User: teabonng

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teabonng10
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Posts by teabonng

<prev • 24 results • page 1 of 3 • next >
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Histone modification patterns
... Hi Everyone, Can anyone refer me to a good reference that shows evidence that genes that belong to the same regulatory pathway have similar histone modification patterns that can be statistically analyzed? Thank you. ...
chromatin pattern written 14 days ago by teabonng10
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PPI networks in disease vs. healthy
... Hi Everyone, I was reading about some PPIs recently. Please excuse if my question is too simple. My question is, if i reconstruct PPIs from healthy and diseased individuals from omics data, would you expect that the reconstructed PPIs will be different, even if only a few nodes? ...
ppi networks written 17 days ago by teabonng10 • updated 16 days ago by Kevin Blighe35k
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Comment: C: Machine learning predictor has no correlation with output variable
... Hi Jean-Karim, Thank you for your help. I would just like to further clarify, since the logistic regression takes into account the individual contributions of each feature, but I did not add any interaction terms. In this case, I'm not sure if i can say that there is some interaction among the fea ...
written 7 weeks ago by teabonng10
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Machine learning predictor has no correlation with output variable
... Hi Everyone, I built a logistic regression classifier for predicting genes that has around 75% accuracy. Predictor A is a transcription factor that is a top predictor. However, when I look at the the scatterplot there is absolutely no correlation and the positive and negative examples show the same ...
machine learning written 7 weeks ago by teabonng10 • updated 7 weeks ago by Jean-Karim Heriche17k
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Comment: C: Neural networks feature importance
... Hi karl.stamm, Can you provide an example on how to adapt Garson's algorithm for multiple neurons? Can I calculate the importances with respect to each neuron instead? Thanks ...
written 12 weeks ago by teabonng10
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Neural networks feature importance
... Hi everyone, I am using a neural network with two output neurons for my omics data to predict the binary classification of genes. It is important in the study to know the feature importance. I know that the Garson's algorithm and connection weights algorithm are used in neural networks with one hid ...
neural network written 3 months ago by teabonng10 • updated 3 months ago by karl.stamm3.4k
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Comment: C: Data Transformations for machine learning
... Hi Kevin, Thanks for your reply. I have decided to log transform all the features. Then do the standardization so that they have more or less the same range. Then use as input for the neural network. Would this make sense? Thanks, teabonng ...
written 4 months ago by teabonng10
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Comment: C: Data Transformations for machine learning
... Hi Wouter, My input features are normalized feature counts based on ChIP-Seq data, which I wish to use for logistic regression. However, the different features have different distributions, and I am new to machine learning and I would like to get insights on whether it is valid to use some of the r ...
written 4 months ago by teabonng10
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Data Transformations for machine learning
... Hi, I have multiple features as input for machine learning. My input features are normalized feature counts based on ChIP-Seq data, which I wish to use for logistic regression and neural network. However, the different features have different distributions, and I am new to machine learning and I wo ...
machine learning data transformation written 4 months ago by teabonng10
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ChIP-Seq Read Counts
... Hi Everyone, I am very new to ChIP-Seq analysis, but i will be analyzing data from multiple studies. However, some ChIP seq studies do not have Input to compare the distribution of mapped reads, so I cannot do peak calling. In this case, is it common practice to simply get the normalized counts (li ...
chip-seq written 5 months ago by teabonng10

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