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GROBID is a machine learning library for extracting, parsing, and re-structuring raw documents such as PDF into structured XML/TEI encoded documents with a particular focus on technical and scientific publications. First developments started in 2008 as a hobby. In 2011 the tool has been made available in open source. Work on GROBID has been steady as a side project since the beginning and is expected to continue as such. Header extraction and parsing from article in PDF format. The...

TCNs exhibit longer memory than recurrent architectures with the same capacity. Performs better than LSTM/GRU on a vast range of tasks (Seq. MNIST, Adding Problem, Copy Memory, Word-level PTB...). Parallelism (convolutional layers), flexible receptive field size (possible to specify how far the model can see), stable gradients (backpropagation through time, vanishing gradients). The usual way is to import the TCN layer and use it inside a Keras model. The receptive field is defined as the...

FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a...

mlpy is a Python module for Machine Learning built on top of NumPy/SciPy and of GSL. mlpy provides high-level functions and classes allowing, with few lines of code, the design of rich workflows for classification, regression, clustering and feature selection. mlpy is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 3. mlpy is available both for Python >=2.6 and Python 3.X.