on this commit, i found that label: 3\13\18\21\24 are overfitting, which means these classes has high corelationship with the 10 columns data. so next step i will shrink the 33 classes to 5 classes,
and continue to jump into solutions of overfitting problems.

so after commit[500c0aa46f223ddf033f39b35b152be79006b326],
let's jump into folder [data_with_shrinked_label],
and the labels are mapped as:
3\13\18\21\24 -----> 0/1/2/3/4

to be overfitting

commit 8372f6f558538d686d2b117bd276421226252a70
Date: Wed May 30 14:39:54 2018 +0800

after 200 epochs, the five classes overfitted very slowly,
so i added 3 layers with 100 units per layer,
and after 6000 epochs, 5 classes all overfitted.

many articles suggested that,
initialization of input and do batch norm can accelerate the convergency.
i applied input init and batch norm at the very first time.
and the effection has not been estimated,
because i didn't try the model without initializations of input and without batch norm.

as to the exploding and vanishing problem,
i also implemented he-kaiming weights init for relu activation funcs
i printed the units of the last two layers in this version,
and seeing that the units value are not too large or too small

it's worthwhile to mention that, i am using adam optimizer,
which means it has adventages cause of the momentum and RMS probability mechanism in it.

overfitting judgement

it's the very first destination of neuro network adjustment: to be overfitting.
if u don't know how to judge overfitting, u won't know weather u arrived the first target.
i judge overfitting easily by precision-recall rate of the last batch of every epoch.
after thousands of epochs, the output is like: epoch:[4861]
precision_rate:
[ 0.91525424 0.96342856 0.80000001 0.90322578 0.84210527]
recall_rate:
[ 0.77142859 0.99059927 0.66666669 0.875 0.94117647]
f1_score:
[ 0.83720922 0.97682494 0.72727269 0.88888878 0.88888884]
epoch:[4862]
precision_rate:
[ 0.80327868 0.96351194 0.80000001 0.83870965 0.83765113]
recall_rate:
[ 0.89090908 0.98599768 0.5 0.89655173 0.91856062]
f1_score:
[ 0.84482753 0.97462511 0.61538458 0.86666656 0.87624204]

so it's overfitting .
while the standard way to judge overfitting is give the train set and dev set accurracy a contrast.
just like:

epoch:[44]
precision_rate:
[ 0.60000002 0.94438136 0.66666669 0.53488374 0.77464789]
[ 0.58031088 0.94480139 0.51428574 0.65151513 0.7652247 ]
recall_rate:
[ 0.94117647 0.97082847 0.66666669 0.95833331 0.88709676]
[ 0.93723851 0.97176331 0.69230771 0.88356167 0.86638135]
f1_score:
[ 0.73282439 0.95742232 0.66666663 0.68656713 0.82706761]
[ 0.71679991 0.95809263 0.59016389 0.74999988 0.81266713]

training set and dev set has nearly the same accuracy

after thousands of epochs, i am supprised to find that,
there isn't a big gap between the training and testing accuracy:
f1_score: [ 0.77358478 0.97388268 0.83333331 0.9523809 0.86861306] [ 0.72908366 0.95363641 0.62499994 0.77655673 0.75324053]

so firstly i change the traing set measure strategy .
formally, i jus look at the precision-recall rate of the last batch of every epoch.
now, i make a prediction of the entire training set and calculate the precision-recall rate.
so now i use the standard way of overfitting judgement: training set accuarcy vs dev set accuarcy.

now the accuracy of training set changes smoothly from epoch to epoch.
epoch:[54]
f1_score:
[ 0.77388775 0.96709293 0.82253087 0.84310782 0.8334958 ]
[ 0.78799999 0.96371841 0.73469383 0.80272108 0.83031219]
epoch:[55]
f1_score:
[ 0.78775996 0.96933049 0.81846625 0.84646732 0.83268845]
[ 0.77992266 0.96576035 0.69230765 0.79715294 0.82712758]
epoch:[56]
f1_score:
[ 0.77206451 0.96964955 0.82556379 0.84699982 0.83193547]
[ 0.78068405 0.96725875 0.70588231 0.8188405 0.82594156]

model gradient checking

even at the very first epoch, the accuracy of the training and dev set are very high.
so i suspected that is there any bug in the model, so i inversed the dev label,
the accuracy of dev set became very low:

epoch:[15]
precision_rate:
[ 0.72294486 0.94651884 0.80645162 0.79794079 0.75523823]
[ 0.27372262 0.05391454 0.25 0.21710527 0.22925226]
recall_rate:
[ 0.81091332 0.99103498 0.69984448 0.84033614 0.90678781]
[ 0.01994151 0.28017884 0.00150981 0.00856253 0.29414865]
f1_score:
[ 0.76440644 0.96826541 0.74937546 0.81858987 0.82410353]
[ 0.03717471 0.09042806 0.0030015 0.01647528 0.25767717]
epoch:[16]
precision_rate:
[ 0.72139692 0.93869275 0.82889736 0.82721323 0.75196791]
[ 0.26394051 0.06506365 0.2 0.1970803 0.23665048]
recall_rate:
[ 0.80770355 0.99342096 0.67807156 0.78774738 0.91101015]
[ 0.01887796 0.34277198 0.00100654 0.00700571 0.30838165]
f1_score:
[ 0.76211452 0.96528172 0.74593663 0.80699795 0.82388377]
[ 0.03523572 0.10936755 0.002003 0.01353044 0.26779577]

and i printed the training cost of every batch of every epoch,
the cost goes down very quikly.
so the gradient descent behavior of the model is normal.

wishing to get the big gap

actrually, i still didn't see a big gap between training set and dev set accuracy.
there are 2 reasons for that:

1. ceiling has been reached according to the co-relationship limit between data and label.
2. there is still avoidable bias,
   that's means training set accuracy could be improved by more neuro units and more epochs.

after i added layers, the gap finally came back:
epoch:[2283]
precision_rate:
[ 0.98406488 0.99627608 0.99072641 0.99287474 0.96681172]
[ 0.68888891 0.94044811 0.63999999 0.828125 0.75998122]
recall_rate:
[ 0.99110007 0.99624628 0.99688959 0.98210895 0.97745955]
[ 0.64853555 0.95824569 0.61538464 0.72602737 0.76937705]
f1_score:
[ 0.98756987 0.99626112 0.99379838 0.98746246 0.9721064 ]
[ 0.66810334 0.94926339 0.62745088 0.77372253 0.76465017]

solve the overfitting issue