Big Data Analytics in Healthcare Homework 1

CSE6250: Big Data Analytics in Healthcare
Homework 1

• You can use 2 days of late submission throughout the semester ONLY for homeworks.
• Discussion is encouraged, but each student must write his/her own answers and explicitly mention any collaborators.
• Each student is expected to respect and follow the GT Honor Code. We will apply
anti-cheating software to check for plagiarism. Any one who is flagged by the
software will automatically receive 0 for the homework and be reported to the college.
• Please type the submission with LATEX or Microsoft Word. We will not accept hand
written submissions.
• Please do not change the filenames and function definitions in the skeleton
code provided, as this will cause the test scripts to fail and you will receive no points
in those failed tests. Built-in modules of python and the following libraries - pandas,
numpy, scipy, scikit-learn can be used.
• It is your responsibility to make sure that all code and other deliverables are in the
correct format and that your submission compiles and runs. We will not manually
check your code (not feasible given the class size). Thus non-runnable code in our
test environment will directly lead to 0 score without comments.
Overview
Preparing the data, computing basic statistics and constructing simple models are essential
steps for data science practice. In this homework, you will use clinical data as raw input
to perform Mortality Prediction. For this homework, Python programming will be
required. See the attached skeleton code as a start-point for the programming questions.
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Also, you need to make a single PDF file (homework1 answer.pdf ) of a compiled
document for non-programming questions.
1 CITI Certification [10 points]
During this course, we will be working with the MIMIC database. MIMIC, although deidentified, still contains detailed information regarding the clinical care of patients, and must
be treated with appropriate care and respect. In order to obtain access, it is necessary to
finish the MIMIC CITI program training provided by MIT and get the certificate.
1. Navigate to the website: https://www.citiprogram.org/index.cfm?pageID=154&
icat=0&ac=0. Under Register, select ”Massachusetts Institute of Technology Affiliate”
as your organization affiliation (not ”independent learner”) and create your account
with your GT email address (required).
2. Follow the links to add a Massachusetts Institute of Technology Affiliates course. In the
Human Subjects training category, select the ”Data or Specimens Only Research”
course
3. Complete the course and save your completion report, which lists all modules completed
with dates and scores.
Solution: Please include your certificates named Certif icate MIMIC.pdf as the submission
format we provided at the end.
About Raw Data
Navigate to homework1/data/train. There are three CSV files which will be the input data
in this homework.
The data provided in events.csv are event sequences. Each line of this file consists of a
tuple with the format (patient id, event id, event description, timestamp, value).
For example,
1053 , DIAG319049 , Acute respiratory failure ,2924 -10 -08 ,1.0
1053 , DIAG197320 , Acute renal failure syndrome ,2924 -10 -08 ,1.0
1053 , DRUG19122121 , Insulin ,2924 -10 -08 ,1.0
1053 , DRUG19122121 , Insulin ,2924 -10 -11 ,1.0
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -08 ,3.000
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -08 ,3.690
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -09 ,3.240
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -10 ,3.470
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• patient id: De-identified patient identiers. For example, the patient in the example
above has patient id 1053.
• event id: Clinical event identifiers. For example, DRUG19122121 means that a drug
with RxNorm code as 19122121 was prescribed to the patient. DIAG319049 means
the patient was diagnosed of disease with SNOMED code of 319049 and LAB3026361
means that the laboratory test with a LOINC code of 3026361 was conducted on the
patient.
• event description: Shows the description of the clinical event. For example, DIAG319049
is the code for Acute respiratory failure and DRUG19122121 is the code for Insulin.
• timestamp: the date at which the event happened. (Here the timestamp is not a real
date.)
• value: Contains the value associated to an event. See Table 1 for the detailed description.
event type sample event id value meaning example
diagnostic code DIAG319049 diagnosed with a certain disease, value always be 1.0
1.0
drug consumption DRUG19122121 prescribed a certain
medication, value will
always be 1.0
1.0
laboratory test LAB3026361 test conducted on a
patient and its value
3.690
Table 1: Event sequence value explanation
The data provided in mortality events.csv contains the patient ids of only the deceased
people. They are in the form of a tuple with the format (patient id, timestamp, label). For
example,
37 ,3265 -12 -31 ,1
40 ,3202 -11 -11 ,1
The timestamp indicates the death date of a deceased person and a label of 1 indicates
death. Patients that are not mentioned in this file are considered alive.
The event feature map.csv is a map from an event id (SNOMED, LOINC and RxNorm)
to an integer index. This file contains (idx, event id) pairs for all event ids.
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Python and dependencies
In this homework, we will work on Python 3.6.5 environment. If you do not have a python
distribution installed yet, we recommend installing Anaconda (or miniconda) with Python
3.6.5. We provide homework1/environment.yml which contains a list of libraries needed to
set environment for this homework. You can use it to create a copy of conda ‘environment’
(http://conda.pydata.org/docs/using/envs.html#use-environment-from-file). If you already
have your own Python development environment (it should be Python 3.6.5), please refer to
this file to find necessary libraries, which is used to set the same coding/grading environment.
Alternatively, we have prepared the docker environment. You are highly encouraged to set
the environment ready ASAP following the tutorials of this link, which you might use often
in later homework. Please also activate environment.yml when needed in coding.
Running the tests
Test cases are provided for every module in this homework and operate on a subset of the
data. To run a test, execute the following commands from the base folder i.e. homework1. If
any of the test cases fail, an error will be shown. For example to test the statistics computed,
the following command should be executed:
nosetests tests / test_statistics . py -- nologcapture
A single test can also be run using this syntax:
nosetests tests / < filename : < test_method -- nologcapture
Remember to use the right filename and test method in above command line. For more
information about basic usage of nosetests, please refer to this LINK
2 Descriptive Statistics [10 points]
Before starting analytic modeling, it is a good practice to get descriptive statistics of the
input raw data. In this section, you need to write code that computes various metrics on
the data described previously. A skeleton code is provided to you as a starting point.
The definition of terms used in the result table are described below:
• Event count: Number of events recorded for a given patient. Note that every line in
the input file is an event.
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• Encounter count: Count of unique dates on which a given patient visited the hospital.
All the events - DIAG, LAB and DRUG - should be considered as hospital visiting
events.
• Record length: Duration (in number of days) between the first event and last event
for a given patient.
For example, if the first event is on 2014-05-21 and the last event is on 2014-05-24, the
duration is 3 days. If a patient has only one event, the duration is 0.
a. Complete src/event statistics.py to implement the required statistics.
Please be aware that you are NOT allowed to change the filename and any existing function declarations. Only numpy, scipy, scikit-learn and other built-in modules
of python will be available for you to use. The use of pandas library is suggested.
b. Use events.csv and mortality events.csv provided in data/train as input and fill
Table 2 with actual values. Include this table in homework1 answer.pdf
Metric Deceased patients Alive patients Function to complete
Event Count event count metrics
1. Average Event Count
2. Max Event Count
3. Min Event Count
Encounter Count encounter count metrics
1. Average Encounter Count
2. Max Encounter Count
3. Min Encounter Count
Record Length record length metrics
1. Average Record Length
2. Max Record Length
3. Min Record Length
Table 2: Descriptive statistics for alive and dead patients
Deliverable: src/event statistics.py, homework1 answer.pdf [10 points]
3 Feature construction [30 points]
It is a common practice to convert raw data into a standard data format before running real
machine learning models. In this section, you will work on src/etl.py file and implement the
necessary python functions in this script. You will work with events.csv, mortality events.csv
and event feature map.csv files provided in data/train folder. The use of pandas library
in this question is recommended. Listed below are a few concepts you need to know before
beginning feature construction (for details please refer to lectures).
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• Observation Window: The time interval you will use to identify relevant events. Only
events present in this window should be included while constructing feature vectors.
The size of observation window is 2000 days.
• Prediction Window: A fixed time interval that is to be used to make the prediction.
Events in this interval should not be included in constructing feature vectors. The size
of prediction window is 30 days.
• Index date: The day on which mortality is to be predicted. Index date is evaluated as
follows:
– For deceased patients: Index date is 30 days prior to the death date (timestamp
field) in data/train/mortality events.csv.
– For alive patients: Index date is the last event date in data/train/events.csv for
each alive patient.
Note: In the test etl.py test, please be careful the format of trailing space and line
breaks issue we provide in the test feature order. Adding a trailing blanks is not required
in solution but adding it will not hurt grading. Line breaks are mandatory for grading.
Step - a. Compute the index date [8 points]
Use the definition provided above to compute the index date for all patients. Complete the
method calculate index date provided in src/etl.py .
Deliverable: src/etl.py, deliverables/etl index dates.csv
Step - b. Filter events [5 points]
Consider an observation window (2000 days) and prediction window (30 days). Remove
the events that occur outside the observation window. Complete the method f ilter events
provided in src/etl.py .
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Deliverable: src/etl.py, deliverables/etl filtered events.csv
c. Aggregate events [10 points]
To create features suitable for machine learning, we will need to aggregate the events for
each patient as follows:
• sum values for diagnostics and medication events (i.e. event id starting with DIAG
and DRUG).
• count occurences for lab events (i.e. event id starting with LAB).
Each event type will become a feature and we will directly use event id as feature name.
For example, given below raw event sequence for a patient,
1053 , DIAG319049 , Acute respiratory failure ,2924 -10 -08 ,1.0
1053 , DIAG197320 , Acute renal failure syndrome ,2924 -10 -08 ,1.0
1053 , DRUG19122121 , Insulin ,2924 -10 -08 ,1.0
1053 , DRUG19122121 , Insulin ,2924 -10 -11 ,1.0
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -08 ,3.000
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -08 ,3.690
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -09 ,3.240
1053 , LAB3026361 , Erythrocytes in Blood ,2924 -10 -10 ,3.470
We can get feature value pairs(event id, value) for this patient with ID 1053 as
( DIAG319049 , 1.0)
( DIAG197320 , 1.0)
( DRUG19122121 , 2.0)
( LAB3026361 , 4)
You will notice there are certain events with no entries in the values column. Handle these missing values by removing all events with null values while
constructing the features. Next, replace each event id with the feature id provided in
data/train/event feature map.csv
(708 , 1.0)
(306 , 1.0)
(2475 , 2.0)
(3030 , 3.35)
Further, in machine learning algorithm like logistic regression, it is important to normalize different features into the same scale using an approach like min-max normalization
(hint: we define min(x) is always 0, i.e. the scale equation become x/max(x)). Complete
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the method aggregate events provided in src/etl.py .
Deliverable: src/etl.py and deliverables/etl aggregated events.csv
d. Save in SVMLight format [7 points]
If the dimensionality of a feature vector is large but the feature vector is sparse (i.e. it has
only a few nonzero elements), sparse representation should be employed. In this problem
you will use the provided data for each patient to construct a feature vector and represent
the feature vector in SVMLight format.
< line .=. < target < feature : < value < feature : < value
< target .=. 1 | 0
< feature .=. < integer
< value .=. < float
The target value and each of the feature/value pairs are separated by a space character.
Feature/value pairs MUST be ordered by increasing feature number. Features with value
zero can be skipped. For example, the feature vector in SVMLight format will look like:
1 2:0.5 3:0.12 10:0.9 2000:0.3
0 4:1.0 78:0.6 1009:0.2
1 33:0.1 34:0.98 1000:0.8 3300:0.2
1 34:0.1 389:0.32
where, 1 or 0 will indicate whether the patient is alive or dead i.e. the label and it will
be followed by a series of feature-value pairs sorted by the feature index (idx) value.
Deliverable: src/etl.py, deliverables/features svmlight.train and deliverables/features.train
4 Predictive Modeling [45 points]
4.1 Model Creation [15 points]
In the previous section, you constructed feature vectors for patients to be used as training
data in various predictive models (classifiers). Now you will use this training data (deliverables/features svmlight.train) in 3 predictive models.
a. Implement Logistic Regression, SVM and Decision Tree. Skeleton code is provided in
src/models partb.py, src/models partc.py.
b. Report performance metrics on the training data (deliverables/features svmlight.train).
Skeleton code is provided in src/models partb.py. You will evaluate and report the perfor8
mance of your predictive models based on the metrics listed in Table 3. Include this table
in homework1 answer.pdf
Model Accuracy AUC Precision Recall F-Score
Logistic Regression
SVM
Decision Tree
Table 3: Model performance on training data
c. Evaluate your predictive models on a separate test dataset in data/features svmlight.validate
(binary labels are provided in that svmlight file as the first field). Skeleton code is provided
in src/models partc.py. You will report the performance of your predictive models based on
the metrics listed in Table 4. Include this table in homework1 answer.pdf
Model Accuracy AUC Precision Recall F-Score
Logistic Regression
SVM
Decision Tree
Table 4: Model performance on test data
d. Based on the performance metrics on training and test data, please propose some
strategies to improve the test performance and also provide the justification for your recommendation. For example, the strategies can be “gather more training data” or “do parameter
tuning more on the algorithms”.
Deliverable: src/models partb.py, src/models partc.py, homework1 answer.pdf
[15 points]
4.2 Model Validation [10 points]
In order to fully utilize the available data and obtain more reliable results, machine learning
practitioners use cross-validation to evaluate and improve their predictive models. You will
demonstrate using two cross-validation strategies against Logistic Regression.
• K-fold: Divide all the data into k groups of samples. Each time 1
k
samples will be used
as test data and the remaining samples as training data.
• Randomized K-fold: Iteratively random shuffle the whole dataset and use top specific
percentage of data as training and the rest as test.
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a. Implement the two cross-validation strategies in src/cross.py.
1. K-fold: Use the number of iterations k=5;
2. Randomized K-fold: Use a test data percentage of 20% and k=5 for the number of
iterations for Randomized
b. Report the average Accuracy and AUC in Table 5. Include this table in homework1 answer.pdf
CV strategy Accuracy AUC
K-Fold
Randomized
Table 5: Cross Validation
NOTE: You will use the features that you constructed in Section 3 as the entire dataset
for this problem.
Deliverable: src/cross.py, homework1 answer.pdf [10 points]
4.3 Creating Your Best Model [15 points]
In this part, you will create your own best predictive model and set of features to attempt
to obtain better performance compared to what you just worked on. You are advised to
try out different things to improve the performance of your predictive model. One may try
out new features, or use feature selection techniques to reduce the feature set, or tune the
parameters of the predictive model or try ensemble techniques. However, one must not
change the observation window and prediction window.
You should use the data available in data/train to construct features and train your
predictive model. It is advisable to use cross validation and AUC as the metric to determine the relative performance of your model. Your final model will be evaluated on a
(separate) test set for which the labels are unknown to you. The events in the observation
window corresponding to the test patients are available in data/test/events.csv. If you are
using the same features as in Section 3 for the test set, you may use the feature map in
data/test/event feature map.csv.
a. Implement your predictive model in src/my model.py. You are free to use your own
features and predictive model. Please ensure that your predicted labels are either 0 or 1.
Report your features of the test patients in deliverables/test features.txt. Submit your predictions in the form of a csv file (patient id, predicted label) in deliverables/my predictions.csv
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b. Write a short paragraph on your best predictive model (based on cross validation
and AUC) and the other models that you tried. What was the rationale behind your approach? Did your model perform better than in the previous section? Include this in
homework1 answer.pdf
Deliverable 1: deliverables/test features.txt
(Refer to the skeleton code for the required format)
Deliverable 2: src/my model.py
Deliverable 3: deliverables/my predictions.csv
4.4 Kaggle [5 + up to 5 bonus points]
Kaggle is a platform for predictive modelling and analytics competitions. Submit your
soft-labeled CSV prediction file (Y prediction is in the range of [0,1]) you implemented in
4.3 to a kaggle competition created specifically for this assignment to compete with your
fellow classmates. A gatech.edu email address is required to participate; follow the sign up
directions using your university email address or if you already have an account, change the
email on your existing account via your profile settings so you can participate. Make sure
your display name (not necessarily your username) matches either your actual full name or
your GT account username so your kaggle submission can be linked back to Canvas(Do
NOT use nickname, otherwise we do not know whom takes this competition and your score
won’t count in this case).
Evaluation criteria is AUC. The predicted label is a soft label, which represents the
possibility of mortality for each patient you predict. The label range is between 0 and 1. 50%
of the data is used for the public leaderboard where you can receive feedback on your model.
The final private leaderboard will use the remaining 50% of the data and will determine your
final class ranking. More specific details can be found on the kaggle competition website.
Score at least 0.6 AUC to receive 5 points of credit. Additional bonus points can be
received for your performance according to the following:
• Top 10%: 5 bonus points
• Top 15%: 4 bonus points
• Top 20%: 3 bonus points
• Top 25%: 2 bonus points
• Top 30%: 1 bonus point
Percentages are based on the entire class size, not just those who submit to kaggle.
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5 Submission [5 points]
The folder structure of your submission should be as below. You can use the tree command
to dispay and verify the folder structure is as seen below. All modified src code should
be in src folder. You should not change the given function names in source code.
All other unrelated files will be discarded during testing and you will get ZERO
score for Submission part. Make sure your codes com compile/run normally,
otherwise you will get full penalty without comments
< your gtid - < your gt account - hw1
| - - Certificate_MIMIC . pdf
| - - homework1_answer . pdf
| - - src
| - - event_statistics . py
| - - etl . py
| - - models_partb . py
| - - models_partc . py
| - - cross . py
| - - utils . py
| - - my_model . py
| - - deliverables
| - - etl_index_dates . csv
| - - etl_filtered_events . csv
| - - etl_aggregated_events . csv
| - - features_svmlight . train
| - - features . train
| - - test_features . txt
| - - my_predictions . csv
Create a tar archive of the folder above with the following command and submit the tar file
(should have one folder named ’< yourGT id -< yourGT account -hw1’ inside the .tar.gz
file).
tar - czvf < your GTid - < your GT account - hw1 . tar . gz \
< your GTid - < your GT account - hw1
Example submission: 901234567-gburdell3-hw1.tar.gz
Common Errors which are not accepted:
• Underscore: 901234567 gburdell3 hw1.tar.gz
• Zip file: zip your files and rename it
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