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1. Mean-return-time phase of a stochastic oscillator provides an approximate renewal description for the associated point process

   https://doi.org/10.1007/s00422-022-00920-1  

   Holzhausen, Konstantin; Ramlow, Lukas; Pu, Shusen; Thomas, Peter J.; Lindner, Benjamin (February 2022, Biological Cybernetics)

   Abstract Stochastic oscillations can be characterized by a corresponding point process; this is a common practice in computational neuroscience, where oscillations of the membrane voltage under the influence of noise are often analyzed in terms of the interspike interval statistics, specifically the distribution and correlation of intervals between subsequent threshold-crossing times. More generally, crossing times and the corresponding interval sequences can be introduced for different kinds of stochastic oscillators that have been used to model variability of rhythmic activity in biological systems. In this paper we show that if we use the so-called mean-return-time (MRT) phase isochrons (introduced by Schwabedal and Pikovsky) to count the cycles of a stochastic oscillator with Markovian dynamics, the interphase interval sequence does not show any linear correlations, i.e., the corresponding sequence of passage times forms approximately a renewal point process. We first outline the general mathematical argument for this finding and illustrate it numerically for three models of increasing complexity: (i) the isotropic Guckenheimer–Schwabedal–Pikovsky oscillator that displays positive interspike interval (ISI) correlations if rotations are counted by passing the spoke of a wheel; (ii) the adaptive leaky integrate-and-fire model with white Gaussian noise that shows negative interspike interval correlations when spikes are counted in the usual way by the passage of a voltage threshold; (iii) a Hodgkin–Huxley model with channel noise (in the diffusion approximation represented by Gaussian noise) that exhibits weak but statistically significant interspike interval correlations, again for spikes counted when passing a voltage threshold. For all these models, linear correlations between intervals vanish when we count rotations by the passage of an MRT isochron. We finally discuss that the removal of interval correlations does not change the long-term variability and its effect on information transmission, especially in the neural context. 

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2. Exact sampling for some multi-dimensional queueing models with renewal input

   https://doi.org/10.1017/apr.2019.45  

   Blanchet, Jose; Pei, Yanan; Sigman, Karl (December 2019, Advances in Applied Probability)

   Abstract Using a result of Blanchet and Wallwater (2015) for exactly simulating the maximum of a negative drift random walk queue endowed with independent and identically distributed (i.i.d.) increments, we extend it to a multi-dimensional setting and then we give a new algorithm for simulating exactly the stationary distribution of a first-in–first-out (FIFO) multi-server queue in which the arrival process is a general renewal process and the service times are i.i.d.: the FIFO GI/GI/ c queue with $$ 2 \leq c \lt \infty$$ . Our method utilizes dominated coupling from the past (DCFP) as well as the random assignment (RA) discipline, and complements the earlier work in which Poisson arrivals were assumed, such as the recent work of Connor and Kendall (2015). We also consider the models in continuous time, and show that with mild further assumptions, the exact simulation of those stationary distributions can also be achieved. We also give, using our FIFO algorithm, a new exact simulation algorithm for the stationary distribution of the infinite server case, the GI/GI/ $$\infty$$ model. Finally, we even show how to handle fork–join queues, in which each arriving customer brings c jobs, one for each server. 

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3. Dynamic Modeling of Spike Count Data With Conway-Maxwell Poisson Variability

   https://doi.org/10.1162/neco_a_01593  

   Wei, Ganchao; Stevenson, Ian H. (June 2023, Neural Computation)

   Abstract In many areas of the brain, neural spiking activity covaries with features of the external world, such as sensory stimuli or an animal's movement. Experimental findings suggest that the variability of neural activity changes over time and may provide information about the external world beyond the information provided by the average neural activity. To flexibly track time-varying neural response properties, we developed a dynamic model with Conway-Maxwell Poisson (CMP) observations. The CMP distribution can flexibly describe firing patterns that are both under- and overdispersed relative to the Poisson distribution. Here we track parameters of the CMP distribution as they vary over time. Using simulations, we show that a normal approximation can accurately track dynamics in state vectors for both the centering and shape parameters (λ and ν). We then fit our model to neural data from neurons in primary visual cortex, “place cells” in the hippocampus, and a speed-tuned neuron in the anterior pretectal nucleus. We find that this method outperforms previous dynamic models based on the Poisson distribution. The dynamic CMP model provides a flexible framework for tracking time-varying non-Poisson count data and may also have applications beyond neuroscience. 

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4. Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics

   https://doi.org/10.1093/molbev/msaa049  

   Tao, Qiqing; Barba-Montoya, Jose; Huuki, Louise A; Durnan, Mary Kathleen; Kumar, Sudhir; Thorne, Jeffrey (March 2020, Molecular Biology and Evolution)

   Abstract The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared with those from simple models is yet to be quantified for contemporary data sets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa, we found that the use of the simplest models can produce divergence time estimates and credibility intervals similar to those obtained from the complex models applied in the original studies. This result is surprising because the use of simple models underestimates sequence divergence for all the data sets analyzed. We found three fundamental reasons for the observed robustness of time estimates to model complexity in many practical data sets. First, the estimates of branch lengths and node-to-tip distances under the simplest model show an approximately linear relationship with those produced by using the most complex models applied on data sets with many sequences. Second, relaxed clock methods automatically adjust rates on branches that experience considerable underestimation of sequence divergences, resulting in time estimates that are similar to those from complex models. And, third, the inclusion of even a few good calibrations in an analysis can reduce the difference in time estimates from simple and complex models. The robustness of time estimates to model complexity in these empirical data analyses is encouraging, because all phylogenomics studies use statistical models that are oversimplified descriptions of actual evolutionary substitution processes. 

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5. Enhancing reinforcement learning models by including direct and indirect pathways improves performance on striatal dependent tasks

   https://doi.org/10.1371/journal.pcbi.1011385  

   Blackwell, Kim T.; Doya, Kenji (August 2023, PLOS Computational Biology)

   Cai, Ming Bo (Ed.)

   A major advance in understanding learning behavior stems from experiments showing that reward learning requires dopamine inputs to striatal neurons and arises from synaptic plasticity of cortico-striatal synapses. Numerous reinforcement learning models mimic this dopamine-dependent synaptic plasticity by using the reward prediction error, which resembles dopamine neuron firing, to learn the best action in response to a set of cues. Though these models can explain many facets of behavior, reproducing some types of goal-directed behavior, such as renewal and reversal, require additional model components. Here we present a reinforcement learning model, TD2Q, which better corresponds to the basal ganglia with two Q matrices, one representing direct pathway neurons (G) and another representing indirect pathway neurons (N). Unlike previous two-Q architectures, a novel and critical aspect of TD2Q is to update the G and N matrices utilizing the temporal difference reward prediction error. A best action is selected for N and G using a softmax with a reward-dependent adaptive exploration parameter, and then differences are resolved using a second selection step applied to the two action probabilities. The model is tested on a range of multi-step tasks including extinction, renewal, discrimination; switching reward probability learning; and sequence learning. Simulations show that TD2Q produces behaviors similar to rodents in choice and sequence learning tasks, and that use of the temporal difference reward prediction error is required to learn multi-step tasks. Blocking the update rule on the N matrix blocks discrimination learning, as observed experimentally. Performance in the sequence learning task is dramatically improved with two matrices. These results suggest that including additional aspects of basal ganglia physiology can improve the performance of reinforcement learning models, better reproduce animal behaviors, and provide insight as to the role of direct- and indirect-pathway striatal neurons. 

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