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                                            lkqnaruto

Question on crf layer, why loop through batch before crf layer?

> Hi @lkqnaruto , > > By interleaved zeros and ones, I meant a mask like `[0, 1, 0, 1, 1, 0, 0, 0, 1, ...]` instead of `[1, 1,...

For cases like O->I, should I manually set the corresponding entries in the transition probability matrix to zero?

> Hi @lkqnaruto , Yes, you can do that if you want to initialize the CRF layer with such constraints, but the pytorch-crf library does not expose an API for...

For cases like O->I, should I manually set the corresponding entries in the transition probability matrix to zero?

> Yes, I believe so. I see it as a form of model initialization similar to [adjusting the bias terms of a classification layer to produce the prior probabilities of...

Is it possible to enforce constraint on transition matrix of CRF?

I'm referring to the CRF layer in the BiLSTM and BERT

Is it possible to enforce constraint on transition matrix of CRF?

> They both use the CRF implemented in [pytorch-crf](https://pytorch-crf.readthedocs.io/en/stable/#torchcrf.CRF). Does it appear to natively support what you are trying to do? I don't think it is support what I want...

Is it possible to enforce constraint on transition matrix of CRF?

> I am not sure. If you create or obtain a torch-compatible CRF implementation that does what you need, I may be able to discuss with you how to use...

Is it possible to enforce constraint on transition matrix of CRF?

> None of the CRFs used in medaCy are implemented within medaCy, so the only changes one would make to medaCy code would be replacing the CRF implementations imported from...

How to choose reference data? Should test data and refernce data coming from the same group? like using control group to infer control group cell types, using disease group to infer disease group labels?

@LTLA Thank you for the reply. I wonder when you say "A drug isn't going to cause cells to change their broad identities", do you mean statistically or biologically? And...

How to choose reference data? Should test data and refernce data coming from the same group? like using control group to infer control group cell types, using disease group to infer disease group labels?

@thank you. If the drug or disease indeed triggers differentiation, does the multi reference strategy still work? And the truth is I have no idea whether there will be any...