How to use Machine Learning to discover important biomarkers in an unbalanced small data set Announcing the arrival of Valued Associate #679: Cesar Manara Planned maintenance scheduled April 17/18, 2019 at 00:00UTC (8:00pm US/Eastern) 2019 Moderator Election Q&A - Questionnaire 2019 Community Moderator Election ResultsRegression for binary classification and AUC metricHow to deal with a machine learning model which affects future ground truth data?Data representation (NoSQL database?) for a medical studyHandling data imbalance and class number for classificationHow to classify parametric curves?How do I control for some patients providing multiple samples in my training data?Can we make two separate models vs one for classification?Multivariate time Series classification - One classBuilding a minimal encoding of nominal labels from numerical featuresoversampling data with subclass
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How to use Machine Learning to discover important biomarkers in an unbalanced small data set
Announcing the arrival of Valued Associate #679: Cesar Manara
Planned maintenance scheduled April 17/18, 2019 at 00:00UTC (8:00pm US/Eastern)
2019 Moderator Election Q&A - Questionnaire
2019 Community Moderator Election ResultsRegression for binary classification and AUC metricHow to deal with a machine learning model which affects future ground truth data?Data representation (NoSQL database?) for a medical studyHandling data imbalance and class number for classificationHow to classify parametric curves?How do I control for some patients providing multiple samples in my training data?Can we make two separate models vs one for classification?Multivariate time Series classification - One classBuilding a minimal encoding of nominal labels from numerical featuresoversampling data with subclass
$begingroup$
I have a project which I am just starting out, I am only just learning machine learning and statistics so I am somewhat unsure as to what approaches will be good to start off with, and I am sorry if this does not belong here.
The data set is of different patients carrying a certain disease and each patient has different biomarkers and physical measurements such as heart rate at different time points, until death, if they do die. I was told that the goal was to identify the key features, which would be associated with a a patient dying.
I only have 33 patients, and only 16 of them have died. But disregarding patient the biomarkers came from I have 300 odd time slots, I first tried to approach it as a binary classification problem, classifying the 'death' point from other points. The problems were:
- The data imbalance and,
- How to you interpret the models to discover most important features.
For imbalance, I tried SMOTE oversampling with didn't work as I thought, then I randomly under-sampled, which gave decent results but the data set was even smaller, so I wasn't sure if its a good idea.
Simple binary classification models like Gaussian Naive Bayes and Logistic Regression did okay even with the imbalanced data, but they don't (at least as far as I know) give a way to discern feature importance..
So my main questions are:
What's the best way to approach this problem, or in general what kind of approaches work when you want to identify most influential features (data measurements).
If I do want to approach it as a binary classification problem what approaches can I take to combat class imbalance?
machine-learning data-mining
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
asked Apr 1 at 20:06
InfinityInfinity
1
$endgroup$
add a comment |
$begingroup$
I have a project which I am just starting out, I am only just learning machine learning and statistics so I am somewhat unsure as to what approaches will be good to start off with, and I am sorry if this does not belong here.
The data set is of different patients carrying a certain disease and each patient has different biomarkers and physical measurements such as heart rate at different time points, until death, if they do die. I was told that the goal was to identify the key features, which would be associated with a a patient dying.
I only have 33 patients, and only 16 of them have died. But disregarding patient the biomarkers came from I have 300 odd time slots, I first tried to approach it as a binary classification problem, classifying the 'death' point from other points. The problems were:
- The data imbalance and,
- How to you interpret the models to discover most important features.
For imbalance, I tried SMOTE oversampling with didn't work as I thought, then I randomly under-sampled, which gave decent results but the data set was even smaller, so I wasn't sure if its a good idea.
Simple binary classification models like Gaussian Naive Bayes and Logistic Regression did okay even with the imbalanced data, but they don't (at least as far as I know) give a way to discern feature importance..
So my main questions are:
What's the best way to approach this problem, or in general what kind of approaches work when you want to identify most influential features (data measurements).
If I do want to approach it as a binary classification problem what approaches can I take to combat class imbalance?
machine-learning data-mining
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
asked Apr 1 at 20:06
InfinityInfinity
1
$endgroup$
1
$begingroup$
I think you need to be a bit more specific on what your questions is or it will be difficult to provide you with helpful answers
$endgroup$
– oW_♦
Apr 1 at 20:56
$begingroup$
You are going to have a hard time getting solid results for testing biomarkers with sample sizes that low unless that effect sizes are huge. The number of different measurements doesn't really increase statistical power very much. You might want to look at prior research on "severity of illness" to get an idea of what has already been discovered. There is quite a bit already done in the intensive care literature using various techniques.
$endgroup$
– 42-
Apr 2 at 0:13
add a comment |
$begingroup$
I have a project which I am just starting out, I am only just learning machine learning and statistics so I am somewhat unsure as to what approaches will be good to start off with, and I am sorry if this does not belong here.
The data set is of different patients carrying a certain disease and each patient has different biomarkers and physical measurements such as heart rate at different time points, until death, if they do die. I was told that the goal was to identify the key features, which would be associated with a a patient dying.
I only have 33 patients, and only 16 of them have died. But disregarding patient the biomarkers came from I have 300 odd time slots, I first tried to approach it as a binary classification problem, classifying the 'death' point from other points. The problems were:
- The data imbalance and,
- How to you interpret the models to discover most important features.
For imbalance, I tried SMOTE oversampling with didn't work as I thought, then I randomly under-sampled, which gave decent results but the data set was even smaller, so I wasn't sure if its a good idea.
Simple binary classification models like Gaussian Naive Bayes and Logistic Regression did okay even with the imbalanced data, but they don't (at least as far as I know) give a way to discern feature importance..
So my main questions are:
What's the best way to approach this problem, or in general what kind of approaches work when you want to identify most influential features (data measurements).
If I do want to approach it as a binary classification problem what approaches can I take to combat class imbalance?
machine-learning data-mining
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
asked Apr 1 at 20:06
InfinityInfinity
1
$endgroup$
I have a project which I am just starting out, I am only just learning machine learning and statistics so I am somewhat unsure as to what approaches will be good to start off with, and I am sorry if this does not belong here.
The data set is of different patients carrying a certain disease and each patient has different biomarkers and physical measurements such as heart rate at different time points, until death, if they do die. I was told that the goal was to identify the key features, which would be associated with a a patient dying.
I only have 33 patients, and only 16 of them have died. But disregarding patient the biomarkers came from I have 300 odd time slots, I first tried to approach it as a binary classification problem, classifying the 'death' point from other points. The problems were:
- The data imbalance and,
- How to you interpret the models to discover most important features.
For imbalance, I tried SMOTE oversampling with didn't work as I thought, then I randomly under-sampled, which gave decent results but the data set was even smaller, so I wasn't sure if its a good idea.
Simple binary classification models like Gaussian Naive Bayes and Logistic Regression did okay even with the imbalanced data, but they don't (at least as far as I know) give a way to discern feature importance..
So my main questions are:
What's the best way to approach this problem, or in general what kind of approaches work when you want to identify most influential features (data measurements).
If I do want to approach it as a binary classification problem what approaches can I take to combat class imbalance?
machine-learning data-mining
machine-learning data-mining
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
asked Apr 1 at 20:06
InfinityInfinity
1
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
asked Apr 1 at 20:06
InfinityInfinity
1
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
edited Apr 2 at 1:30
Stephen Rauch♦
1,52551330
1,52551330
asked Apr 1 at 20:06
InfinityInfinity
1
asked Apr 1 at 20:06
InfinityInfinity
1
asked Apr 1 at 20:06
InfinityInfinity
1
1
1
$begingroup$
I think you need to be a bit more specific on what your questions is or it will be difficult to provide you with helpful answers
$endgroup$
– oW_♦
Apr 1 at 20:56
$begingroup$
You are going to have a hard time getting solid results for testing biomarkers with sample sizes that low unless that effect sizes are huge. The number of different measurements doesn't really increase statistical power very much. You might want to look at prior research on "severity of illness" to get an idea of what has already been discovered. There is quite a bit already done in the intensive care literature using various techniques.
$endgroup$
– 42-
Apr 2 at 0:13
add a comment |
1
$begingroup$
I think you need to be a bit more specific on what your questions is or it will be difficult to provide you with helpful answers
$endgroup$
– oW_♦
Apr 1 at 20:56
$begingroup$
You are going to have a hard time getting solid results for testing biomarkers with sample sizes that low unless that effect sizes are huge. The number of different measurements doesn't really increase statistical power very much. You might want to look at prior research on "severity of illness" to get an idea of what has already been discovered. There is quite a bit already done in the intensive care literature using various techniques.
$endgroup$
– 42-
Apr 2 at 0:13
1
1
$begingroup$
I think you need to be a bit more specific on what your questions is or it will be difficult to provide you with helpful answers
$endgroup$
– oW_♦
Apr 1 at 20:56
$begingroup$
I think you need to be a bit more specific on what your questions is or it will be difficult to provide you with helpful answers
$endgroup$
– oW_♦
Apr 1 at 20:56
$begingroup$
You are going to have a hard time getting solid results for testing biomarkers with sample sizes that low unless that effect sizes are huge. The number of different measurements doesn't really increase statistical power very much. You might want to look at prior research on "severity of illness" to get an idea of what has already been discovered. There is quite a bit already done in the intensive care literature using various techniques.
$endgroup$
– 42-
Apr 2 at 0:13
$begingroup$
You are going to have a hard time getting solid results for testing biomarkers with sample sizes that low unless that effect sizes are huge. The number of different measurements doesn't really increase statistical power very much. You might want to look at prior research on "severity of illness" to get an idea of what has already been discovered. There is quite a bit already done in the intensive care literature using various techniques.
$endgroup$
– 42-
Apr 2 at 0:13
add a comment |
1 Answer
1
active
oldest
votes
$begingroup$
If your goal is to identify important features, I would say go for a Decision Tree which inherently calculates importance/separation capability of the features while selecting them for splitting the internal nodes. You can also go for an ensemble of decision trees such as RandomForest which will return feature importance based on their average impurity reduction throughout all its trees.
This article can help you set up a basic experiment.
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
$endgroup$
add a comment |
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$begingroup$
If your goal is to identify important features, I would say go for a Decision Tree which inherently calculates importance/separation capability of the features while selecting them for splitting the internal nodes. You can also go for an ensemble of decision trees such as RandomForest which will return feature importance based on their average impurity reduction throughout all its trees.
This article can help you set up a basic experiment.
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
$endgroup$
add a comment |
$begingroup$
If your goal is to identify important features, I would say go for a Decision Tree which inherently calculates importance/separation capability of the features while selecting them for splitting the internal nodes. You can also go for an ensemble of decision trees such as RandomForest which will return feature importance based on their average impurity reduction throughout all its trees.
This article can help you set up a basic experiment.
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
$endgroup$
add a comment |
$begingroup$
If your goal is to identify important features, I would say go for a Decision Tree which inherently calculates importance/separation capability of the features while selecting them for splitting the internal nodes. You can also go for an ensemble of decision trees such as RandomForest which will return feature importance based on their average impurity reduction throughout all its trees.
This article can help you set up a basic experiment.
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
$endgroup$
If your goal is to identify important features, I would say go for a Decision Tree which inherently calculates importance/separation capability of the features while selecting them for splitting the internal nodes. You can also go for an ensemble of decision trees such as RandomForest which will return feature importance based on their average impurity reduction throughout all its trees.
This article can help you set up a basic experiment.
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
answered Apr 1 at 22:25
Sajid AhmedSajid Ahmed
315
315
add a comment |
add a comment |
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I think you need to be a bit more specific on what your questions is or it will be difficult to provide you with helpful answers
$endgroup$
– oW_♦
Apr 1 at 20:56
$begingroup$
You are going to have a hard time getting solid results for testing biomarkers with sample sizes that low unless that effect sizes are huge. The number of different measurements doesn't really increase statistical power very much. You might want to look at prior research on "severity of illness" to get an idea of what has already been discovered. There is quite a bit already done in the intensive care literature using various techniques.
$endgroup$
– 42-
Apr 2 at 0:13