Pretraining for Large-Scale Functional Connectome Fingerprinting Supports Generalization and Transfer Learning in Functional Neuroimaging.
The 5 matches
- [1] § Materials and Methods › Data and preprocessing ↔ preproc_model_embedding_code.zip/preproc_model_embedding_code/embedding_generation_script.py, lines 179–226 · score 0.81 · global signal, fMRIPrep, CSF, detrended, overlap, preprocessing
- [2] § Materials and Methods › Model architecture and pretraining ↔ preproc_model_embedding_code.zip/preproc_model_embedding_code/brain2vec_model_arch.py, lines 39–140 · score 0.75 · weight decay, class weighting, cross entropy, Adam, loss, epochs
- [3] § Materials and Methods › Data and preprocessing ↔ preproc_model_embedding_code.zip/preproc_model_embedding_code/embedding_generation_script.py, lines 44–48 · score 0.64 · minimal preprocessing, AOMIC PIOP1, fMRIPrep, derivatives
- [4] § Materials and Methods › Transfer-learning experiments: identification of new individuals ↔ preproc_model_embedding_code.zip/preproc_model_embedding_code/brain2vec_model_arch.py, lines 39–140 · score 0.62 · weight decay, cross entropy, momentum, model embedding, class, linear
- [5] § Materials and Methods › Model architecture and pretraining ↔ preproc_model_embedding_code.zip/preproc_model_embedding_code/brain2vec_model_arch.py, lines 149–258 · score 0.56 · PyTorch, ReLU, lightning, affine, leaky, momentum
Paper
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The authors' code
Python · 358 lines · 13 KB · no license · 3 matches
- #!/usr/bin/env python3
- # -*- coding: utf-8 -*-
- import pytorch_lightning as pl
- from pytorch_lightning.callbacks.early_stopping import EarlyStopping
- import torchmetrics
- from sklearn.utils.class_weight import compute_class_weight
- import os
- from pathlib import Path
- import torch
- from torch.utils.data import Dataset, DataLoader
- import torch.nn as nn
- import torch.nn.functional as F
- import torch.optim as optim
- # import glob
- import numpy as np
- # import seaborn as sns
- import pandas as pd
- import matplotlib.pyplot as plt
- from tqdm import tqdm
- # this code might occasionally borrow code, approaches or generally draw inspiration from https://github.com/hltcoe/xvectors
- # Function to initialize model weights (called by the hltcoe xvec github code)
- def init_weight(model):
- for m in model.modules():
- if isinstance(m, nn.Linear) or isinstance(m, nn.Conv1d):
- nn.init.kaiming_normal_(m.weight, a=0.01) # default negative slope of LeakyReLU
- elif isinstance(m, nn.BatchNorm1d):
- if m.affine:
- nn.init.constant_(m.weight, 1)
- nn.init.constant_(m.bias, 0)
- class b2v_FFwdNN_uniform_layer_sizes(pl.LightningModule):
- def __init__(self, input_dim, n_layers: int = 4, layer_dim: int = 1024, embedding_dim: int = 1024, dropout_rate: float = 0.0, nclasses: int = 2,class_weights: list = [1,1], batch_size: int = 16, lr: float = 0.001):
- super().__init__()
- self.save_hyperparameters()
- self.batch_size = batch_size # can be tuned by pytorchlightning
- self.lr = lr # can be tuned by pytorchlightning
- self.n_layers = n_layers
- self.dropout_rate = dropout_rate
- self.input_dim = input_dim
- self.layer_dim = layer_dim
- self.embedding_dim = embedding_dim
- self.nclasses = nclasses
- self.class_weights = class_weights
- self.base_net = torch.nn.Sequential()
- self.base_net.add_module('layer1_linear', nn.Linear(self.input_dim, self.layer_dim))
- self.base_net.add_module('layer1_relu', nn.LeakyReLU(inplace=True))
- self.base_net.add_module('layer1_batchnorm', nn.BatchNorm1d(self.layer_dim, momentum=0.1,affine=False))
- self.base_net.add_module('layer1_dropout',nn.Dropout(p=self.dropout_rate))
- if self.n_layers > 1:
- for ix, ll in enumerate(list(range(1,self.n_layers))):
- self.base_net.add_module('layer'+ str(ll+1) + '_linear', nn.Linear(self.layer_dim, self.layer_dim))
- self.base_net.add_module('layer'+ str(ll+1) + '_relu', nn.LeakyReLU(inplace=True))
- self.base_net.add_module('layer'+ str(ll+1) + '_batchnorm', nn.BatchNorm1d(self.layer_dim, momentum=0.1,affine=False))
- self.base_net.add_module('layer'+ str(ll+1) + '_dropout',nn.Dropout(p=self.dropout_rate))
- self.embed1_linear = nn.Linear(self.layer_dim ,self.embedding_dim)
- self.embed1_relu = nn.LeakyReLU(inplace=True)
- self.embed1_batchnorm = nn.BatchNorm1d(self.embedding_dim, momentum=0.1,affine=False)
- self.output = nn.Linear(self.embedding_dim, self.nclasses)
- init_weight(self)
- self.softmax = nn.Softmax(dim=1);
- # Metrics
- self.train_accuracy = torchmetrics.Accuracy(num_classes=self.nclasses, task = "multiclass")
- self.val_accuracy = torchmetrics.Accuracy(num_classes=self.nclasses, task = "multiclass")
- def forward(self, x):
- base_out = self.base_net.forward(x.float())
- x = self.embed1_linear(base_out)
- x = self.embed1_relu(x)
- embed = self.embed1_batchnorm(x)
- out_logit = self.output(embed)
- out_softmax = self.softmax(out_logit)
- return out_logit, out_softmax, embed, base_out
- def configure_optimizers(self):
- optimizer = optim.Adam(self.parameters(), lr=self.lr, weight_decay=1e-4)
- lr_schedulers = {'scheduler': torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, mode='min',patience=3,verbose=True),
- 'monitor': 'val_loss'}
- return [optimizer], [lr_schedulers]
- def training_step(self, batch, batch_idx):
- x, y, y_str, f_path = batch
- output = self(x)
- y_hat_logits = output[0]
- y_hat_softmax = output[1]
- _, predicted = torch.max(y_hat_softmax, 1)
- loss = F.cross_entropy(y_hat_logits, y, weight=self.class_weights.to(self.device))
- # logging
- self.train_accuracy(predicted, y)
- self.log('train_loss', loss, batch_size = self.batch_size)
- self.log('train_accuracy', self.train_accuracy, on_step=True, prog_bar=True, on_epoch=True, batch_size = self.batch_size)
- return { 'loss': loss, 'preds': predicted, 'targets': y }
- def validation_step(self, batch, batch_idx):
- x, y, y_str, f_path = batch
- output = self(x)
- y_hat_logits = output[0]
- y_hat_softmax = output[1]
- _, predicted = torch.max(y_hat_softmax, 1)
- val_loss = F.cross_entropy(y_hat_logits, y, weight=self.class_weights.to(self.device))
- # logging
- self.val_accuracy(predicted, y)
- self.log('val_loss', val_loss, batch_size = self.batch_size)
- self.log('val_accuracy', self.val_accuracy, on_step=False, prog_bar=True, on_epoch=True, batch_size = self.batch_size)
- return { 'val_loss': val_loss, 'preds': predicted, 'targets': y }
- class b2v_FFwdNN_decrease_layer_sizes(pl.LightningModule):
- def __init__(self, input_dim, n_layers: int = 4, layer_dim: int = 1024, embedding_dim: int = 1024, dropout_rate: float = 0.0, nclasses: int = 2,class_weights: list = [1,1], batch_size: int = 16, lr: float = 0.001):
- super().__init__()
- self.save_hyperparameters()
- self.batch_size = batch_size # can be tuned by pytorchlightning
- self.lr = lr # can be tuned by pytorchlightning
- self.n_layers = n_layers
- self.dropout_rate = dropout_rate
- self.input_dim = input_dim
- self.layer_dim = layer_dim
- self.embedding_dim = embedding_dim
- self.nclasses = nclasses
- self.class_weights = class_weights
- self.base_net = torch.nn.Sequential()
- self.base_net.add_module('layer1_linear', nn.Linear(self.input_dim, self.layer_dim))
- self.base_net.add_module('layer1_relu', nn.LeakyReLU(inplace=True))
- self.base_net.add_module('layer1_batchnorm', nn.BatchNorm1d(self.layer_dim, momentum=0.1,affine=False))
- self.base_net.add_module('layer1_dropout',nn.Dropout(p=self.dropout_rate))
- self.prev_l_size = self.layer_dim
- self.next_l_size = int( self.prev_l_size / 2 )
- if self.n_layers > 1:
- for ix, ll in enumerate(list(range(1,self.n_layers))):
- self.base_net.add_module('layer'+ str(ll+1) + '_linear', nn.Linear(self.prev_l_size, self.next_l_size))
- self.base_net.add_module('layer'+ str(ll+1) + '_relu', nn.LeakyReLU(inplace=True))
- self.base_net.add_module('layer'+ str(ll+1) + '_batchnorm', nn.BatchNorm1d(self.next_l_size, momentum=0.1,affine=False))
- self.base_net.add_module('layer'+ str(ll+1) + '_dropout',nn.Dropout(p=self.dropout_rate))
- self.prev_l_size = self.next_l_size
- self.next_l_size = int( self.prev_l_size / 2 )
- self.embed1_linear = nn.Linear( self.prev_l_size ,self.embedding_dim)
- self.embed1_relu = nn.LeakyReLU(inplace=True)
- self.embed1_batchnorm = nn.BatchNorm1d(self.embedding_dim, momentum=0.1,affine=False)
- self.output = nn.Linear(self.embedding_dim, self.nclasses)
- init_weight(self)
- self.softmax = nn.Softmax(dim=1);
- # Metrics
- self.train_accuracy = torchmetrics.Accuracy(num_classes=self.nclasses, task = "multiclass")
- self.val_accuracy = torchmetrics.Accuracy(num_classes=self.nclasses, task = "multiclass")
- def forward(self, x):
- base_out = self.base_net.forward(x.float())
- x = self.embed1_linear(base_out)
- x = self.embed1_relu(x)
- embed = self.embed1_batchnorm(x)
- out_logit = self.output(embed)
- out_softmax = self.softmax(out_logit)
- return out_logit, out_softmax, embed, base_out
- def configure_optimizers(self):
- optimizer = optim.Adam(self.parameters(), lr=self.lr, weight_decay=1e-4)
- lr_schedulers = {'scheduler': torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, mode='min',patience=3,verbose=True),
- 'monitor': 'val_loss'}
- return [optimizer], [lr_schedulers]
- def training_step(self, batch, batch_idx):
- x, y, y_str, f_path = batch
- output = self(x)
- y_hat_logits = output[0]
- y_hat_softmax = output[1]
- _, predicted = torch.max(y_hat_softmax, 1)
- loss = F.cross_entropy(y_hat_logits, y, weight=self.class_weights.to(self.device))
- # logging
- self.train_accuracy(predicted, y)
- self.log('train_loss', loss, batch_size = self.batch_size)
- self.log('train_accuracy', self.train_accuracy, on_step=True, prog_bar=True, on_epoch=True, batch_size = self.batch_size)
- return { 'loss': loss, 'preds': predicted, 'targets': y }
- def validation_step(self, batch, batch_idx):
- x, y, y_str, f_path = batch
- output = self(x)
- y_hat_logits = output[0]
- y_hat_softmax = output[1]
- _, predicted = torch.max(y_hat_softmax, 1)
- val_loss = F.cross_entropy(y_hat_logits, y, weight=self.class_weights.to(self.device))
- # logging
- self.val_accuracy(predicted, y)
- self.log('val_loss', val_loss, batch_size = self.batch_size)
- self.log('val_accuracy', self.val_accuracy, on_step=False, prog_bar=True, on_epoch=True, batch_size = self.batch_size)
- return { 'val_loss': val_loss, 'preds': predicted, 'targets': y }
- class b2v_FFwdNN_embed_only(pl.LightningModule):
- def __init__(self, input_dim, embedding_dim: int = 1024, nclasses: int = 2, dropout_rate: float = 0.0,class_weights: list = [1,1], batch_size: int = 16, lr: float = 0.001):
- super().__init__()
- self.save_hyperparameters()
- self.batch_size = batch_size # can be tuned by pytorchlightning
- self.lr = lr # can be tuned by pytorchlightning
- self.dropout_rate = dropout_rate
- self.input_dim = input_dim
- self.embedding_dim = embedding_dim
- self.nclasses = nclasses
- self.class_weights = class_weights
- self.embed1_linear = nn.Linear(self.input_dim ,self.embedding_dim)
- self.embed1_relu = nn.LeakyReLU(inplace=True)
- self.embed1_batchnorm = nn.BatchNorm1d(self.embedding_dim, momentum=0.1,affine=False)
- self.embed1_do = nn.Dropout(p=self.dropout_rate)
- self.output = nn.Linear(self.embedding_dim, self.nclasses)
- init_weight(self)
- self.softmax = nn.Softmax(dim=1);
- # Metrics
- self.train_accuracy = torchmetrics.Accuracy(num_classes=self.nclasses, task = "multiclass")
- self.val_accuracy = torchmetrics.Accuracy(num_classes=self.nclasses, task = "multiclass")
- def forward(self, x):
- x = self.embed1_linear(x.float())
- x = self.embed1_relu(x)
- x = self.embed1_batchnorm(x)
- embed = x
- x = self.embed1_do(x)
- out_logit = self.output(x)
- out_softmax = self.softmax(out_logit)
- return out_logit, out_softmax, embed
- def configure_optimizers(self):
- optimizer = optim.Adam(self.parameters(), lr=self.lr, weight_decay=1e-4)
- lr_schedulers = {'scheduler': torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, mode='min',patience=3,verbose=True),
- 'monitor': 'val_loss'}
- return [optimizer], [lr_schedulers]
- def training_step(self, batch, batch_idx):
- x, y, y_str, f_path = batch
- output = self(x)
- y_hat_logits = output[0]
- y_hat_softmax = output[1]
- _, predicted = torch.max(y_hat_softmax, 1)
- loss = F.cross_entropy(y_hat_logits, y, weight=self.class_weights.to(self.device))
- # logging
- self.train_accuracy(predicted, y)
- self.log('train_loss', loss, batch_size = self.batch_size)
- self.log('train_accuracy', self.train_accuracy, on_step=True, prog_bar=True, on_epoch=True, batch_size = self.batch_size)
- return { 'loss': loss, 'preds': predicted, 'targets': y }
- def validation_step(self, batch, batch_idx):
- x, y, y_str, f_path = batch
- output = self(x)
- y_hat_logits = output[0]
- y_hat_softmax = output[1]
- _, predicted = torch.max(y_hat_softmax, 1)
- val_loss = F.cross_entropy(y_hat_logits, y, weight=self.class_weights.to(self.device))
- # logging
- self.val_accuracy(predicted, y)
- self.log('val_loss', val_loss, batch_size = self.batch_size)
- self.log('val_accuracy', self.val_accuracy, on_step=False, prog_bar=True, on_epoch=True, batch_size = self.batch_size)
- return { 'val_loss': val_loss, 'preds': predicted, 'targets': y }
brain2vec_model_arch.py, no license · at the source
Overview
Abstract
Functional MRI (fMRI) currently supports a limited application space stemming from modest dataset sizes, large interindividual variability, and heterogeneity among scanning protocols. These constraints have made it difficult for fMRI researchers to take full advantage of modern deep-learning tools that have revolutionized other fields such as NLP, speech transcription, and image recognition. To help address these issues, we scaled up functional connectome fingerprinting as a neural network pretraining task, drawing inspiration from speaker recognition research, to learn a generalizable representation of brain function. This approach achieves strong performance for neural fingerprinting on a previously unseen scale, across multiple public fMRI datasets (individual recognition from held-out scan sessions, 93% on MPI-Leipzig, 94% on NKI-Rockland, 73% on OASIS-3, and 99% on HCP). Performance is maintained even when evaluation scan duration is truncated to <2 min. We show that this representation can also generalize to support accurate neural fingerprinting for completely new datasets and participants of either sex not used in training. Finally, we demonstrate that the representation learned by the network encodes features related to individual variability that partially transfers to new tasks. These results support the development of scalable transfer-learning approaches for future clinical and cognitive neuroimaging applications.
Reproduced under the paper's license (CC BY), from the paper cited above.
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Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
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- preproc_model_embedding_
code.zip/ , Python, 358 lines, 3 matchespreproc_model_embedding_ code/ brain2vec_model_arch.py - preproc_model_embedding_
code.zip/ , Python, 309 lines, 2 matchespreproc_model_embedding_ code/ embedding_generation_scr ipt.py
The paper's code and data availability statement is in the Data section.
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Data
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Data Availability
All data used in this report are publicly accessible via https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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Version 2, 28 September 2026
- Funding: added Eli Lilly and Company; Johns Hopkins University; National Institutes of Health: P30 NS09857781, P30-AG066444, UL1‐TR000448, R01EB009352, R01AG043434, P01AG026276, 1U54‐MH‐091657, P01 AG003991, P50 AG00561, TR000448, AG003991, AG066444, AG026276; McDonnell Center for Systems Neuroscience: R01 EB009352, P01 AG026276, P30 NS09857781, R01 AG043434, P01 AG003991, 1U54MH091657, P50 AG00561, UL1 TR000448; Avid Radiopharmaceuticals
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 4 keywords, 8 MeSH terms, 96 references.
Cite
This paper
Ogg, M., & Kitchell, L. (2026). Pretraining for Large-Scale Functional Connectome Fingerprinting Supports Generalization and Transfer Learning in Functional Neuroimaging. eNeuro, 13(8), ENEURO.0370-25.2026. https://
BibTeX
@article{ogg2026pretrain
author = {Ogg, Mattson and Kitchell, Lindsey},
title = {{Pretraining for Large-Scale Functional Connectome Fingerprinting Supports Generalization and Transfer Learning in Functional Neuroimaging}},
journal = {eNeuro},
year = {2026},
month = aug,
volume = {13},
number = {8},
pages = {ENEURO.0370--25.2026},
publisher = {Society for Neuroscience},
issn = {2373-2822},
doi = {10.1523/
url = {https://
pmid = {42527301},
pmcid = {PMC13505883}
}
RIS
TY - JOUR
AU - Ogg, Mattson
AU - Kitchell, Lindsey
TI - Pretraining for Large-Scale Functional Connectome Fingerprinting Supports Generalization and Transfer Learning in Functional Neuroimaging
T2 - eNeuro
J2 - eNeuro
PY - 2026
DA - 2026/
VL - 13
IS - 8
SP - ENEURO.0370
EP - 25.2026
SN - 2373-2822
PB - Society for Neuroscience
DO - 10.1523/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1523/
"type": "article-journal",
"title": "Pretraining for Large-Scale Functional Connectome Fingerprinting Supports Generalization and Transfer Learning in Functional Neuroimaging",
"container-title": "eNeuro",
"author": [
{
"family": "Ogg",
"given": "Mattson"
},
{
"family": "Kitchell",
"given": "Lindsey"
}
],
"container-title-short":
"volume": "13",
"issue": "8",
"page": "ENEURO.0370-25.2026",
"DOI": "10.1523/
"PMID": "42527301",
"PMCID": "PMC13505883",
"ISSN": "2373-2822",
"publisher": "Society for Neuroscience",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
24
]
]
}
}
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