binn 0.0.2

A package to generate and interpret biologically informed neural networks.

Biologically Informed Neural Network (BINN)

BINN documentation is avaiable here.

The BINN-package allows you to create a sparse neural network from a pathway and input file. The examples presented in notebooks use the Reactome pathway database and a proteomic dataset to generate the neural network. It also allows you to train and interpret the network using SHAP. Plotting functions are also available for generating sankey plots. The article presenting the BINN can currently be found at bioRxiv.

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Usage

First, a network is created. This is the network that will be used to create the sparse BINN.

from binn import BINN, Network
import pandas as pd

input_data = pd.read_csv("../data/test_data.tsv", sep="\t")
translation = pd.read_csv("../data/translation.tsv", sep="\t")
pathways = pd.read_csv("../data/pathways.tsv", sep="\t")

network = Network(
    input_data=input_data,
    pathways=pathways,
    mapping=translation,
    verbose=True
)

The BINN can thereafter be generated using the network:

binn = BINN(
    pathways=network,
    n_layers=4,
    dropout=0.2,
    validate=False,
)

An sklearn wrapper is also available:

from binn import BINNClassifier

binn = BINNClassifier(
    pathways=network,
    n_layers=4,
    dropout=0.2,
    validate=True,
    epochs=10,
    threads=10,
    logger=SuperLogger("logs/test")
)

This generates the Pytorch sequential model:

Sequential(
  (Layer_0): Linear(in_features=446, out_features=953, bias=True)
  (BatchNorm_0): BatchNorm1d(953, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
  (Dropout_0): Dropout(p=0.2, inplace=False)
  (Tanh 0): Tanh()
  (Layer_1): Linear(in_features=953, out_features=455, bias=True)
  (BatchNorm_1): BatchNorm1d(455, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
  (Dropout_1): Dropout(p=0.2, inplace=False)
  (Tanh 1): Tanh()
  (Layer_2): Linear(in_features=455, out_features=162, bias=True)
  (BatchNorm_2): BatchNorm1d(162, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
  (Dropout_2): Dropout(p=0.2, inplace=False)
  (Tanh 2): Tanh()
  (Layer_3): Linear(in_features=162, out_features=28, bias=True)
  (BatchNorm_3): BatchNorm1d(28, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
  (Dropout_3): Dropout(p=0.2, inplace=False)
  (Tanh 3): Tanh()
  (Output layer): Linear(in_features=28, out_features=2, bias=True)
)

Example input

Test data - this file should contain a column with the feature names (quantmatrix or some matrix containing input column - in this case "Protein")

PeptideSequence	Protein (this is our input column)
VDRDVAPGTLC(UniMod:4)DVAGWGIVNHAGR	P00746
VDRDVAPGTLC(UniMod:4)DVAGWGIVNHAGR	P00746
VDTVDPPYPR	P04004
AVTEQGAELSNEER	P27348
VDVIPVNLPGEHGQR	P02751

Pathways file - this file should contain the mapping used to create the connectivity in the hidden layers.

parent (target)	child (source)
R-BTA-109581	R-BTA-109606
R-BTA-109581	R-BTA-169911
R-BTA-109581	R-BTA-5357769
R-BTA-109581	R-BTA-75153
R-BTA-109582	R-BTA-140877

Translation file - this file is alternative, but is useful if some translation is needed to map the input features to the pathways in the hiddenn layers. In this case, it is used to map proteins (UniProt IDs) to pathways (Reactome IDs).

input (UniProd IDs)	translation (Reactome IDs)
A0A075B6P5	R-HSA-166663
A0A075B6P5	R-HSA-173623
A0A075B6P5	R-HSA-198933
A0A075B6P5	R-HSA-202733
A0A075B6P5	R-HSA-2029481

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Plotting

Plotting a subgraph starting from a node generates the plot: A compelte sankey may look like this:

Installation

The package can be installed and built from source with git.

git clone [e-mail]:InfectionMedicineProteomics/BINN.git
pip install -e BINN/

Testing

The software has been tested on desktop machines running Windows 10/Linux (Ubuntu). Small networks are not RAM-intensive and all experiments have been run comfortably with 16 GB RAM.

Contributors

Erik Hartman, infection medicine proteomics, Lund University

Aaron Scott, infection medicine proteomics, Lund University

Contact

Erik Hartman - [e-mail]