Optimal Estimation of Change in a Population of Parameters. (arXiv:1911.12568v1 [cs.LG])

Paired estimation of change in parameters of interest over a population plays a central role in several application domains including those in the social sciences, epidemiology, medicine and biology. In these domains, the size of the population under study is often very large, however, the number of observations available per individual in the population is…

On the Asymptotic, Near-Equilibrium Sensory Response. (arXiv:1307.6445v5 [q-bio.NC] UPDATED)

The asymptotic, near-equilibrium neural response of the sensory periphery can be derived theoretically using information theory, asymptotic Bayesian statistics and a theory of complex systems. Almost no biological knowledge is required. The theoretical approach shows good agreement with experimental data across different sensory modalities and animal species. The theory is reminiscent of statistical physics.

Lineage EM Algorithm for Inferring Latent States from Cellular Lineage Trees. (arXiv:1806.00215v4 [q-bio.PE] UPDATED)

Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such phenomena, it is indispensable to identify the phenotype of each cell and its inheritance. Although recent advancements in microfluidic…

Cholinergic switch between two types of slow waves in cerebral cortex. (arXiv:1810.00816v3 [q-bio.NC] UPDATED)

Sleep slow waves are known to participate in memory consolidation, yet slow waves occurring under anesthesia present no positive effects on memory. Here, we shed light onto this paradox, based on a combination of extracellular recordings in vivo, in vitro, and computational models. We find two types of slow waves, based on analyzing the temporal…

Assessing the accuracy of direct-coupling analysis for RNA contact prediction. (arXiv:1812.07630v4 [q-bio.QM] UPDATED)

Many non-coding RNAs are known to play a role in the cell directly linked to their structure. Structure prediction based on the sole sequence is however a challenging task. On the other hand, thanks to the low cost of sequencing technologies, a very large number of homologous sequences are becoming available for many RNA families.…

Evolutionary dynamics with game transitions. (arXiv:1905.10269v2 [q-bio.PE] UPDATED)

The environment has a strong influence on a population’s evolutionary dynamics. Driven by both intrinsic and external factors, the environment is subject to continual change in nature. To capture an ever-changing environment, we consider a model of evolutionary dynamics with game transitions, where individuals’ behaviors together with the games they play in one time step…

Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization. (arXiv:1905.11036v2 [q-bio.MN] UPDATED)

While cooperativity in ligand-induced receptor dimerization has been linked with receptor-receptor couplings via minimal representations of physical observables, effects arising from higher-order oligomer (e.g., trimer and tetramer) formations of unobserved receptors have received less attention. Here, we propose a dimerization model of ligand-induced receptors in multivalent form representing physical observables under basis vectors of various…

Inference under random limit bootstrap measures. (arXiv:1911.12779v1 [econ.EM])

Asymptotic bootstrap validity is usually understood as consistency of the distribution of a bootstrap statistic, conditional on the data, for the unconditional limit distribution of a statistic of interest. From this perspective, randomness of the limit bootstrap measure is regarded as a failure of the bootstrap. We show that such limiting randomness does not necessarily…

Dynamic Optimal Choice When Rewards are Unbounded Below. (arXiv:1911.13025v1 [econ.TH])

We propose a new approach to solving dynamic decision problems with rewards that are unbounded below. The approach involves transforming the Bellman equation in order to convert an unbounded problem into a bounded one. The major advantage is that, when the conditions stated below are satisfied, the transformed problem can be solved by iterating with…

Semiparametric Quantile Models for Ascending Auctions with Asymmetric Bidders. (arXiv:1911.13063v1 [econ.EM])

The paper proposes a parsimonious and flexible semiparametric quantile regression specification for asymmetric bidders within the independent private value framework. Asymmetry is parameterized using powers of a parent private value distribution, which is generated by a quantile regression specification. As noted in Cantillon (2008), this covers and extends models used for efficient collusion, joint bidding…