Brain cognition gaps reveal associations with dopamine and factors related to brain health through artificial intelligence prediction of functional connectome.
The 6 matches
- [1] § Materials and methods › Deep neural network model › Enhanced residual block ↔ train_densenet_fc_age.py, lines 235–315 · score 0.78 · squared error, Keras, loss, momentum, TensorFlow, MSE
- [2] § Materials and methods › Deep neural network model ↔ train_densenet_fc_age.py, lines 200–209 · score 0.60 · BatchNormalization, enhanced residual block, transition, layer, ReLU
- [3] § Materials and methods › Deep neural network model ↔ train_densenet_fc_age.py, lines 212–232 · score 0.57 · Batch normalization, dense block, DenseNet, linear, layer, ReLU
- [4] § Materials and methods › Deep neural network model ↔ train_densenet_fc_age.py, lines 1–50 · score 0.54 · DenseNet, attention block, HFAB, ERB, training
- [5] § Results › AI-driven predictive modeling of cognition scores from the functional connectome ↔ train_densenet_fc_age.py, lines 235–315 · score 0.53 · absolute error, square error, MAE, MSE, scores, trained
- [6] § Materials and methods › Deep neural network model › Enhanced residual block ↔ train_densenet_fc_age.py, lines 179–187 · score 0.51 · ReLU, residual block, ERB, maps
Paper
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The authors' code
Python · 347 lines · 14 KB · CC-BY-4.0 · 6 matches
- #!/usr/bin/env python
- """
- train_densenet_fc_age.py
- Train a DenseNet-style CNN with attention blocks (HFAB/ERB) to predict a
- continuous target (e.g. age, episodic-memory score) from square functional
- connectivity (FC) matrices stored as .mat files.
- M. Esmaeili et al. (2026), Brain-Cognitive Gaps in relation to Dopamine and Health-related Factors: Insights from AI-Driven Functional Connectome Predictions, eLife Sciences Publications, Ltd, 2025. https://doi.org/10.7554/eLife.104053.1
- Example
- -------
- python train_densenet_fc_age.py \
- --data-dir /path/to/FC_Movie \
- --labels-csv /path/to/WM_AGE.csv \
- --subject-id-col SubjectID \
- --target-col AGE \
- --runs-per-subject 3 \
- --output-dir ./runs/densenet_age_run1
- Requirements: see requirements.txt (TensorFlow >= 2.10, scikit-learn, scipy,
- pandas, numpy).
- """
- from __future__ import annotations
- import argparse
- import json
- import logging
- import re
- import sys
- from dataclasses import dataclass
- from pathlib import Path
- from typing import Optional
- import numpy as np
- import pandas as pd
- import scipy.io
- import tensorflow as tf
- from sklearn.metrics import mean_absolute_error, mean_squared_error, r2_score
- from sklearn.model_selection import GroupShuffleSplit
- from tensorflow.keras import Model
- from tensorflow.keras.layers import Conv2D, Dropout, Flatten, Input, MaxPool2D
- from tensorflow.keras.layers import BatchNormalization, ReLU, concatenate, multiply, add
- logging.basicConfig(
- level=logging.INFO,
- format="%(asctime)s [%(levelname)s] %(message)s",
- datefmt="%Y-%m-%d %H:%M:%S",
- )
- log = logging.getLogger("densenet_fc")
- # Data loading
- @dataclass
- class Sample:
- filepath: Path
- subject_id: str
- target: float
- def extract_subject_id(filepath: Path) -> str:
- """
- Parse a subject identifier out of a .mat filename / path.
- *** ADAPT THIS TO YOUR ACTUAL NAMING CONVENTION. ***
- The default assumes filenames contain a token like 'sub-0012' or
- 'subject012'. This is the single most important function to check before
- trusting any results: silent subject/label mismatches are the easiest
- way to get numbers that look plausible but are meaningless.
- """
- match = re.search(r"(sub(?:ject)?-?\d+)", filepath.stem, flags=re.IGNORECASE)
- if not match:
- raise ValueError(
- f"Could not extract a subject ID from '{filepath.name}'. "
- "Update extract_subject_id() to match your file naming scheme."
- )
- return match.group(1).lower()
- def build_sample_index(
- data_dir: Path,
- labels_csv: Path,
- subject_id_col: str,
- target_col: str,
- ) -> list[Sample]:
- """
- Build an explicit, verifiable list of (filepath, subject_id, target)
- triples by joining .mat files to the labels CSV on subject ID.
- """
- df = pd.read_csv(labels_csv)
- if subject_id_col not in df.columns or target_col not in df.columns:
- raise ValueError(
- f"labels CSV must contain columns '{subject_id_col}' and "
- f"'{target_col}'. Found columns: {list(df.columns)}"
- )
- df[subject_id_col] = df[subject_id_col].astype(str).str.lower()
- label_lookup = dict(zip(df[subject_id_col], df[target_col].astype(float)))
- mat_files = sorted(data_dir.glob("**/*.mat"))
- if not mat_files:
- raise FileNotFoundError(f"No .mat files found under {data_dir}")
- samples: list[Sample] = []
- skipped = 0
- for fp in mat_files:
- try:
- sid = extract_subject_id(fp)
- except ValueError as exc:
- log.warning("Skipping file: %s", exc)
- skipped += 1
- continue
- if sid not in label_lookup:
- log.warning("No label found for subject '%s' (file: %s) -- skipping.", sid, fp.name)
- skipped += 1
- continue
- samples.append(Sample(filepath=fp, subject_id=sid, target=label_lookup[sid]))
- if skipped:
- log.warning("%d of %d files were skipped due to missing/unmatched labels.", skipped, len(mat_files))
- log.info("Matched %d FC-map files to labels across %d unique subjects.",
- len(samples), len({s.subject_id for s in samples}))
- if not samples:
- raise RuntimeError("No samples matched between .mat files and labels CSV. Check extract_subject_id().")
- return samples
- def load_matrices(samples: list[Sample], mat_key: str, matrix_size: int) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
- """Load all FC matrices into a single float32 array, plus targets and group (subject) IDs."""
- n = len(samples)
- data = np.zeros((n, matrix_size, matrix_size), dtype="float32")
- targets = np.zeros(n, dtype="float32")
- groups = np.empty(n, dtype=object)
- for i, s in enumerate(samples):
- mat = scipy.io.loadmat(s.filepath)
- if mat_key not in mat:
- raise KeyError(
- f"Expected key '{mat_key}' not found in {s.filepath.name}. "
- f"Available keys: {[k for k in mat if not k.startswith('__')]}"
- )
- arr = mat[mat_key]
- if arr.shape != (matrix_size, matrix_size):
- raise ValueError(
- f"{s.filepath.name}: expected shape ({matrix_size}, {matrix_size}), got {arr.shape}"
- )
- data[i] = arr
- targets[i] = s.target
- groups[i] = s.subject_id
- data = np.expand_dims(data, axis=-1) # (N, H, W, 1)
- return data, targets, groups
- def group_train_val_split(
- data: np.ndarray, targets: np.ndarray, groups: np.ndarray, val_fraction: float, seed: int
- ):
- """Subject-grouped split so repeat runs from one subject never straddle train/val."""
- splitter = GroupShuffleSplit(n_splits=1, test_size=val_fraction, random_state=seed)
- train_idx, val_idx = next(splitter.split(data, targets, groups))
- log.info(
- "Train/val split: %d train samples (%d subjects), %d val samples (%d subjects).",
- len(train_idx), len(set(groups[train_idx])),
- len(val_idx), len(set(groups[val_idx])),
- )
- return (data[train_idx], targets[train_idx]), (data[val_idx], targets[val_idx])
- # Model
- def enhanced_residual_block(x, n_filters: int):
- """ERB: 1x1 -> 3x3 -> 1x1 convs with two residual additions."""
- conv11 = Conv2D(n_filters, 1, kernel_initializer="he_uniform", padding="same", activation="relu")(x)
- y = Conv2D(n_filters, 3, kernel_initializer="he_uniform", padding="same", activation="relu")(conv11)
- y = add([conv11, y])
- y = Conv2D(n_filters, 1, kernel_initializer="he_uniform", padding="same", activation="relu")(y)
- y = add([conv11, y])
- return y
- def high_freq_attention_block(x, n_filters: int):
- """HFAB: a conv branch gated by a sigmoid attention map derived from an ERB."""
- branch = Conv2D(n_filters, 3, kernel_initializer="he_uniform", padding="same", activation="relu")(x)
- y = ReLU()(branch)
- y = enhanced_residual_block(y, n_filters)
- y = ReLU()(y)
- y = Conv2D(n_filters, 3, kernel_initializer="he_uniform", padding="same", activation="relu")(y)
- y = tf.keras.activations.sigmoid(y)
- return multiply([y, branch])
- def dense_block(x, n_filters: int, n_layers: int, dropout: float):
- for _ in range(n_layers):
- y = Conv2D(n_filters, 3, kernel_initializer="he_uniform", activation="relu", padding="same")(x)
- y = Conv2D(n_filters, 3, kernel_initializer="he_uniform", activation="relu", padding="same")(y)
- if dropout > 0:
- y = Dropout(dropout)(y)
- x = concatenate([y, x])
- return x
- def transition_layer(x, n_filters: int, dropout: float):
- n_channels = x.shape[-1] // 2
- x = Conv2D(n_channels, 3, kernel_initializer="he_uniform", activation="relu", padding="same")(x)
- x = BatchNormalization()(x)
- x = MaxPool2D(pool_size=5, strides=1, padding="same")(x)
- x = enhanced_residual_block(x, n_filters)
- x = high_freq_attention_block(x, n_filters)
- if dropout > 0:
- x = Dropout(dropout)(x)
- return x
- def build_densenet(
- input_shape: tuple[int, int, int],
- n_outputs: int = 1,
- n_filters: int = 16,
- block_depths: tuple[int, ...] = (2, 6, 6, 2),
- dropout: float = 0.2,
- ) -> Model:
- inputs = Input(input_shape)
- x = BatchNormalization()(inputs)
- x = Conv2D(n_filters, 3, strides=1, kernel_initializer="he_uniform", activation="relu", padding="same")(x)
- for n_layers in block_depths:
- x = high_freq_attention_block(x, n_filters)
- x = dense_block(x, n_filters, n_layers, dropout)
- x = transition_layer(x, n_filters, dropout)
- x = Flatten()(x)
- if dropout > 0:
- x = Dropout(dropout)(x)
- outputs = tf.keras.layers.Dense(n_outputs, activation="linear")(x)
- return Model(inputs, outputs, name="densenet_fc_regressor")
- # Training / evaluation
- def train(args: argparse.Namespace) -> None:
- tf.random.set_seed(args.seed)
- np.random.seed(args.seed)
- output_dir = Path(args.output_dir)
- output_dir.mkdir(parents=True, exist_ok=True)
- with open(output_dir / "run_config.json", "w") as f:
- json.dump(vars(args), f, indent=2, default=str)
- samples = build_sample_index(
- data_dir=Path(args.data_dir),
- labels_csv=Path(args.labels_csv),
- subject_id_col=args.subject_id_col,
- target_col=args.target_col,
- )
- data, targets, groups = load_matrices(samples, mat_key=args.mat_key, matrix_size=args.matrix_size)
- log.info("Loaded data array: %s, target range [%.3f, %.3f]", data.shape, targets.min(), targets.max())
- (train_x, train_y), (val_x, val_y) = group_train_val_split(
- data, targets, groups, val_fraction=args.val_fraction, seed=args.seed
- )
- # Standardize target using train-set statistics only (avoids leakage).
- target_mean, target_std = train_y.mean(), train_y.std() + 1e-8
- train_y_norm = (train_y - target_mean) / target_std
- val_y_norm = (val_y - target_mean) / target_std
- model = build_densenet(
- input_shape=(args.matrix_size, args.matrix_size, 1),
- n_outputs=1,
- n_filters=args.n_filters,
- dropout=args.dropout,
- )
- model.summary(print_fn=log.info)
- optimizer = tf.keras.optimizers.Adam(learning_rate=args.learning_rate) if args.optimizer == "adam" \
- else tf.keras.optimizers.SGD(learning_rate=args.learning_rate, momentum=0.9)
- model.compile(optimizer=optimizer, loss="mean_absolute_error", metrics=["mse"])
- callbacks = [
- tf.keras.callbacks.ModelCheckpoint(
- filepath=str(output_dir / "best_model.keras"),
- monitor="val_loss", save_best_only=True, verbose=1,
- ),
- tf.keras.callbacks.EarlyStopping(
- monitor="val_loss", patience=args.early_stopping_patience,
- restore_best_weights=True, verbose=1,
- ),
- tf.keras.callbacks.ReduceLROnPlateau(
- monitor="val_loss", factor=0.5, patience=max(5, args.early_stopping_patience // 2), verbose=1,
- ),
- tf.keras.callbacks.CSVLogger(str(output_dir / "training_history.csv")),
- ]
- history = model.fit(
- train_x, train_y_norm,
- validation_data=(val_x, val_y_norm),
- batch_size=args.batch_size,
- epochs=args.epochs,
- callbacks=callbacks,
- verbose=2,
- )
- # Final held-out evaluation, in original target units.
- val_pred_norm = model.predict(val_x, batch_size=args.batch_size).ravel()
- val_pred = val_pred_norm * target_std + target_mean
- mae = mean_absolute_error(val_y, val_pred)
- rmse = mean_squared_error(val_y, val_pred, squared=False)
- r2 = r2_score(val_y, val_pred)
- log.info("Held-out validation -- MAE: %.4f, RMSE: %.4f, R^2: %.4f", mae, rmse, r2)
- metrics = {"val_mae": mae, "val_rmse": rmse, "val_r2": r2,
- "target_mean": float(target_mean), "target_std": float(target_std)}
- with open(output_dir / "final_metrics.json", "w") as f:
- json.dump(metrics, f, indent=2)
- model.save(output_dir / "final_model.keras")
- log.info("Saved final model and metrics to %s", output_dir)
- # CLI
- def parse_args(argv: Optional[list[str]] = None) -> argparse.Namespace:
- p = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
- p.add_argument("--data-dir", required=True, type=str, help="Directory containing .mat FC-map files (searched recursively).")
- p.add_argument("--labels-csv", required=True, type=str, help="CSV file with subject IDs and target values.")
- p.add_argument("--subject-id-col", default="SubjectID", type=str, help="Column name for subject ID in labels CSV.")
- p.add_argument("--target-col", default="AGE", type=str, help="Column name for the regression target in labels CSV.")
- p.add_argument("--mat-key", default="IMG_temp", type=str, help="Key inside each .mat file holding the FC matrix.")
- p.add_argument("--matrix-size", default=273, type=int, help="Side length of the (square) FC matrix.")
- p.add_argument("--output-dir", default="./run_output", type=str, help="Where to write model checkpoints, logs, metrics.")
- p.add_argument("--val-fraction", default=0.2, type=float, help="Fraction of subjects held out for validation.")
- p.add_argument("--n-filters", default=16, type=int, help="Base channel width for the network.")
- p.add_argument("--dropout", default=0.2, type=float, help="Dropout rate used throughout the network.")
- p.add_argument("--batch-size", default=16, type=int)
- p.add_argument("--epochs", default=400, type=int)
- p.add_argument("--learning-rate", default=1e-3, type=float)
- p.add_argument("--optimizer", default="adam", choices=["adam", "sgd"])
- p.add_argument("--early-stopping-patience", default=25, type=int)
- p.add_argument("--seed", default=0, type=int)
- return p.parse_args(argv)
- def main() -> None:
- args = parse_args()
- log.info("Starting run with config: %s", vars(args))
- train(args)
- if __name__ == "__main__":
- sys.exit(main())
train_densenet_fc_age.py at commit 40d54fc, under CC-BY-4.0 · at the source
Overview
- Department of Electrical Engineering and Computer Science, University of Stavanger, Stavanger, Norway
- Department of Diagnostic Imaging, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
- Aging Research Center, Karolinska Institute and Stockholm University, Solna, Sweden
- Department of Diagnostics and Intervention, Diagnostic Radiology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, Umeå, Sweden
- Department of Psychology, Florida State University, Tallahassee, United States
Abstract
A key question in human neuroscience is to understand how individual differences in brain function relate to cognitive differences. However, the optimal condition of brain function to study between-person differences in cognition remains unclear. While many studies have developed objective biomarkers to accurately predict intelligence and general cognition, consensus on domain-specific markers has not yet emerged. Brain age has been proposed as a potential candidate, but recent research suggests that brain age offers minimal additional information on cognitive decline beyond what chronological age provides, prompting a shift toward approaches focused directly on cognitive prediction. Using a deep learning approach, we evaluated the predictive power of the functional connectome during various states (resting state, movie-watching, and n-back) on episodic memory and working memory performance. Our findings show that connectomes during tasks, especially during movie-watching, predict individual differences across cognitive domains, while resting state connectomes predict episodic memory meaningfully. Furthermore, individuals with a negative brain cognition gap (where brain predictions underestimate actual performance) exhibited lower physical activity and higher cardiovascular risk compared to those with a positive gap. This shows that knowledge of the brain cognition gap provides insights into factors contributing to cognitive resilience. Further, lower PET-derived measures of dopamine binding were linked to a greater brain cognition gap, mediated by regional functional variability. Together, our findings highlight the importance of brain state in connectome-based cognitive prediction and introduce the brain cognition gap as a potentially informative, dopamine-modulated marker of vulnerability to compromise brain function.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 6 matches between paragraphs and lines of code.
MorEsm/AI-based-Prediction-of-Cognitive-Function
40d54fc2665482db688562207d989d924d7ecdc7, 27 August 2026Availability: 1 check, the latest on 26 September 2026: the link answers
- 26 September 2026: the link answers
3 files
- train_densenet_fc_age.py
, Python, 347 lines, 6 matches - LICENSE, License, 18 lines
- README.md, Text, 29 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 1 script, each with its path and the digest of its content;
- 6 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability
The scripts used for developing the model are available at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 10 authors, 1 keyword, 14 MeSH terms, 4 funders, 141 references.
Cite
This paper
Esmaeili, M., Bjørkeli, E. B., Pedersen, R., Falahati, F., Johansson, J., Nordin, K., Karalija, N., Bäckman, L., Nyberg, L., & Salami, A. (2026). Brain cognition gaps reveal associations with dopamine and factors related to brain health through artificial intelligence prediction of functional connectome. eLife, 14, RP104053. https://
BibTeX
@article{esmaeili2026bra
author = {Esmaeili, Morteza and Bjørkeli, Erin Beate and Pedersen, Robin and Falahati, Farshad and Johansson, Jarkko and Nordin, Kristin and Karalija, Nina and Bäckman, Lars and Nyberg, Lars and Salami, Alireza},
title = {{Brain cognition gaps reveal associations with dopamine and factors related to brain health through artificial intelligence prediction of functional connectome}},
journal = {eLife},
year = {2026},
month = sep,
volume = {14},
pages = {RP104053},
publisher = {eLife Sciences Publications, Ltd},
issn = {2050-084X},
doi = {10.7554/
url = {https://
pmid = {42684829},
pmcid = {PMC13537765}
}
RIS
TY - JOUR
AU - Esmaeili, Morteza
AU - Bjørkeli, Erin Beate
AU - Pedersen, Robin
AU - Falahati, Farshad
AU - Johansson, Jarkko
AU - Nordin, Kristin
AU - Karalija, Nina
AU - Bäckman, Lars
AU - Nyberg, Lars
AU - Salami, Alireza
TI - Brain cognition gaps reveal associations with dopamine and factors related to brain health through artificial intelligence prediction of functional connectome
T2 - eLife
J2 - eLife
PY - 2026
DA - 2026/
VL - 14
SP - RP104053
SN - 2050-084X
PB - eLife Sciences Publications, Ltd
DO - 10.7554/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.7554/
"type": "article-journal",
"title": "Brain cognition gaps reveal associations with dopamine and factors related to brain health through artificial intelligence prediction of functional connectome",
"container-title": "eLife",
"author": [
{
"family": "Esmaeili",
"given": "Morteza"
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"family": "Bjørkeli",
"given": "Erin Beate"
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"family": "Falahati",
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"given": "Jarkko"
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"given": "Lars"
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],
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"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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2
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]
}
}
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