budach / pysster Goto Github PK
View Code? Open in Web Editor NEWpysster: Learning Sequence And Structure Motifs In Biological Sequences Using Convolutional Neural Networks
License: MIT License
pysster: Learning Sequence And Structure Motifs In Biological Sequences Using Convolutional Neural Networks
License: MIT License
Hi,
I'm having trouble adding dense layers of with different neuron numbers. For instance, if I would like 3 hidden layers of widths 300, 100, 30 - is there a way to initialize a pysster model to handle this?
Thank you for your help!
Todo: remove the keras dependency and switch to tf.keras when Tensorflow 2.0 is released.
Hi, just spotted a small issue with the documentation of utils.annotate_structures - as well as H,I,M,S forgi can output F (fiveprime) and T (threeprime) as labels, it might be good if this was mentioned to avoid confusion.
Simply replacing all occurrences of from keras
with from tensorflow.python.keras
works like a charm - no crashes - BUT: the loss on my data sets doesn't improve over time anymore. Other users observe similar behavior (tensorflow/tensorflow#15026, tensorflow/tensorflow#15831).
I will try again with a future tensorflow version. Having one less dependency is always nice.
Hi I was wondering if adding a tensorboard option is planned.
For each kernel, there are a lot of indidivual output files to look at right now (sequence logo, violin plots, positional enrichment plots). I guess it would be convenient to generate an html summary showing all plots to get a quick overview by just scrolling through that single html document.
Hello, may I ask if it is possible to provide the structure strings for the data sets in /tutorials/rbp/data/ obtained via ViennaRNA python bindings (in the measure_rbp_pysster.py)?
I tried to do this by running the measure_rbp_pysster.py file but I have trouble installing the ViennaRNA and cannot resolve the installation problem.
Thank you very much.
When training two pysster Model objects with the same seed, model weights are not equal anymore with keras 2.3.0. Respective tests have been disabled for now. Might not need a fix, since we want to switch to tf.keras anyway.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.