Benchmarking criteria to determine latent linear dimensionality in neural data.
The 19 matches · 5 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
- [1] § Results ↔ MATLAB Package/simulate_data_matrix.m, lines 1–113 · score 0.80 · decay factor, soft normalization, noise distribution, noise factor, varied, tuning
- [2] § Methods › Simulations ↔ MATLAB Package/simulate_data_matrix.m, lines 1–113 · score 0.73 · linear combinations, simulated neural, linear simulations, activation, Gaussian, latent variables
- [3] § Methods › Criteria for dimensionality estimation ↔ MATLAB Package/optimal_SVHT_coef.m, lines 1–68 · score 0.70 · optimal hard threshold, unknown noise, Donoho, Gavish, singular, coefficient
- [4] § Results ↔ MATLAB Package/dimensionality_DEMO.m, lines 8–30 · score 0.69 · decay factor, soft normalization, noise distribution, noise factor, Poisson, Gaussian
- [5] § Methods › Variance decay rate of a matrix ↔ MATLAB Package/simulate_data_matrix.m, lines 181–219 · score 0.69 · power law function, exponential decay, latent variables, simulations, matrices, components
- [6] § Methods › Criteria for dimensionality estimation ↔ MATLAB Package/singval_hard_threshold.m, the whole file · a weak match · score 0.67 · optimal hard threshold, Donoho, Gavish, singular, unknown, coefficient
- [7] § Methods › Criteria for dimensionality estimation ↔ MATLAB Package/kaiser_rule.m, the whole file · a weak match · score 0.67 · Kaiser rule, original variables, variance explained, eigenvalues, scored, PCA
- [8] § Methods › Criteria for dimensionality estimation ↔ MATLAB Package/eval_num_PCs_cross_val.m, lines 88–165 · score 0.66 · bi cross validation, ALS, algorithms, train, fold, iterative
- [9] § Results › Criteria comparison on linear datasets ↔ MATLAB Package/optimal_SVHT_coef.m, lines 1–68 · score 0.66 · low rank, denoised matrix, Hard Thresholding, Donoho, Gavish, Singular
- [10] § Methods › Variance decay rate of a matrix ↔ MATLAB Package/fit_power_law.m, the whole file · a weak match · score 0.64 · power law, fitted, explained variance, exponential, PCs, components
- [11] § Methods › Metrics for criteria comparison ↔ MATLAB Package/simulate_data_matrix.m, lines 304–368 · score 0.63 · noise variance, fake units, variance explained, fitted, R2, scored
- [12] § Methods › Simulations ↔ MATLAB Package/simulate_data_matrix.m, lines 221–260 · score 0.58 · noise matrix, sp, Subtracting, firing, bins, Poisson
- [13] § Methods › Simulations ↔ MATLAB Package/simulate_data_matrix.m, lines 181–219 · score 0.56 · exponential decay, decay factor, orthogonalized, latent variable, scored, simulation
- [14] § Results › Criteria comparison on linear datasets ↔ MATLAB Package/singval_hard_threshold.m, the whole file · a weak match · score 0.56 · optimal Singular, Hard Thresholding, Donoho, Gavish, rank, median
- [15] § Results › The effect of non-linearities on latent structure recovery ↔ MATLAB Package/eval_num_PCs_cross_val.m, lines 1–45 · score 0.54 · cross validation schemes, bi cross validation, deviation, R2, imputation, reconstruction
- [16] § Methods › Simulations ↔ MATLAB Package/dimensionality_DEMO.m, lines 8–30 · score 0.54 · soft normalization, noise distribution, Poisson, Gaussian, latent variable, synthetic
- [17] § Methods › Criteria for dimensionality estimation ↔ MATLAB Package/eval_num_PCs_cross_val.m, lines 88–165 · score 0.54 · bi cross validation, train, predictions, iterations, imputation, reconstruction
- [18] § Methods › Criteria for dimensionality estimation ↔ MATLAB Package/parallel_analysis.m, the whole file · a weak match · score 0.54 · covariance matrix, Parallel, descending, disrupting, eigenvalues, threshold
- [19] § Methods › Simulations ↔ MATLAB Package/simulate_data_matrix.m, lines 221–260 · score 0.50 · firing rate, subtracted, weight, FAKE, scoring, simulation
Paper
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The authors' code
MATLAB · 368 lines · 15 KB · MIT · 7 matches
- function [X, varargout] = simulate_data_matrix(fake_units, time_series_length, num_latent, settings)
- %--------------------------------------------------------------------------
- % SIMULATE_DATA_MATRIX Generate synthetic data with controlled latent structure
- %
- % Designed for generating synthetic neural-like data with known underlying dimensionality and
- % noise characteristics. Simulates a data matrix based on linear combinations of latent variables plus
- % noise. The degree of non-linearity mapping between latent activations and simulated neural activity
- % can be tuned. Other parameters can be varied (see below).
- %
- % Syntax:
- % X = simulate_data_matrix(fake_units, time_series_length, num_latent)
- % [X, output] = simulate_data_matrix(fake_units, time_series_length, num_latent, settings)
- % [X, output, settings] = simulate_data_matrix(fake_units, time_series_length, num_latent, settings)
- %
- % Inputs:
- % fake_units - Number of variables/units to generate (e.g., neurons)
- % time_series_length - Length of time series (number of timepoints)
- % num_latent - Number of latent variables defining data structure
- % settings - (Optional) struct with fields:
- % .gen - Latent generation method: 'random','sine','PCs','dynamical' (default:'random')
- % .noiseDistr - Noise distribution: 'gaussian' or 'poisson' (default:'gaussian')
- % .nonLinAlfa - Non-linearity strength parameter (default:0)
- % .decayFactor - Decay factor for scaling latents (default:0.5)
- % .decayCap - Cap decay to maintain latent structure (default:false)
- % .noiseFactor - Scale factor for noise amplitude (default:1)
- % .equalNoise - Use equal noise across units (default:false)
- % .soft_norm - Use soft normalization instead of z-score (default:false)
- % .display - Plot diagnostic figures (default:false)
- %
- % Outputs:
- % X - Simulated data matrix (time_series_length x fake_units)
- % output - (Optional) struct with fields:
- % .single_L_var - Variance explained by each latent
- % .single_L_SNR - Signal-to-noise ratio for each latent
- % .L_R2s - R-squared values for latent reconstructions
- % .L_var - Total variance explained by linear structure
- % .U_var - Total variance in combined latents
- % .noise_var - Variance explained by noise
- % .nonLinear_var - Variance from non-linear effects
- % .L - Raw latent variables matrix
- % .U - Combined latent representation
- % .noise_matrix - Generated noise matrix
- % .tau - variance decay for X
- % .settings - Copy of input settings
- % .fake_units - Number of units generated
- % .time_series_length - Length of time series
- % .num_latent - Number of latent dimensions
- % settings - (Optional) Copy of settings struct with defaults filled in
- %
- % Example:
- % % Generate 100 units with 5 latents over 1000 timepoints
- % settings = struct('gen','sine','noiseFactor',0.5,'display',true);
- % [X,stats] = simulate_data_matrix(100, 1000, 5, settings);
- %
- % Author: Francesco E. Vaccari, PhD
- % Date: September 24, 2025
- %--------------------------------------------------------------------------
- % --- Handle settings structure input ---
- if nargin < 4
- settings = struct();
- end
- if ~isfield(settings, 'gen') | isnan(settings.gen), settings.gen = 'random'; end
- if ~isfield(settings, 'noiseDistr') | isnan(settings.noiseDistr), settings.noiseDistr = 'gaussian'; end
- if ~isfield(settings, 'nonLinAlfa') | isnan(settings.nonLinAlfa), settings.nonLinAlfa = 0; end
- if ~isfield(settings, 'decayFactor') | isnan(settings.decayFactor), settings.decayFactor = 0.5; end
- if ~isfield(settings, 'decayCap') | isnan(settings.decayCap), settings.decayCap = false; end
- if ~isfield(settings, 'noiseFactor') | isnan(settings.noiseFactor), settings.noiseFactor = 1; end
- if ~isfield(settings, 'equalNoise') | isnan(settings.equalNoise), settings.equalNoise = false; end
- if ~isfield(settings, 'soft_norm') | isnan(settings.soft_norm), settings.soft_norm = false; end
- if ~isfield(settings, 'display') | isnan(settings.display), settings.display = false; end
- % Simulate!
- if settings.decayCap %if decay is capped
- settingsTemp = settings;
- settingsTemp.nonLinAlfa = 0; %set linear simulation
- settingsTemp.display = false;
- while true
- [X, output] = simulate(fake_units, time_series_length, num_latent, settingsTemp);
- % [coeff, score] = pca(X);
- %
- % for k = 1:num_latent
- % Xhat = score(:,1:k)*coeff(:,1:k)';
- % error(k) = sumsqr(output.U - Xhat);
- % end
- [k_opt, vv] = find_optimality(X, output);
- % if error(num_latent) > min(error) %any(output.single_L_SNR < 2/3) %if the last PC contains more noise than signal
- if k_opt ~= num_latent
- settingsTemp.decayFactor = settingsTemp.decayFactor*0.8; %reduce the decayFactor by 10% and run another simulation
- else
- settings.decayFactor = settingsTemp.decayFactor; %set the final decayFactor to be equal to the last one
- break
- end
- end
- else
- [X, output] = simulate(fake_units, time_series_length, num_latent, settings); %run the output simulation
- end
- % Check the number of outputs requested and return accordingly
- if nargout == 2
- varargout{1} = output; % Return the struct as the second output
- elseif nargout == 3
- varargout{1} = output; % Return the struct as the second output
- varargout{2} = settings; % Return the struct as the third output
- end
- function [X, output] = simulate(fake_units, time_series_length, num_latent, settings)
- % Assign settings fields to variables used below without changing any other commands
- gen = settings.gen;
- decayFactor = settings.decayFactor;
- decayCap = settings.decayCap;
- noiseFactor = settings.noiseFactor;
- equalNoise = settings.equalNoise;
- soft_norm = settings.soft_norm;
- display = settings.display;
- tmp_num_latent = num_latent;
- for i = 1:10
- switch gen
- case 'random'
- % Generate random time series (stochastic)
- L = generate_random_time_series(tmp_num_latent, time_series_length);
- case 'sine'
- % Generate sine-wave based time series
- L = generate_random_sine_series(tmp_num_latent, time_series_length);
- case 'PCs'
- % Generate time series based on principal components
- L = generate_random_units_from_PCs(tmp_num_latent, time_series_length);
- case 'dynamical'
- L = generate_random_dynamical_series(tmp_num_latent, time_series_length);
- end
- % Pre-process latent data (z-score, orthogonalize, and z-score again)
- L = zscore(L);
- if rank(L) == num_latent
- break
- else
- tmp_num_latent = tmp_num_latent+1;
- end
- end
- num_latent = rank(L);
- if display
- % Plot statistics of latent variables BEFORE orthogonalization and scaling
- figure
- subplot(1, 3, 1)
- bar(var(L))
- ylabel('Variance')
- xlabel('Dimensions')
- title('Latent Variables Variance')
- subplot(1, 3, 2)
- imagesc(corr(L))
- ylabel('Dimensions')
- xlabel('Dimensions')
- title('Latent Variables Correlation')
- subplot(1, 3, 3)
- for l = 1:size(L, 2)
- plot(L(:, l) + ones(size(L, 1), 1) * 2 * l)
- hold on
- end
- title('Latent Variables Temporal Evolution')
- sgtitle('Generated Real Latent Variables Statistics')
- end
- % Orthogonalize latent variables using PCA (Principal Component Analysis)
- [~, L, ~] = pca(L, 'NumComponents', num_latent);
- L = zscore(L); % Z-score after PCA
- % Apply decay factor to scale latent variables
- SF = exp(-decayFactor * [1:num_latent]); % following a exponential decay
- % SF = [1:num_latent] .^ (-decayFactor); % following a power law function
- SF = SF / sum(SF); % Normalize scaling factors
- for i = 1:num_latent
- L(:, i) = L(:, i) * SF(i);
- end
- if display
- % Plot statistics of latent variables AFTER orthogonalization and scaling
- figure
- subplot(1, 3, 1)
- bar(var(L))
- ylabel('Variance')
- xlabel('Dimensions')
- title('Latent Variables Variance')
- subplot(1, 3, 2)
- imagesc(corr(L))
- ylabel('Dimensions')
- xlabel('Dimensions')
- title('Latent Variables Correlation')
- subplot(1, 3, 3)
- for l = 1:size(L, 2)
- plot(L(:, l) + ones(size(L, 1), 1) * l)
- hold on
- end
- title('Latent Variables Temporal Evolution (After Scaling)')
- sgtitle('Generated Real Latent Variables Statistics AFTER Scaling')
- end
- % Generate random weight matrix W
- W = normrnd(0, 1, num_latent, fake_units); %Draw samples from independent Guassian distributions to avoid directional biases
- % Normalize the weight matrix
- W = W ./ sqrt(sum(W.^2)); % Normalize the columns to have unit norm
- % Create 'U' matrix by combining real_latents with W
- U = L * W;
- % Add non-linearities if required
- if settings.nonLinAlfa > 0
- U = normalize(U,"range", [0 1]); % To be comparable with Altan et al. (2021) procedure
- U = (exp(settings.nonLinAlfa*U)-1) / (exp(settings.nonLinAlfa)-1);
- end
- % Generate noise matrix
- switch settings.noiseDistr
- case 'poisson'
- U = normalize(U,"range", [0 5]); %assuming a 50ms bin, it would correspond to a maximum FR around 100 sp/sec
- noise_matrix = poissrnd(U) - U; % Generate Poisson noise where each element's variance equals its value in U (subtract U since each generated element is expected to be equal to U)
- case 'gaussian'
- noise_matrix = normrnd(0, 1, size(U));
- end
- U = zscore(U); % Z-score 'U' matrix
- noise_matrix = zscore(noise_matrix); % Z-score the noise matrix
- % Adjust noise factor
- noiseFactor = noiseFactor * mean(std(U)./std(noise_matrix)); % Equilibrate noise and signal variances if not already equilibrated
- noise_matrix = noiseFactor * noise_matrix;
- % Apply different noise distribution depending on equalNoise flag
- if equalNoise
- beta = ones(1, fake_units)*0.5; % Equal noise distribution across all units
- else
- beta = normrnd(0.5, 1/6, 1, fake_units);
- beta(beta < 0) = 0; beta(beta > 1) = 1; % Clip values to [0, 1]
- end
- % Add noise to the data matrix X
- X = U .* (1 - beta) + noise_matrix .* beta; % Weighted noise addition
- X = X + abs(min(X)); % Ensure that all values in X are non-negative (firing rate)
- % Apply normalization if specified
- if soft_norm
- X = soft_normalize(X, 2, mean(X, 'all')/2);
- X = X - mean(X); % Center the data
- else
- X = zscore(X); % Standard z-score normalization
- end
- if display
- % Visualize the final simulated data matrix
- figure
- subplot(1, 2, 1)
- imagesc(X)
- colormap('hot')
- colorbar
- caxis([-3 3])
- subplot(1, 2, 2)
- for l = 1:3
- plot(X(:, randi(fake_units, 1, 1)) + ones(size(L, 1), 1) * 3 * l, 'LineWidth', 2)
- hold on
- end
- sgtitle('Simulated Fake Units')
- end
- % Estimate the latent variables' contribution to the data matrix X
- b = L \ X; % Solve the linear system X = real_latents * b
- % Calculate variance explained by each latent variable
- single_L_var = [];
- for i = 1:num_latent
- single_L_var(i) = 100 - (var(X - L(:, i) * b(i, :)) / var(X)) * 100;
- end
- [single_L_var, I] = sort(single_L_var, 'descend'); % Sort by variance explained
- L_R2s = [];
- for i = 1:num_latent
- L_R2s(i) = Rsquared(X, L(:, 1:i) * b(1:i, :));
- end
- L_var = 100 - (var(X - L * b) / var(X)) * 100;
- % Calculate how much the dataset is non-linear
- Xhat = [];
- for j = 1:fake_units
- b = U(:,j) \ X(:,j);
- Xhat = [Xhat, U(:,j)*b];
- end
- U_var = 100 - var(X - Xhat)/var(X)*100;
- nonLinear_var = U_var - L_var;
- % Calculate how much of the dataset is noise
- Xhat = [];
- for j = 1:fake_units
- b = noise_matrix(:,j) \ X(:,j);
- Xhat = [Xhat, noise_matrix(:,j)*b];
- end
- noise_var = 100 - var(X - Xhat)/var(X)*100; % Calculate the real noise variance percentage
- % calculate tau on X
- [tau, ~] = fit_tau(X, false);
- % Perform PCA on the final data matrix X
- [coeff, last_score, latent, tsquared, score_var, mu] = pca(X);
- score_var = score_var'; % Variance explained by each principal component
- if numel(score_var) < fake_units
- score_var = [score_var zeros(1, fake_units-numel(score_var))];
- end
- if display
- % Plot the variance explained by real latent variables vs PCs
- figure
- bar([single_L_var, zeros(1, fake_units - num_latent); score_var]')
- ylabel('Explained Variance')
- hold on
- yyaxis right
- plot(cumsum(single_L_var)) % Cumulative explained variance for real latent variables
- plot(cumsum(score_var)) % Cumulative explained variance for PCs
- legend('True Latent Variance', 'PCs Variance', 'True Latent Variance Cumsum', 'PCs Variance Cumsum')
- xlabel('Dimensions')
- ylabel('Total Explained Variance')
- title(['Data underlying linear structure / linearities = ' num2str(L_var) ...
- ' + nonlinearities = ' num2str(nonLinear_var) ...
- ' + noise = ' num2str(noise_var) '% of the X variance'])
- end
- % --- Return the outputs in a struct ---
- output.single_L_var = single_L_var;
- jj = min([num_latent fake_units]);
- output.single_L_SNR = single_L_var(1:jj)./score_var(1:jj);
- output.L_R2s = [L_R2s];
- output.L_var = L_var;
- output.U_var = U_var;
- output.noise_var = noise_var;
- output.nonLinear_var= nonLinear_var;
- output.L = L;
- output.U = U;
- output.noise_matrix = noise_matrix;
- output.tau = tau;
- output.settings = settings;
- output.fake_units = fake_units;
- output.time_series_length = time_series_length;
- output.num_latent = num_latent;
- end
- end
simulate_data_matrix.m at commit 5b6fb50, under MIT · at the source
Overview
- Department of Biomedical and Neuromotor Sciences, University of Bologna,Bologna, Italy
- Institute of Cognitive Sciences and Technologies, National Research Council,Rome, Italy
- Alma Mater Research Institute for Human-Centered Artificial Intelligence, University of Bologna,Bologna, Italy
Abstract
The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repositories
Its files are read in the Code ↔ Paper reader above, with 19 matches between paragraphs and lines of code.
francescovaccari/Dimensionality-estimation
5b6fb5054f40222b3ed981df73040a50a2081297, 26 September 2025Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
18 files
- MATLAB Package/
dimensionality_DEMO.m , MATLAB, 79 lines, 2 matches - MATLAB Package/
eval_num_PCs_cross_val.m , MATLAB, 281 lines, 3 matches - MATLAB Package/
fit_power_law.m , MATLAB, 77 lines, 1 match - MATLAB Package/
fit_tau.m , MATLAB, 70 lines - MATLAB Package/
generate_random_dynamica , MATLAB, 72 linesl_series.m - MATLAB Package/
generate_random_sine_ser , MATLAB, 40 linesies.m - MATLAB Package/
generate_random_time_ser , MATLAB, 39 linesies.m - MATLAB Package/
generate_random_units_fr , MATLAB, 33 linesom_PCs.m - MATLAB Package/
kaiser_rule.m , MATLAB, 54 lines, 1 match - MATLAB Package/
optimal_SVHT_coef.m , MATLAB, 161 lines, 2 matches - MATLAB Package/
parallel_analysis.m , MATLAB, 65 lines, 1 match - MATLAB Package/
participation_ratio.m , MATLAB, 37 lines - MATLAB Package/
simulate_data_matrix.m , MATLAB, 368 lines, 7 matches - MATLAB Package/
singval_hard_threshold.m , MATLAB, 67 lines, 2 matches - MATLAB Package/
soft_normalize.m , MATLAB, 65 lines - MATLAB Package/
variance_hard_threshold. , MATLAB, 33 linesm - LICENSE, License, 21 lines
- README.md, Text, 94 lines
francescovaccari/Dimensionality-estimation-upper-bound
230df0f1d77e6cef2960ec603a3cdd5c64368310, 26 March 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
5 files
- _utils/
__init__.py , Python, 1 line - _utils/
helpers.py , Python, 442 lines - app.py, Python, 173 lines
- LICENSE, License, 21 lines
- README.md, Text, 131 lines
Code availability statement
The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to the authors' code: francescovaccari/
Dimensionality-estimatio , francescovaccari/n Dimensionality-estimatio n-upper-bound
Read it in the paper: doi.org/10.1038/s41598-026-55225-1.
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:
- 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 19 scripts, each with its path and the digest of its content;
- 19 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
Datasets cited
- crcns.org/
data-sets/ , at CRCNS; found in “Data availability”vc
Data availability statement
The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to a dataset: crcns.org/
data-sets/ vc
Read it in the paper: doi.org/10.1038/s41598-026-55225-1.
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, issue, pages, dates, 7 authors, 7 keywords, 8 MeSH terms, 3 funders, 83 references.
Cite
This paper
Vaccari, F. E., Diomedi, S., Bettazzi, E., Filippini, M., De Vitis, M., Hadjidimitrakis, K., & Fattori, P. (2026). Benchmarking criteria to determine latent linear dimensionality in neural data. Scientific reports, 16(1), 26011. https://
BibTeX
@article{vaccari2026benc
author = {Vaccari, Francesco Edoardo and Diomedi, Stefano and Bettazzi, Edoardo and Filippini, Matteo and De Vitis, Marina and Hadjidimitrakis, Kostas and Fattori, Patrizia},
title = {{Benchmarking criteria to determine latent linear dimensionality in neural data}},
journal = {Scientific reports},
year = {2026},
month = jun,
volume = {16},
number = {1},
pages = {26011},
publisher = {Nature Publishing Group},
issn = {2045-2322},
doi = {10.1038/
url = {https://
pmid = {42259857},
pmcid = {PMC13486701}
}
RIS
TY - JOUR
AU - Vaccari, Francesco Edoardo
AU - Diomedi, Stefano
AU - Bettazzi, Edoardo
AU - Filippini, Matteo
AU - De Vitis, Marina
AU - Hadjidimitrakis, Kostas
AU - Fattori, Patrizia
TI - Benchmarking criteria to determine latent linear dimensionality in neural data
T2 - Scientific reports
J2 - Sci Rep
PY - 2026
DA - 2026/
VL - 16
IS - 1
SP - 26011
SN - 2045-2322
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"given": "Francesco Edoardo"
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{
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"given": "Edoardo"
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"given": "Matteo"
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"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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