Kenneth Latimer

Google Scholar Profile


  • David Zoltowski, Kenneth W. Latimer, Jacob L. Yates, Alexander C. Huk, & Jonathan W. Pillow (2019). Discrete stepping and nonlinear ramping dynamics underlie spiking responses of LIP neurons during decision-making . Neuron, 102(6):1249-1258.   [abstract | link]

    Neurons in LIP exhibit ramping trial-averaged responses during decision-making. Recent work sparked debate over whether single-trial LIP spike trains are better described by discrete "stepping" or continuous "ramping"dynamics. We extended latent dynamical spike train models and used Bayesian model comparison to address this controversy. First, we incorporated non-Poisson spiking into both models and found that more neurons were better described by stepping than ramping, even when conditioned on evidence or choice. Second, we extended the ramping model to include a non-zero baseline and compressive output nonlinearity. This model accounted for roughly as many neurons as the stepping model. However, latent dynamics inferred under this model exhibited high diffusion variance for many neurons, softening the distinction between continuous and discrete dynamics. Results generalized to additional datasets, demonstrating that substantial fractions of neurons are well described by either stepping or nonlinear ramping, which may be less categorically distinct than the original labels implied.

  • Kenneth W. Latimer, Jacob L. Yates, Miriam L. R. Meister, Alexander C. Huk, & Jonathan W. Pillow (2015). Single-trial spike trains in parietal cortex reveal discrete steps during decision-making. Science, 349(6244):184-187.   [abstract | link]
    Related: Technical Comment by Shadlen and colleagues and Our Response

    Neurons in the macaque lateral intraparietal (LIP) area exhibit firing rates that appear to ramp upward or downward during decision-making. These ramps are commonly assumed to reflect the gradual accumulation of evidence toward a decision threshold. However, the ramping in trial-averaged responses could instead arise from instantaneous jumps at different times on different trials. We examined single-trial responses in LIP using statistical methods for fitting and comparing latent dynamical spike-train models. We compared models with latent spike rates governed by either continuous diffusion-to-bound dynamics or discrete “stepping” dynamics. Roughly three-quarters of the choice-selective neurons we recorded were better described by the stepping model. Moreover, the inferred steps carried more information about the animal’s choice than spike counts.

  • Kenneth W. Latimer, Alexander C. Huk, & Jonathan W. Pillow (2015). Bayesian inference for latent stepping and ramping models of spike train data. Chapter in Advanced State Space Methods for Neural and Clinical Data, ed. Zhe Chen, Cambridge University Press.

  • Kenneth W. Latimer, E.J. Chichilnisky, Fred Rieke, & Jonathan W. Pillow (2014). Inferring synaptic conductances from spike trains under a biophysically inspired point process model. Advances in Neural Information Processing Systems, 27:954-962.   [abstract | link | poster]

    A popular approach to neural characterization describes neural responses in terms of a cascade of linear and nonlinear stages: a linear filter to describe stimulus integration, followed by a nonlinear function to convert the filter output to spike rate. However, real neurons respond to stimuli in a manner that depends on the nonlinear integration of excitatory and inhibitory synaptic inputs. Here we introduce a biophysically inspired point process model that explicitly incorporates stimulus-induced changes in synaptic conductance in a dynamical model of neuronal membrane potential. Our work makes two important contributions. First, on a theoretical level, it offers a novel interpretation of the popular generalized linear model (GLM) for neural spike trains. We show that the classic GLM is a special case of our conductance-based model in which the stimulus linearly modulates excitatory and inhibitory conductances in an equal and opposite "push-pull" fashion. Our model can therefore be viewed as a direct extension of the GLM in which we relax these constraints; the resulting model can exhibit shunting as well as hyperpolarizing inhibition, and time-varying changes in both gain and membrane time constant. Second, on a practical level, we show that our model provides a tractable model of spike responses in early sensory neurons that is both more accurate and more interpretable than the GLM. Most importantly, we show that we can accurately infer intracellular synaptic conductances from extracellularly recorded spike trains. We validate these estimates using direct intracellular measurements of excitatory and inhibitory conductances in parasol retinal ganglion cells. The stimulus-dependence of both excitatory and inhibitory conductances can be well described by a linear-nonlinear cascade, with the filter driving inhibition exhibiting opposite sign and a slight delay relative to the filter driving excitation. We show that the model fit to extracellular spike trains can predict excitatory and inhibitory conductances elicited by novel stimuli with nearly the same accuracy as a model trained directly with intracellular conductances.

  • Il Memming Park, Evan Archer, Kenneth W. Latimer, & Jonathan W. Pillow (2013). Universal models for binary spike patterns using centered Dirichlet processes. Advances in Neural Information Processing Systems, 26:2463-2471.   [abstract | link]

    Probabilistic models for binary spike patterns provide a powerful tool for understanding the statistical dependencies in large-scale neural recordings. Maximum entropy (or "maxent") models, which seek to explain dependencies in terms of low-order interactions between neurons, have enjoyed remarkable success in modeling such patterns, particularly for small groups of neurons. However, these models are computationally intractable for large populations, and low-order maxent models have been shown to be inadequate for some datasets. To overcome these limitations, we propose a family of "universal" models for binary spike patterns, where universality refers to the ability to model arbitrary distributions over all 2^m binary patterns. We construct universal models using a Dirichlet process centered on a well-behaved parametric base measure, which naturally combines the flexibility of a histogram and the parsimony of a parametric model. We derive computationally efficient inference methods using Bernoulli and cascaded logistic base measures, which scale tractably to large populations. We also establish a condition for equivalence between the cascaded logistic and the 2nd-order maxent or "Ising" model, making cascaded logistic a reasonable choice for base measure in a universal model. We illustrate the performance of these models using neural data.

  • Benjamin Scholl, Kenneth W. Latimer, & Nicholas J. Priebe (2012). A retinal source of spatial contrast gain control. J. Neurosci, 32(29):9824-9830.   [abstract | link]

    Sensory cortex is able to encode a broad range of stimulus features despite a great variation in signal strength. In cat primary visual cortex (V1), for example, neurons are able to extract stimulus features like orientation or spatial configuration over a wide range of stimulus contrasts. The contrast-invariant spatial tuning found in V1 neuron responses has been modeled as a gain control mechanism, but at which stage of the visual pathway it emerges has remained unclear. Here we describe our findings that contrast-invariant spatial tuning occurs not only in the responses of lateral geniculate nucleus (LGN) relay cells but also in their afferent retinal input. Our evidence suggests that a similar contrast-invariant mechanism is found throughout the stages of the early visual pathway, and that the contrast-invariant spatial selectivity is evident in both retinal ganglion cell and LGN cell responses.


  • Kenneth W. Latimer*, Dylan Barbera*, Michael Sokoletsky, Bshara Awwad, Yonaton Katz, Israel Nelkin, Lampl L, Adrienne L. Fairhall, & Nicholas K. Priebe NJ (2019). Multiple timescales account for adaptive responses across sensory cortices. . bioRxiv.   [abstract | link]

    Sensory systems encounter remarkably diverse stimuli in the external environment. Natural stimuli exhibit timescales and amplitudes of variation that span a wide range. Mechanisms of adaptation, ubiquitous feature of sensory systems, allow for the accommodation of this range of scales. Are there common rules of adaptation across different sensory modalities? We measured the membrane potential responses of individual neurons in the visual, somatosensory and auditory cortices to discrete, punctate stimuli delivered at a wide range of fixed and nonfixed frequencies. We find that the adaptive profile of the response is largely preserved across these three areas, exhibiting attenuation and responses to the cessation of stimulation which are signatures of response to changes in stimulus statistics. We demonstrate that these adaptive responses can emerge from a simple model based on the integration of fixed filters operating over multiple time scales.

  • Kenneth W. Latimer (2019). Nonlinear demixed component analysis for neural population data as a low-rank kernel regression problem . arXiv.   [abstract | link]

    Here I introduce an extension to demixed principal component analysis (dPCA), a linear dimensionality reduction technique for analyzing the activity of neural populations, to the case of nonlinear components. This extension, kernel demixed principal component analysis (kdPCA), relies on kernel least-squares regression techniques, and it resembles kernel-based extensions to standard principal component analysis and canonical correlation analysis. kdPCA includes dPCA as a special case when the kernel is linear. I present simulated examples of high-dimensional neural activity generated from low-dimensional trajectories and compare the results of kdPCA to dPCA. These simulations demonstrate that neurally relevant nonlinearities - such as stimulus-dependent gain and rotations - impede the ability of dPCA to demix neural activity corresponding to experimental parameters. However, kdPCA can still recover interpretable components from such data. Additionally, I apply kdPCA to a neural population previously analyzed by dPCA from rat orbitofrontal cortex during an odor classification task in recovering decision-related activity. The components recovered by kdPCA achieve better generalization and demixing performance compared to dPCA by accounting for a nonlinear interaction between stimulus and decision in the neural activity. In conclusion, simple nonlinear interactions inhibit the ability of linear dimensionality reduction techniques to recover interpretable demixed components in neural data, but this problem can be tackled by nonlinear dimensionality reduction approaches like kdPCA.

  • Kenneth W. Latimer, Fred Rieke, & Jonathan W. Pillow (2018). Inferring synaptic inputs from spikes with a conductance-based neural encoding model . bioRxiv.   [abstract | link]

    A popular approach to the study of information processing in the nervous system is to characterize neural responses in terms of a cascade of linear and nonlinear stages: a linear filter to describe the neuron’s stimulus integration properties, followed by a rectifying nonlinearity to convert filter output to spike rate. However, real neurons integrate stimuli via the modulation of nonlinear excitatory and inhibitory synaptic conductances. Here we introduce a bio-physically inspired point process model with conductance-based inputs. The model provides a novel interpretation of the popular Poisson generalized linear model (GLM) as a special kind of conductance-based model, where excitatory and inhibitory conductances are modulated in a “push-pull” manner so that total conductance remains constant. We relax this constraint to obtain a more general and flexible “conductance-based encoding model” (CBEM), which can exhibit stimulus-dependent fluctuations in gain and dynamics. We fit the model to spike trains of macaque retinal ganglion cells and show that, remarkably, we can accurately infer underlying inhibitory and excitatory conductances, using comparisons to intracellularly measured conductances. Using extracellular data, we corroborate the intracellular finding that synaptic excitation temporally precedes inhibition in retina. We show that the CBEM outperforms the classic GLM at predicting retinal ganglion cell responses to full-field stimuli, generalizes better across contrast levels, and captures inhibition-dependent response properties to spatially structured stimuli. The CBEM provides a powerful tool for gaining insights into the intracellular variables governing spiking, and forges an important link between extracellular characterization methods and biophysically detailed response models.

*, † denote equal contribution.