arXiv subjects

Mika Ala-Korpela

Publications and source records attributed to Mika Ala-Korpela.

3 recordsLinked to original sources

arXiv2024

Multilayer Network of Cardiovascular Diseases and Depression via Multipartite Projection

Cardiovascular diseases (CVD) and depression exhibit significant comorbidity, which is highly predictive of poor clinical outcomes. Yet, the underlying biological pathways remain challenging to decipher, presumably due to the non-linear associations across multiple mechanisms. In this study, we introduced a multipartite projection method based on mutual information correlations to construct multilayer disease networks as a novel approach to explore such intricate relationships. We applied this method to a cross-sectional dataset from a wave of the Young Finns Study, which includes data on CVD and depression, along with related risk factors and two omics of biomarkers: metabolites and lipids. Rather than directly correlating CVD-related phenotypes and depressive symptoms, we extended the notion of bipartite networks to create a multipartite network, linking these phenotypes and symptoms to intermediate biological variables. Projecting from these intermediate variables results in a weighted multilayer network, where each link between CVD and depression variables is marked by its layer (i.e., metabolome or lipidome). Applying this projection method, we identified potential mediating biomarkers that connect CVD with depression. These biomarkers may therefore play significant roles in the biological pathways underlying CVD-depression comorbidity. Additionally, the network projection highlighted sex and BMI as key risk factors, or confounders, in this comorbidity. Our method is scalable to incorporate any number of omics layers and various disease phenotypes, offering a comprehensive, system-level perspective on the biological pathways contributing to comorbidity.

cs.CE↗

arXiv2016

Multiple Output Regression with Latent Noise

In high-dimensional data, structured noise caused by observed and unobserved factors affecting multiple target variables simultaneously, imposes a serious challenge for modeling, by masking the often weak signal. Therefore, (1) explaining away the structured noise in multiple-output regression is of paramount importance. Additionally, (2) assumptions about the correlation structure of the regression weights are needed. We note that both can be formulated in a natural way in a latent variable model, in which both the interesting signal and the noise are mediated through the same latent factors. Under this assumption, the signal model then borrows strength from the noise model by encouraging similar effects on correlated targets. We introduce a hyperparameter for the \emph{latent signal-to-noise ratio} which turns out to be important for modelling weak signals, and an ordered infinite-dimensional shrinkage prior that resolves the rotational unidentifiability in reduced-rank regression models. Simulations and prediction experiments with metabolite, gene expression, FMRI measurement, and macroeconomic time series data show that our model equals or exceeds the state-of-the-art performance and, in particular, outperforms the standard approach of assuming independent noise and signal models.

stat.ML↗

arXiv2013

Bayesian Information Sharing Between Noise And Regression Models Improves Prediction of Weak Effects

We consider the prediction of weak effects in a multiple-output regression setup, when covariates are expected to explain a small amount, less than $\approx 1%$, of the variance of the target variables. To facilitate the prediction of the weak effects, we constrain our model structure by introducing a novel Bayesian approach of sharing information between the regression model and the noise model. Further reduction of the effective number of parameters is achieved by introducing an infinite shrinkage prior and group sparsity in the context of the Bayesian reduced rank regression, and using the Bayesian infinite factor model as a flexible low-rank noise model. In our experiments the model incorporating the novelties outperformed alternatives in genomic prediction of rich phenotype data. In particular, the information sharing between the noise and regression models led to significant improvement in prediction accuracy.

stat.ML↗