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1. Fast animal pose estimation using deep neural networks

Author(s):
Pereira, Talmo D.; Aldarondo, Diego E.; Willmore, Lindsay; Kislin, Mikhail; Wang, Samuel S.-H.; Murthy, Mala; Shaevitz, Joshua W.
Abstract:
Recent work quantifying postural dynamics has attempted to define the repertoire of behaviors performed by an animal. However, a major drawback to these techniques has been their reliance on dimensionality reduction of images which destroys information about which parts of the body are used in each behavior. To address this issue, we introduce a deep learning-based method for pose estimation, LEAP (LEAP Estimates Animal Pose). LEAP automatically predicts the positions of animal body parts using a deep convolutional neural network with as little as 10 frames of labeled data for training. This framework consists of a graphical interface for interactive labeling of body parts and software for training the network and fast prediction on new data (1 hr to train, 185 Hz predictions). We validate LEAP using videos of freely behaving fruit flies (Drosophila melanogaster) and track 32 distinct points on the body to fully describe the pose of the head, body, wings, and legs with an error rate of <3% of the animal's body length. We recapitulate a number of reported findings on insect gait dynamics and show LEAP's applicability as the first step in unsupervised behavioral classification. Finally, we extend the method to more challenging imaging situations (pairs of flies moving on a mesh-like background) and movies from freely moving mice (Mus musculus) where we track the full conformation of the head, body, and limbs.
Type:
Dataset
Issue Date:
30 May 2018

2. March Mathness: Effects of basketball on the brain

Author(s):
Antony, James; McDougle, Sam
Abstract:
Surprise signals a discrepancy between past and current beliefs. It is theorized to be linked to affective experiences, the creation of particularly resilient memories, and segmentation of the flow of experience into discrete perceived events. However, the ability to precisely measure naturalistic surprise has remained elusive. We used advanced basketball analytics to derive a quantitative measure of surprise and characterized its behavioral, physiological, and neural correlates in human subjects observing basketball games. We found that surprise was associated with segmentation of ongoing experiences, as reflected by subjectively perceived event boundaries and shifts in neocortical patterns underlying belief states. Interestingly, these effects differed by whether surprising moments contradicted or bolstered current predominant beliefs. Surprise also positively correlated with pupil dilation, activation in subcortical regions associated with dopamine, game enjoyment, and long-term memory. These investigations support key predictions from event segmentation theory and extend theoretical conceptualizations of surprise to real-world contexts.
Type:
Dataset
Issue Date:
2020

3. Competitive learning modulates memory consolidation during sleep

Author(s):
Antony, James W.; Cheng, Larry Y.; Brooks, Paula P.; Paller, Ken A.; Norman, Kenneth A.
Abstract:
Competition between memories can cause weakening of those memories. Here we investigated memory competition during sleep in human participants by presenting auditory cues that had been linked to two distinct picture-location pairs during wake. We manipulated competition during learning by requiring participants to rehearse picture-location pairs associated with the same sound either competitively (choosing to rehearse one over the other, leading to greater competition) or separately; we hypothesized that greater competition during learning would lead to greater competition when memories were cued during sleep. With separate-pair learning, we found that cueing benefited spatial retention. With competitive-pair learning, no benefit of cueing was observed on retention, but cueing impaired retention of well-learned pairs (where we expected strong competition). During sleep, post-cue beta power (16–30 Hz) indexed competition and predicted forgetting, whereas sigma power (11–16 Hz) predicted subsequent retention. Taken together, these findings show that competition between memories during learning can modulate how they are consolidated during sleep.
Type:
Dataset
Issue Date:
November 2018

4. Sleep spindle refractoriness segregates periods of memory reactivation

Author(s):
Antony, James W.; Piloto, Luis; Wang, Margaret; Brooks, Paula P.; Norman, Kenneth A.; Paller, Ken A.
Abstract:
The stability of long-term memories is enhanced by reactivation during sleep. Correlative evidence has linked memory reactivation with thalamocortical sleep spindles, although their functional role is not fully understood. Our initial study replicated this correlation and also demonstrated a novel rhythmicity to spindles, such that a spindle is more likely to occur approximately 3–6 s following a prior spindle. We leveraged this rhythmicity to test the role of spindles in memory by using real-time spindle tracking to present cues within versus just after the presumptive refractory period; as predicted, cues presented just after the refractory period led to better memory. Our findings demonstrate a precise temporal link between sleep spindles and memory reactivation. Moreover, they reveal a previously undescribed neural mechanism whereby spindles may segment sleep into two distinct substates: prime opportunities for reactivation and gaps that segregate reactivation events.
Type:
Dataset
Issue Date:
4 June 2018

5. Accessing Real-Life Episodic Information from Minutes versus Hours Earlier Modulates Hippocampal and High-Order Cortical Dynamics

Author(s):
Chen, Janice; Honey, Christopher; Simony, Erez; Arcaro, Michael; Norman, Kenneth; Hasson, Uri
Abstract:
It is well known that formation of new episodic memories depends on hippocampus, but in real-life settings (e.g., conversation), hippocampal amnesics can utilize information from several minutes earlier. What neural systems outside hippocampus might support this minutes-long retention? In this study, subjects viewed an audiovisual movie continuously for 25 min; another group viewed the movie in 2 parts separated by a 1-day delay. Understanding Part 2 depended on retrieving information from Part 1, and thus hippocampus was required in the day-delay condition. But is hippocampus equally recruited to access the same information from minutes earlier? We show that accessing memories from a few minutes prior elicited less interaction between hippocampus and default mode network (DMN) cortical regions than accessing day-old memories of identical events, suggesting that recent information was available with less reliance on hippocampal retrieval. Moreover, the 2 groups evinced reliable but distinct DMN activity timecourses, reflecting differences in information carried in these regions when Part 1 was recent versus distant. The timecourses converged after 4 min, suggesting a time frame over which the continuous-viewing group may have relied less on hippocampal retrieval. We propose that cortical default mode regions can intrinsically retain real-life episodic information for several minutes.
Type:
Dataset
Issue Date:
3 August 2015

7. Noise correlations in the human brain and their impact on pattern classification

Author(s):
Bejjanki, Vikranth R.; da Silveira, Rava Azeredo; Cohen, Jonathan D.; Turk-Browne, Nicholas B.
Abstract:
Multivariate decoding methods, such as multivoxel pattern analysis (MVPA), are highly effective at extracting information from brain imaging data. Yet, the precise nature of the information that MVPA draws upon remains controversial. Most current theories emphasize the enhanced sensitivity imparted by aggregating across voxels that have mixed and weak selectivity. However, beyond the selectivity of individual voxels, neural variability is correlated across voxels, and such noise correlations may contribute importantly to accurate decoding. Indeed, a recent computational theory proposed that noise correlations enhance multivariate decoding from heterogeneous neural populations. Here we extend this theory from the scale of neurons to functional magnetic resonance imaging (fMRI) and show that noise correlations between heterogeneous populations of voxels (i.e., voxels selective for different stimulus variables) contribute to the success of MVPA. Specifically, decoding performance is enhanced when voxels with high vs. low noise correlations (measured during rest or in the background of the task) are selected during classifier training. Conversely, voxels that are strongly selective for one class in a GLM or that receive high classification weights in MVPA tend to exhibit high noise correlations with voxels selective for the other class being discriminated against. Furthermore, we use simulations to show that this is a general property of fMRI data and that selectivity and noise correlations can have distinguishable influences on decoding. Taken together, our findings demonstrate that if there is signal in the data, the resulting above-chance classification accuracy is modulated by the magnitude of noise correlations.
Type:
Dataset
Issue Date:
August 2017

9. Spike Trains of Retinal Ganglion Cells Viewing a Repeated Natural Movie

Author(s):
Berry II, Michael J.
Abstract:
This archive contains spike trains simultaneously recorded from ganglion cells in the tiger salamander retina with a multi-electrode array while viewing a repeated natural movie clip. These data have been analyzed in previous papers, notably Puchalla et al. Neuron 2005 and Schneidman et al. Nature 2006.
Type:
Dataset
Issue Date:
8 March 2022

10. The Structured `Low Temperature' Phase of the Retinal Population Code

Author(s):
Ioffe, Mark Lev; Berry II, Michael J.
Abstract:
Recent advances in experimental techniques have allowed the simultaneous recordings of populations of hundreds of neurons, fostering a debate about the nature of the collective structure of population neural activity. Much of this debate has focused on the empirical findings of a phase transition in the parameter space of maximum entropy models describing the measured neural probability distributions, interpreting this phase transition to indicate a critical tuning of the neural code. Here, we instead focus on the possibility that this is a first-order phase transition which provides evidence that the real neural population is in a `structured', collective state. We show that this collective state is robust to changes in stimulus ensemble and adaptive state. We find that the pattern of pairwise correlations between neurons has a strength that is well within the strongly correlated regime and does not require fine tuning, suggesting that this state is generic for populations of 100+ neurons. We find a clear correspondence between the emergence of a phase transition, and the emergence of attractor-like structure in the inferred energy landscape. A collective state in the neural population, in which neural activity patterns naturally form clusters, provides a consistent interpretation for our results.
Type:
Dataset
Issue Date:
2017

13. Attention and awareness in the dorsal attention network

Author(s):
Wilterson, Andrew; Nastase, Samuel; Bio, Branden; Guterstam, Arvid; Graziano, Michael
Abstract:
The attention schema theory (AST) posits a specific relationship between subjective awareness and attention, in which awareness is the control model that the brain uses to aid in the endogenous control of attention. We proposed that the right temporoparietal junction (TPJ) is involved in that interaction between awareness and attention. In previous experiments, we developed a behavioral paradigm in human subjects to manipulate awareness and attention. The paradigm involved a visual cue that could be used to guide a shift of attention to a target stimulus. In task 1, subjects were aware of the visual cue, and their endogenous control mechanism was able to use the cue to help control attention. In task 2, subjects were unaware of the visual cue, and their endogenous control mechanism was no longer able to use it to control attention, even though the cue still had a measurable effect on other aspects of behavior. Here we tested the two tasks while scanning brain activity in human volunteers. We predicted that the right TPJ would be active in relation to the cue in task 1, but not in task 2. This prediction was confirmed. The right TPJ was active in relation to the cue in task 1; it was not measurably active in task 2; the difference was significant. In our interpretation, the right TPJ is involved in a complex interaction in which awareness aids in the control of attention.
Type:
Dataset
Issue Date:
2020

14. Integrative Mechanisms of Social Attention

Author(s):
Bio, Branden; Graziano, Michael
Abstract:
Monitoring the attention of others is fundamental to social cognition. Most of the literature on the topic assumes that our social cognitive machinery is tuned specifically to the gaze direction of others as a proxy for attention. This standard assumption reduces attention to an externally visible parameter. Here we show that this assumption is wrong and a deeper, more meaningful representation is involved. We presented subjects with two cues about the attentional state of a face: direction of gaze and emotional expression. We tested whether people relied predominantly on one cue, the other, or both. If the traditional view is correct, then the gaze cue should dominate. Instead, people employed a variety of strategies, some relying on gaze, some on expression, and some on an integration of cues. We also assessed people’s social cognitive ability using two, independent, standard tests. If the traditional view is correct, then social cognitive ability, as assessed by the independent tests, should correlate with the degree to which people successfully use the gaze cue to judge the attention state of the face. Instead, social cognitive ability correlated best with the degree to which people successfully integrated the cues together, instead of with the use of any one specific cue. The results suggest a rethink of a fundamental component of social cognition: monitoring the attention of others involves constructing a deep model that is informed by a combination of cues. Attention is a rich process and monitoring the attention of others involves a similarly rich representation.
Type:
Dataset
Issue Date:
22 July 2021

16. Reductions in Retrieval Competition Predict the Benefit of Repeated Testing

Author(s):
Rafidi, Nicole S; Hulbert, Justin C; Brooks, Paula P; Norman, Kenneth A
Abstract:
Repeated testing (as opposed to repeated study) leads to improved long-term memory retention, but the mechanism underlying this improvement remains controversial. In this work, we test the hypothesis that retrieval practice benefits subsequent recall by reducing competition from related memories. This hypothesis implies that the degree of reduction in competition between retrieval practice attempts should predict subsequent memory for the practiced items. To test this prediction, we collected electroencephalography (EEG) data across two sessions. In the first session, participants practiced selectively retrieving exemplars from superordinate semantic categories (high competition), as well as retrieving the names of the superordinate categories from exemplars (low competition). In the second session, participants repeatedly studied and were then tested on Swahili-English vocabulary. One week after session two, participants were again tested on the vocabulary. We trained a within-subject classifier on the data from session one to distinguish high and low competition states. We then used this classifier to measure competition across multiple retrieval practice attempts in the second session. The degree to which competition decreased for a given vocabulary word predicted whether that item was subsequently remembered in the third session. These results are consistent with the hypothesis that repeated testing improves retention by reducing competition.
Type:
Dataset
Issue Date:
April 2018

18. Attentional Modulation of Brain Responses to Primary Appetitive and Aversive Stimuli

Author(s):
Cara L. Buck; Jonathan D. Cohen; Field, Brent; Daniel Kahneman; Samuel M. McClure; Leigh E. Nystrom
Abstract:
Studies of subjective well-being have conventionally relied upon self-report, which directs subjects’ attention to their emotional experiences. This method presumes that attention itself does not influence emotional processes, which could bias sampling. We tested whether attention influences experienced utility (the moment-by-moment experience of pleasure) by using functional magnetic resonance imaging (fMRI) to measure the activity of brain systems thought to represent hedonic value while manipulating attentional load. Subjects received appetitive or aversive solutions orally while alternatively executing a low or high attentional load task. Brain regions associated with hedonic processing, including the ventral striatum, showed a response to both juice and quinine. This response decreased during the high-load task relative to the low-load task. Thus, attentional allocation may influence experienced utility by modulating (either directly or indirectly) the activity of brain mechanisms thought to represent hedonic value.
Type:
Dataset, Software, and text
Issue Date:
11 February 2015

19. The 21st year: transcription, motif list, and relation score

Author(s):
Chang, Claire H. C.; Lazaridi, Christina; Yeshurun, Yaara; Norman, Kenneth A.; Hasson, Uri
Abstract:
This study examined how the brain dynamically updates event representations by integrating new information over multiple minutes while segregating irrelevant input. A professional writer custom-designed a narrative with two independent storylines, interleaving across minute-long segments (ABAB). In the last (C) part, characters from the two storylines meet and their shared history is revealed. Part C is designed to induce the spontaneous recall of past events, upon the recurrence of narrative motifs from A/B, and to shed new light on them. Our fMRI results showed storyline-specific neural patterns, which were reinstated (i.e. became more active) during storyline transitions. This effect increased along the processing timescale hierarchy, peaking in the default mode network. Similarly, the neural reinstatement of motifs was found during part C. Furthermore, participants showing stronger motif reinstatement performed better in integrating A/B and C events, demonstrating the role of memory reactivation in information integration over intervening irrelevant events.
Type:
Dataset and text
Issue Date:
2021

20. Dynamic reconfiguration of the default mode network during narrative comprehension

Author(s):
Simony, Erez; Honey, Christopher; Chen, Janice; Lositsky, Olga; Yeshurun, Yaara; Wiesel, Ami; Hasson, Uri
Abstract:
Does the default mode network (DMN) reconfigure to encode information about the changing environment? This question has proven difficult, because patterns of functional connectivity reflect a mixture of stimulus-induced neural processes, intrinsic neural processes and non-neuronal noise. Here we introduce inter-subject functional correlation (ISFC), which isolates stimulus-dependent inter-regional correlations between brains exposed to the same stimulus. During fMRI, we had subjects listen to a real-life auditory narrative and to temporally scrambled versions of the narrative. We used ISFC to isolate correlation patterns within the DMN that were locked to the processing of each narrative segment and specific to its meaning within the narrative context. The momentary configurations of DMN ISFC were highly replicable across groups. Moreover, DMN coupling strength predicted memory of narrative segments. Thus, ISFC opens new avenues for linking brain network dynamics to stimulus features and behaviour.
Type:
Dataset
Issue Date:
18 July 2016

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