Brief text on Kevin’s paper.
Brief text on Alex’s paper.
- Benjamin B. Scott*, Christine M. Constantinople*, Athena Akrami, Timothy D. Hanks, Carlos D. Brody and David W. Tank, Fronto-parietal cortical circuits encode accumulated evidence with a diversity of timescales. Neuron, 2017
Brief text on Ben and Christine’s paper.
- Benjamin B. Scott*, Christine M. Constantinople*, Jeffrey C. Erlich, David W. Tank and Carlos D. Brody, Sources of noise during accumulation of evidence in unrestrained and voluntarily head-restrained rats. eLife, 2015;4:e11308
Many models of decision-making process include an “evidence accumulation” stage: evidence for or against different options is gradually accumulated over time, and it is the result of that accumulation process that drives the final decision. In these models (including work from our own lab), it is usually assumed that noise from inputs at different timepoints is independent of each other, in which case the total variance would increase linearly with the number of inputs. But is that true? Using a visual flashes accumulation task, we found that the data was better described by a model in which variance increased as the square of the number of inputs. In other words, the standard deviation scales linearly with the number of inputs, similar to “scalar variability” models used for numerical and time interval estimation. This result held both for freely moving rats and for head-restrained rats; the latter suggests the phenomenon can be investigated using cellular-resolution two-photon microscopy.
- Charles D. Kopec, Jeffrey C. Erlich, and Bingni W. Brunton, Karl Deisseroth, and Carlos D. Brody, Cortical and subcortical contributions to short-term memory for orienting movements. Neuron, (online) (2015)
Short-term memory is an essential higher cognitive function, allowing us to mentally store information, and thereby separate sensory input from motor output. Guided by previous neural recordings conducted in the rat FOF by Jeff Erlich et al. 2011 during a simple memory guided orienting task, we sought to test the hypothesis that activity in the rat FOF is causally maintaining the rat’s choice for its upcoming motor act. Surprisingly, as information encoded in the FOF increased, the ability to perturb the rat’s choice by disrupting that information decreased. We conducted the same experiments on the deep motor layers of the superior colliculus (SC) and found nearly identical results. In order to reconcile these seemingly contradictory optogenetic and electrophysiological results we adapted a simple mutually inhibiting dynamical attractor network model. At the start of a trial the network resides on the unstable hill separating two basins of attraction, at this point there is little information encoded, but unilateral inactivation of either the FOF or SC can easily push the network off the hill into one of the attractors, biasing the decision. Later, during the memory delay period, when the network resides in one of the attractors, there is a large amount of information encoded, but now the same perturbation is insufficient to push the network out of the attractor. These results provide the first direct causal test that short-term memory is maintained by a network distributed across cortical and subcortical regions and is well characterized by attractor dynamics.
- Chunyu A. Duan, Jeffrey C. Erlich, and Carlos D. Brody, Requirement of prefrontal and midbrain regions for rapid executive control of behavior in the rat. Neuron, 86 (6): 1491-1503 (2015)
Executive control, defined by flexible sensorimotor remapping in response to changing environmental demands, is a remarkable feature of adaptive behavior, and is predominantly studied in primates and putatively mediated by the prefrontal cortex (PFC). To study executive control in the rat, graduating student Ann Duan, together with Jeff and Carlos, developed a novel behavior in which subjects are cued, on each trial, to apply a sensorimotor association to orient either toward a visual target (“Pro”) or away from it (“Anti”). Multiple behavioral asymmetries suggest that Anti behavior is cognitively demanding while Pro is easier to learn and perform. This is consistent with a prominent hypothesis in the primate literature that Anti requires prefrontal cortex (PFC), whereas Pro could be mediated by midbrain superior colliculus (SC). First author Ann Duan directly tested this hypothesis via reversible inactivation of the PFC or SC during task performance. Pharmacological inactivation of rat medial PFC supported its expected role in Anti. Remarkably, bilateral SC inactivation substantially impaired Anti while leaving Pro essentially intact. Moreover, SC inactivation eliminated the performance cost of switching from Anti to Pro tasks. Our results establish a rodent model of single-trial sensorimotor remapping and suggest a critical role for SC in the cognitively demanding Anti task.
- Jeffrey C. Erlich, Bingni W. Brunton, Chunyu A. Duan, Timothy D. Hanks, and Carlos D. Brody, Distinct behavioral effects of prefrontal and parietal cortex inactivations on an accumulation of evidence task in the rat. eLife, 2015; 4:e05457
Numerous brain regions have been shown to have neural correlates of gradually accumulating evidence for decision-making, but the causal roles of these regions in decisions driven by accumulation of evidence have yet to be determined. Here, in rats performing an auditory evidence accumulation task, we inactivated the frontal orienting fields (FOF) and posterior parietal cortex (PPC), two rat cortical regions that have neural correlates of accumulating evidence and that have been proposed as central to decision-making. We used a detailed model of the decision process to analyze the effect of inactivations. Inactivation of the FOF induced substantial performance impairments that were quantitatively best described as an impairment in the output pathway of an evidence accumulator with a long integration time constant (>240 ms). In contrast, we found a minimal role for PPC in decisions guided by accumulating auditory evidence, even while finding a strong role for PPC in internally-guided decisions.
- Timothy D. Hanks*, Charles D. Kopec*, Bingni W. Brunton, Chunyu A. Duan, Jeffrey C. Erlich, and Carlos D. Brody, Distinct relationships of parietal and prefrontal cortices to evidence accumulation. Nature, Advance Online Publication (2015)
Tim Hanks and Chuck Kopec took our temporal accumulation of auditory evidence decision task (“Poisson Clicks”, Brunton et al. 2013), and used it to investigate encoding of accumulating evidence in posterior parietal cortex (PPC) and frontal orienting fields (FOF) of rats. The paper develops a new method to estimate tuning curves for accumulating evidence, allowing us to plot firing rate as a function of value of the accumulated evidence. This method revealed that while PPC encoded accumulating evidence in a graded manner, the FOF did so in a more binary-like categorical manner, more consistent with encoding response selection (“if the GO signal came now, which of the two options does the accumulated evidence tell me I should choose?”) than with encoding the gradually accumulating evidence itself.
Information about response selection needs to be read out, and will affect behavior, only around the time of the GO signal. Such an encoding thus predicts that perturbing the FOF should have an effect only if the perturbation occurs at the time of the GO signal. High time-resolution optogenetic inactivation of the FOF confirmed this prediction, supporting the idea that the FOF is part of transforming accumulated evidence into a categorical choice, but is not part of the gradually accumulating evidence process itself.
- Scott, BW, Brody CD, and Tank DW, Cellular Resolution Functional Imaging in Behaving Rats using Voluntary Head Restraint. Neuron, 80:1-14 (2013)
Ben Scott, a postdoc in the Brody and Tank labs, developed a system for voluntary head-fixation in rats. Based on the principles of kinematic mounts often used in optics, the system allows precise re-positioning of a rat’s head, across multiple trials of a behavior, with an accuracy of a few microns. This enables cellular-resolution calcium imaging in behaving rats. In addition, because the rats engage the system voluntarily, the approach is amenable to high-throughput training. Thanks to Ben’s work, we can now use the lab’s training facility to teach voluntarily head-fixing rats to perform complex cognitive behaviors requiring many months to train. We are using this is to perform the first cellular-resolution imaging assays of neural activity involved in higher cognitive processes.
- Brunton BW, Botvinivk MM, Brody CD,Rats and Humans can Optimally Accumulate Evidence for Decision-making. Science, 340:95-98 (2013)
Where do imperfections in decision-making come from? And can rats perform gradual accumulation of evidence for decision-making, like primates do? This paper describes a decision-making task that is particularly well-suited to detailed quantitative modeling and analysis. Using this task together with a trial-by-trial model of the behavior, first-author Bing Brunton showed that rats, like humans, can gradually accumulate evidence for decision-making, and that their evidence accumulator is optimal in the sense of being noiseless and lossless. Thus imperfections in decision-making all came from imperfections in sensory processing, none from the evidence accumulation process.The modeling and analysis methods Bing developed are the most statistically powerful approach to date for characterizing properties of decision-making processes. The approach can be readily applied to other decision-making tasks and modalities, and provides a moment-by-moment, trial-by-trial estimate of the subject’s internal estimate of the accumulating evidence.
Nature published a News and Views piece on our paper.
- Erlich JC, Bialek M, Brody CD. A cortical substrate for memory-guided orienting in the rat. Neuron, 72(2):330-343 (2011)
Do rats have a brain region homologous to the primate Frontal Eye Fields (FEF)? We trained rats to perform memory-guided orienting, and used that to investigate the functional role of the rat’s Frontal Orienting Fields (FOF). Memory-guided orienting is a classic task in which a transient sensory cue tells you in which direction you should orient, but you must withhold your motion over a delay period, until a “go” cue arrives. (You must therefore keep either the sensory cue or your intended motion in memory during the delay period.) First-author Jeff Erlich recorded in the Frontal Orienting Fields (FOF), a rat cortical area that has been suggested as homologous to the primate FEF. Just as in the primate FEF, he found persistent neural activity during the delay period that predicts the subject’s subsequent orienting motion. Again as in the primate FEF, Jeff found that pharmacological inactivation of the FOF impairs memory-guided orienting markedly more than it impairs sensory-guided orienting. Our data support the rat FOF / primate FEF homology. Full Description.
- Pai S, Erlich JC, Kopec C, Brody CD. Minimal impairment in a rat model of duration discrimination following excitotoxic lesions of primary auditory and prefrontal cortices. Front. Syst. Neurosci. 5:74.(2011)
Which brain areas are involved in time discrimination? Using the same behavioral protocol and stimuli, rats were trained to either discriminate high versus low tones, or discriminate long versus short durations. First-author Shraddha Pai then lesioned either the auditory cortex (ACx) or the medial prefontal cortex (mPFC). ACx lesions led to a clear impairment in frequency discrimination, but no impairment in the matched duration discrimination task. mPFC lesions led to no detectable impairment in either task. The data suggests that time discrimination may bypass both ACx and mPFC.
- Kopec CD, Bowers AC, Pai S, Brody CD. Semi-automated atlas-based analysis of brain histological sections. J Neurosci Methods. 196(1):12-19 (2011)
Quantifying the location and/or number of features in a histological section of the brain currently requires one to first, manually register a corresponding section from a tissue atlas onto the experimental section and second, count the features. No automated method exists for the first process (registering), and most automated methods for the second process (feature counting) operate reliably only in a high signal-to-noise regime. To reduce experimenter bias and inconsistencies and increase the speed of these analyses, we developed Atlas Fitter, a semi-automated, open-source MatLab-based software package that assists in rapidly registering atlas panels onto histological sections. We also developed CellCounter, a novel fully automated cell counting algorithm that is designed to operate on images with non-uniform background intensities and low signal-to-noise ratios.
- Machens CK, Romo R, Brody CD. Functional, but not anatomical, separation of “what” and “when” in prefrontal cortex. J Neurosci. 30(1):350-360. (2010)
How do populations of neurons multiplex different types of information? Recordings in prefrontal cortices typically show neurons that have responses that depend on multiple aspects of the task being performed, and that are highly heterogeneous: although each neuron is reliable, no two neurons are alike. Faced with datasets of recordings of hundreds of such neurons, people often first use principal components analysis (PCA), so as to look at a reduced number of dimensions that captures most of the variance. But PCA doesn’t orient its axes in order to clearly distinguish task components. In this paper, we describe a method to automatically find the orientation of the PC axes that best distinguish between the components of the task we’re interested in. This allows a particularly clear and intelligible view of the data.
- Kopec CD, Brody CD. 2010. Human performance on the temporal bisection task. Brain Cogn. 74(3): 262-72.
- Jun JK, Miller P, Hernández A, Zainos A, Lemus L, Brody CD, Romo R.Heterogenous population coding of a short-term memory and decision task. J Neurosci. 30(3):916-929. (2010)
- Chow SS, Romo R, Brody CD. Context-dependent modulation of functional connectivity: secondary somatosensory cortex to prefrontal cortex connections in two-stimulus-interval discrimination tasks. J Neurosci. 29(22):7238-7245. (2009)
[this section on older papers needs filling in]
- Machens, C.K., R. Romo, and C.D. Brody. 2005. Flexible control of mutual inhibition: a neural model of two-interval discrimination. Science 307: 1121–1124.
- Hopfield, J.J., and C.D. Brody. 2004. Learning rules and network repair in spike-timing-based computation networks. Proc. Natl. Acad. Sci. USA 101: 337–342.
- Brody, C.D., and J.J. Hopfield. 2003. Simple networks for spike-timing-based computation, with application to olfactory processing. Neuron 37: 843–852.
- Hopfield, J.J., and C.D. Brody. 2001. What is a moment? Transient synchrony as a collective mechanism for spatiotemporal integration. Proc. Natl. Acad. Sci. USA 98: 1282–1287.