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Systems Biology

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Machine learning alternative to systems biology should not solely depend on data.

Briefings in bioinformatics
In recent years, artificial intelligence (AI)/machine learning has emerged as a plausible alternative to systems biology for the elucidation of biological phenomena and in attaining specified design objective in synthetic biology. Although considered...

Guided interactive image segmentation using machine learning and color-based image set clustering.

Bioinformatics (Oxford, England)
MOTIVATION: Over the last decades, image processing and analysis have become one of the key technologies in systems biology and medicine. The quantification of anatomical structures and dynamic processes in living systems is essential for understandi...

Physically constrained neural networks for inferring physiological system models.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Systems biology and systems neurophysiology in particular have recently emerged as powerful tools for a number of key applications in the biomedical sciences. Nevertheless, such models are often based on complex combinations of multiscale (and possib...

Prediction of whole-cell transcriptional response with machine learning.

Bioinformatics (Oxford, England)
MOTIVATION: Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments to cover all possible combinations of perturbations is infeasible. In this paper, we prese...

A Practical Guide to Integrating Multimodal Machine Learning and Metabolic Modeling.

Methods in molecular biology (Clifton, N.J.)
Complex, distributed, and dynamic sets of clinical biomedical data are collectively referred to as multimodal clinical data. In order to accommodate the volume and heterogeneity of such diverse data types and aid in their interpretation when they are...

Computational Systems Biology and Artificial Intelligence.

Methods in molecular biology (Clifton, N.J.)
Aware of the rapid evolution of computational systems biology (CSB), which is the focus of this book, we address the emergence of artificial intelligence (AI). Consequently, one of the main purposes of this Introduction is to assess where the relatio...

Personal Dense Dynamic Data Clouds Connect Systems Biomedicine to Scientific Wellness.

Methods in molecular biology (Clifton, N.J.)
The dramatic convergence of molecular biology, genomics, proteomics, metabolomics, bioinformatics, and artificial intelligence has provided a substrate for deep understanding of the biological basis of health and disease. Systems biology is a holisti...

Training with Small Medical Data: Robust Bayesian Neural Networks for Colon Cancer Overall Survival Prediction.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Fast and accurate cancer prognosis stratification models are essential for treatment designs. Large labeled patient data can power advanced deep learning models to obtain precise predictions. However, since fully labeled patient data are hard to acqu...

Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease.

Database : the journal of biological databases and curation
Omics technologies offer great promises for improving our understanding of diseases. The integration and interpretation of such data pose major challenges, calling for adequate knowledge models. Disease maps provide curated knowledge about disorders'...

Ciliate behavior: blueprints for dynamic cell biology and microscale robotics.

Molecular biology of the cell
Place a drop of pond water under the microscope, and you will likely find an ocean of extraordinary and diverse single-celled organisms called . This remarkable group of single-celled organisms wield microtubules, active systems, electrical signaling...