An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology. De Martino, A. and De Martino, D. 4(4):e00596.
An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology [link]Paper  doi  abstract   bibtex   
A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data.
@article{demartinoIntroductionMaximumEntropy2018,
  title = {An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology},
  author = {De Martino, Andrea and De Martino, Daniele},
  date = {2018-04-01},
  journaltitle = {Heliyon},
  shortjournal = {Heliyon},
  volume = {4},
  pages = {e00596},
  issn = {2405-8440},
  doi = {10.1016/j.heliyon.2018.e00596},
  url = {https://doi.org/10.1016/j.heliyon.2018.e00596},
  urldate = {2019-09-19},
  abstract = {A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data.},
  keywords = {~INRMM-MiD:z-2SPWWDXM,data-transformation-modelling,entropy,statistics},
  number = {4}
}
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