Related papers: A Maximum Entropy Approach to Defining Cell State
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
Optimisation problems in science and engineering typically involve finding the ground state (i.e. the minimum energy configuration) of a cost function with respect to many variables. If the variables are corrupted by noise then this…
Statistical model checking avoids the exponential growth of states associated with probabilistic model checking by estimating properties from multiple executions of a system and by giving results within confidence bounds. Rare properties…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
This paper presents a statistical parser for natural language that obtains a parsing accuracy---roughly 87% precision and 86% recall---which surpasses the best previously published results on the Wall St. Journal domain. The parser itself…
During a spontaneous change, a macroscopic physical system will evolve towards a macro-state with more realizations. This observation is at the basis of the Statistical Mechanical version of the Second Law of Thermodynamics, and it provides…
The paper examines and critiques the expression of entropy as the logarithm of the number of quantum states of a physical system. Boltzmann method of expressing entropy as the logarithm of the number of states of a gas with a given total…
Maximum entropy principle (MEP) offers an effective and unbiased approach to inferring unknown probability distributions when faced with incomplete information, while neural networks provide the flexibility to learn complex distributions…
In single-cell RNA sequencing (scRNA-seq) analysis, a key challenge is inferring hidden cellular dynamics from static cell snapshots. Various computational methods have been developed to address this, focusing on perspectives like…
Maximum Entropy models can be inferred from large data-sets to uncover how collective dynamics emerge from local interactions. Here, such models are employed to investigate neurons recorded by multielectrode arrays in the human and monkey…
Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…
The Maximum Entropy Method (MEM) is a popular data analysis technique based on Bayesian inference, which has found various applications in the research literature. While the MEM itself is well-grounded in statistics, I argue that its…
We quantify the amount of regulation required to control growth in living cells by a Maximum Entropy approach to the space of underlying metabolic states described by genome-scale models. Results obtained for E. coli and human cells are…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
The purpose of this study was to investigate how the entropy of a neuron cell can be measured using membrane ion current signals, which were recorded from neurons in the mouse medial prefrontal cortex (mPFC). The sample entropy and the…
In this paper, we propose a maximum entropy method for predicting disease risks. It is based on a patient's medical history with diseases coded in ICD-10 which can be used in various cases. The complete algorithm with strict mathematical…
Topological and metric entropies of the DNA sequences from different organisms were calculated. Obtained results were compared each other and with ones of corresponding artificial sequences. For all envisaged DNA sequences there is a…
Simplified mechanistic models in ecology have been criticized for the fact that a good fit to data does not imply the mechanism is true: pattern does not equal process. In parallel, the maximum entropy principle (MaxEnt) has been applied in…
Numerical methods for the description of nonequilibrium many-particle quantum systems such as equation of motion techniques often cannot compute the full statistics of observables but only moments of it, such as mean, variance and…
The determination of block-entropies is a well established method for the investigation of discrete data, also called symbols (7). There is a large variety of such symbolic sequences, ranging from texts written in natural languages,…