Publications - Nan Chen

gFlora: a topology-aware method to discover functional co-response groups in soil microbial communities

Nan Chen, Merlijn Schram, Doina Bucur

IEEE Transactions on Computational Biology and Bioinformatics, 2024 Spotlight

Microorganisms such as bacteria perform critical functions in the soil ecosystem: they mediate essential carbon, nitrogen, and nutrient cycling processes in soils. To manage the health and functions of soils, it is important to understand which soil functions are related the most to which microbial taxa—but this taxon-to-function link is difficult to discover because of the size and complexity of the soil ecosystem. A feasible solution is to discover functional links at the level of groups instead of individuals, using observational data of both taxa abundance and soil function indicators. We thus aim to learn the functional co-response group: a group of taxa whose co-response effect (the representative characteristic of the whole functional group) co-responds (associates well statistically) to a functional variable. Unlike the existing method, we model the soil microbial community as an ecological co-occurrence network with the taxa as nodes (weighted by their abundance) and their relationships (a combination from both spatial and functional ecological aspects) as edges (weighted by the strength of the relationships). Then, we design a method called gFlora which notably uses graph convolution over this co-occurrence network to compute the co-response effect of the group, such that the network topology is also considered in the discovery process. We evaluate gFlora on four real-world soil microbiome datasets (bacteria and nematodes combined with two soil functions: nitrogen mineralization and crop yield). gFlora outperforms the competing method on all evaluation metrics, and it discovers new functional evidence for taxa which were so far under-studied. We show that the graph convolution is crucial to taxa with relatively low abundance (thus removing the bias towards taxa with higher abundance), and the discovered bacteria of different genera are distributed in the co-occurrence network but remain tightly connected among themselves, demonstrating that topologically they fill different but collaborative functional roles in the ecological community.

[Paper] [Code]

gFlora: a topology-aware method to discover functional co-response groups in soil microbial communities

Nan Chen, Merlijn Schram, Doina Bucur

IEEE Transactions on Computational Biology and Bioinformatics, 2024 Spotlight

Microorganisms such as bacteria perform critical functions in the soil ecosystem: they mediate essential carbon, nitrogen, and nutrient cycling processes in soils. To manage the health and functions of soils, it is important to understand which soil functions are related the most to which microbial taxa—but this taxon-to-function link is difficult to discover because of the size and complexity of the soil ecosystem. A feasible solution is to discover functional links at the level of groups instead of individuals, using observational data of both taxa abundance and soil function indicators. We thus aim to learn the functional co-response group: a group of taxa whose co-response effect (the representative characteristic of the whole functional group) co-responds (associates well statistically) to a functional variable. Unlike the existing method, we model the soil microbial community as an ecological co-occurrence network with the taxa as nodes (weighted by their abundance) and their relationships (a combination from both spatial and functional ecological aspects) as edges (weighted by the strength of the relationships). Then, we design a method called gFlora which notably uses graph convolution over this co-occurrence network to compute the co-response effect of the group, such that the network topology is also considered in the discovery process. We evaluate gFlora on four real-world soil microbiome datasets (bacteria and nematodes combined with two soil functions: nitrogen mineralization and crop yield). gFlora outperforms the competing method on all evaluation metrics, and it discovers new functional evidence for taxa which were so far under-studied. We show that the graph convolution is crucial to taxa with relatively low abundance (thus removing the bias towards taxa with higher abundance), and the discovered bacteria of different genera are distributed in the co-occurrence network but remain tightly connected among themselves, demonstrating that topologically they fill different but collaborative functional roles in the ecological community.

[Paper] [Code]

EleMi: A Robust Method to Infer Soil Ecological Networks with Better Community Structure

Nan Chen, Doina Bucur

International Conference on Complex Networks (CompleNet), 2024

Soil ecological networks enable us to better understand the complex interactions among a great number of organisms in soil. Soil communities are biotic groups with similar environmental and resource preferences. Community detection thus provides insights into the mechanisms of the soil ecosystem. Therefore, inferring ecological networks with clear community structure is essential for investigating the soil ecosystem. We propose Elastic net regularized Multi-regression (EleMi), a new method to infer soil ecological networks. To better find the community structure, EleMi does not infer pairwise interactions, but considers all organisms simultaneously. Specifically, it regresses the abundance of all other taxa to one taxon (with shared parameters across soil samples) and employs Elastic net to avoid over-sparsity and stochasticity. The results on both synthetic and real biotic data show that EleMi is more robust and can infer ecological networks with clearer community structure.

[Paper] [Code]

EleMi: A Robust Method to Infer Soil Ecological Networks with Better Community Structure

Nan Chen, Doina Bucur

International Conference on Complex Networks (CompleNet), 2024

Soil ecological networks enable us to better understand the complex interactions among a great number of organisms in soil. Soil communities are biotic groups with similar environmental and resource preferences. Community detection thus provides insights into the mechanisms of the soil ecosystem. Therefore, inferring ecological networks with clear community structure is essential for investigating the soil ecosystem. We propose Elastic net regularized Multi-regression (EleMi), a new method to infer soil ecological networks. To better find the community structure, EleMi does not infer pairwise interactions, but considers all organisms simultaneously. Specifically, it regresses the abundance of all other taxa to one taxon (with shared parameters across soil samples) and employs Elastic net to avoid over-sparsity and stochasticity. The results on both synthetic and real biotic data show that EleMi is more robust and can infer ecological networks with clearer community structure.

[Paper] [Code]

Association between cognitive impairments and aberrant dynamism of overlapping brain sub-networks in unmedicated major depressive disorder: A resting-state MEG study

Shuming Zhong*, Nan Chen*, Shunkai Lai, ..., Yanbin Jia (* equal contribution)

Journal of Affective Disorders, 2023

2024

gFlora: a topology-aware method to discover functional co-response groups in soil microbial communities

gFlora: a topology-aware method to discover functional co-response groups in soil microbial communities

EleMi: A Robust Method to Infer Soil Ecological Networks with Better Community Structure

EleMi: A Robust Method to Infer Soil Ecological Networks with Better Community Structure

2023

Association between cognitive impairments and aberrant dynamism of overlapping brain sub-networks in unmedicated major depressive disorder: A resting-state MEG study

Association between cognitive impairments and aberrant dynamism of overlapping brain sub-networks in unmedicated major depressive disorder: A resting-state MEG study

2022

Altered temporal reachability highlights the role of sensory perception systems in major depressive disorder

Altered temporal reachability highlights the role of sensory perception systems in major depressive disorder

2021

Estimation of discriminative multimodal brain network connectivity using message-passing-based nonlinear network fusion

Estimation of discriminative multimodal brain network connectivity using message-passing-based nonlinear network fusion

Calcarine as a bridge between brain function and structure in irritable bowel syndrome: A multiplex network analysis

Calcarine as a bridge between brain function and structure in irritable bowel syndrome: A multiplex network analysis

Inter-hemispheric functional connections are more vulnerable to attack than structural connection in patients with irritable bowel syndrome

Inter-hemispheric functional connections are more vulnerable to attack than structural connection in patients with irritable bowel syndrome

Integration of a novel attribute and classical topology metrics of hyper-networks for automatic diagnosis of Major depressive disorder

Integration of a novel attribute and classical topology metrics of hyper-networks for automatic diagnosis of Major depressive disorder

Age-associated differences of modules and hubs in brain functional networks

Age-associated differences of modules and hubs in brain functional networks

2020

Decreased dynamism of overlapping brain sub-networks in major depressive disorder

Decreased dynamism of overlapping brain sub-networks in major depressive disorder