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18 views3 pages

Untitled Document

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qk149248
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Deep Learning in Single-Cell and Spatial Transcriptomics Data

Analysis: Advances and Challenges from a Data Science Perspective


Shuang Ge, Shuqing Sun, Huan Xu, Qiang Cheng, Zhixiang Ren

Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)

The development of single-cell and spatial transcriptomics has revolutionized our capacity to
investigate cellular properties, functions, and interactions in both cellular and spatial contexts.
However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell
sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty,
obscuring the underlying biological signals. Second, these data often encompass multiple modalities,
including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse
data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while
the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets
are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately
reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis
methods struggle to deal with the various challenges presented by intricate biological networks. Deep
learning has emerged as a powerful tool capable of handling high-dimensional complex data and
automatically identifying meaningful patterns, offering significant promise in addressing these
challenges. This review systematically analyzes these challenges and discusses related deep learning
approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58
computational methods, and evaluated their performance on the respective modeling tasks. Finally, we
highlight three areas for future development from a technical, dataset, and application perspective.
This work will serve as a valuable resource for understanding how deep learning can be effectively
utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address
emerging challenges.

[2] arXiv:2412.03628 [pdf, other]

Effect of Simulated Space Conditions on functional Connectivity


Parshuram N Aarotale, Jaydip Desai

Comments: Biomedical science instrumentation Journal

Subjects: Neurons and Cognition (q-bio.NC); Human-Computer Interaction (cs.HC)

Long duration spaceflight missions can affect the cognitive and behavioral activities of astronauts due
to changes in gravity. The microgravity significantly impacts the central nervous system physiology
which causes the degradation in the performance and lead to potential risk in the space exploration.
The aim of this study was to evaluate functional connectivity at simulated space conditions using an
unloading harness system to mimic the body-weight distribution related to Earth, Mars, and
International Space Station. A unity model with six directional arrows to imagine six different motor
imagery tasks associated with arms and legs were designed for the Oculus Rift S virtual reality headset
for testing. An Electroencephalogram (EEG) and functional near infrared spectroscopy (fNIRS) signals
were recorded from 10 participants in the distributed weight conditions related to Earth, Mars, and
International Space station using the this http URL fNIRS system at sampling rate of 500 Hz. The
magnitude squared coherence were estimated from left vs right hemisphere of the brain that represents
functional connectivity. The EEG coherence was the higher which shows the strong functional
connectivity and fNIRS coherence was lower shows weak functional connectivity between left vs right
hemisphere of the brain, during all the tasks and trials irrespective of the simulated space conditions.
Further analysis of functional connectivity needed between the intra-regions of the brain.

[3] arXiv:2412.03744 [pdf, html, other]

A novel approach to differential expression analysis of co-occurrence


networks for small-sampled microbiome data
Nandini Gadhia, Michalis Smyrnakis, Po-Yu Liu, Damer Blake, Melanie Hay, Anh Nguyen,
Dominic Richards, Dong Xia, Ritesh Krishna

Comments: 12 pages, 7 figures, under review for a special issue of ACM/IEEE TCBB journal

Subjects: Quantitative Methods (q-bio.QM)

Graph-based machine learning methods are useful tools in the identification and prediction of variation
in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an
accelerating research area in pharmacogenomics. In this article, a novel graph theoretic approach is
proposed to infer a co-occurrence network from 16S microbiome data. The approach is specialised to
handle datasets containing a small number of samples. Small datasets exacerbate the significant
challenges faced by biological data, which exhibit properties such as sparsity, compositionality, and
complexity of interactions. Methodologies are also proposed to enrich and statistically filter the
inferred networks. The utility of the proposed method lies in that it extracts an informative network
from small sampled data that is not only feature-rich, but also biologically meaningful and statistically
significant. Although specialised for small data sets, which are abundant, it can be generally applied to
any small-sampled dataset, and can also be extended to integrate multi-omics data. The proposed
methodology is tested on a data set of chickens vaccinated against and challenged by the protozoan
parasite Eimeria tenella. The raw genetic reads are processed, and networks inferred to describe the
ecosystems of the chicken intestines under three different stages of disease progression. Analysis of
the expression of network features derive biologically intuitive conclusions from purely statistical
methods. For example, there is a clear evolution in the distribution of node features in line with the
progression of the disease. The distributions also reveal clusters of species interacting mutualistically
and parasitically, as expected. Moreover, a specific sub-network is found to persist through all
experimental conditions, representative of a persistent microbiome.

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