Resource retrieval

Get the pre-trained net:

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NetModel parameters

This model consists of a family of individual nets, each identified by a specific parameter combination. Inspect the available parameters:

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Pick a non-default net by specifying the parameters:

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Pick a non-default uninitialized net:

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Basic usage

Given a piece of text, BioBERT net produces a sequence of feature vectors of size 768, which corresponds to the sequence of input words or subwords:

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Obtain dimensions of the embeddings:

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Visualize the embeddings:

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Transformer architecture

Each input text segment is first tokenized into words or subwords using a word-piece tokenizer and additional text normalization. Integer codes called token indices are generated from these tokens, together with additional segment indices:

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For each input subword token, the encoder yields a pair of indices that corresponds to the token index in the vocabulary and the index of the sentence within the list of input sentences:

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The list of tokens always starts with special token index 102, which corresponds to the classification index. Also the special token index 103 is used as a separator between the different text segments. Each subword token is also assigned a positional index:

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A lookup is done to map these indices to numeric vectors of size 768:

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For each subword token, these three embeddings are combined by summing elements with ThreadingLayer:

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The transformer architecture then processes the vectors using 12 structurally identical self-attention blocks stacked in a chain:

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The key part of these blocks is the attention module comprising of 12 parallel self-attention transformations, also called “attention heads.” Each head uses an AttentionLayer at its core:

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BioBERT uses self-attention, where the embedding of a given subword depends on the full input text. The following figure compares self-attention (lower left) to other types of connectivity patterns that are popular in deep learning:

Sentence analogies

Define a sentence embedding net that takes the last feature vector from BioBERT subword embeddings (as an arbitrary choice):

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Define a list of sentences in two broad categories (food and music):

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Precompute the embeddings for a list of sentences:

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Visualize the similarity between the sentences using the net as a feature extractor:

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Net information

Inspect the number of parameters of all arrays in the net:

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Obtain the total number of parameters:

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Obtain the layer type counts:

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Display the summary graphic:

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Export to MXNet

Export the net into a format that can be opened in MXNet:

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Export also creates a net.params file containing parameters:

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Get the size of the parameter file:

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