About

David Gire is a professor associated with the field of psychology, with a focus on neurobiology and sensory processing. His research centers on understanding how brains utilize noisy, fluctuating sensory signals from the environment to guide behaviors such as finding food and avoiding danger. He investigates the precise coding of relevant information in spatial and temporal patterns of neural activity, which is essential for adaptive behavior. His work involves exploring complex circuits of synaptic interactions between populations of neurons, particularly during active sensing and exploration of the environment. Gire employs a variety of techniques including electrophysiology, multiphoton imaging, optogenetics, and automated behavioral analysis to connect neural activity to behavior. His research aims to define the neural circuit operations that support complex and flexible behavioral responses to natural sensory stimuli. His contributions advance the mechanistic understanding of neural coding during active sensing, which has implications for developing targeted therapeutics for psychiatric and neurodegenerative disorders.

Research topics

• Artificial Intelligence
• Computer Science
• Psychology
• Neuroscience
• Cognitive psychology
• Transport engineering
• Engineering
• Cognitive science
• Biology
• Computer vision
• Chemistry
• Epistemology

Selected publications

• Octopus track chemosensory plumes to find food

  PLoS ONE · 2025-10-08 · 1 citations

  articleOpen accessSenior authorCorresponding

  Chemosensory plume-guided navigation, tracking a chemical plume to its source, is a primordial behavior used by many animals to search beyond the visual range. Here we report the first laboratory observations of octopuses performing this behavior, demonstrating that they can use chemosensory plumes to find food. In a three-station discrimination task carried out in the dark, octopus showed a strong preference to move upstream towards the food-baited target, supporting the hypothesis that they are performing chemosensory plume-guided search. When seeking a single baited target, also in the dark, octopuses not only preferred to move upstream towards the food source, but they also displayed characteristic motions associated with odor-gated rheotaxis, a commonly used chemosensory tracking strategy used by many animals, which includes pausing, switchbacks, and across-stream redirections to the bait. Additionally, when approaching single baited stations the octopus often made fast reactive lunging motions. The observation of these fast arm-aligned motions (FAAM), taken together with the observation that the octopus did not have a characteristic body axis orientation to the bait, as would be expected if bilaterally symmetric organs such as the olfactory organs guided this behavior, supports the hypothesis that the suckers are the primary chemosensory organs driving octopus chemosense-guided behaviors.

  PublisherDOI

• Octopus can use odor plumes to find food

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-06

  preprintOpen accessSenior author

  Abstract Odor-plume-guided navigation, tracking an odor plume to its source, is a primordial behavior used by most animals to search beyond the visual range. Here we report the first laboratory observations of octopuses performing this behavior, demonstrating that they can use odor plumes to find food. In a three-station discrimination task carried out in the dark, octopus showed a strong preference to move upstream towards the food-baited target, supporting the hypothesis that they are performing odor-guided search. When seeking a single baited target, also in the dark, octopuses not only preferred to move upstream towards the food source, but they also displayed characteristic motions associated with odor-gated rheotaxis, a commonly used odor tracking strategy used by many animals, which includes pausing, switchbacks, and across-stream redirections to the bait. Additionally, when approaching single baited stations the octopus often made reactive fast lunging motions. The observation of these fast arm-aligned motions (FAAM), taken together with the observation that the octopus did not have a characteristic body axis orientation to the bait, as would be expected if bilaterally symmetric organs such as the olfactory pits guided this behavior, supports the hypothesis that the suckers are the primary chemosensory organs driving octopus odor-guided behaviors.

  PublisherOA PDFDOI

• The spiking output of the mouse olfactory bulb encodes large-scale temporal features of natural odor environments

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-05 · 6 citations

  preprintOpen accessSenior authorCorresponding

  In natural odor environments, odor travels in plumes. Odor concentration dynamics change in characteristic ways across the width and length of a plume. Thus, spatiotemporal dynamics of plumes have informative features for animals navigating to an odor source. Population activity in the olfactory bulb (OB) has been shown to follow odor concentration across plumes to a moderate degree (Lewis et al., 2021). However, it is unknown whether the ability to follow plume dynamics is driven by individual cells or whether it emerges at the population level. Previous research has explored the responses of individual OB cells to isolated features of plumes, but it is difficult to adequately sample the full feature space of plumes as it is still undetermined which features navigating mice employ during olfactory guided search. Here we released odor from an upwind odor source and simultaneously recorded both odor concentration dynamics and cellular response dynamics in awake, head-fixed mice. We found that longer timescale features of odor concentration dynamics were encoded at both the cellular and population level. At the cellular level, responses were elicited at the beginning of the plume for each trial, signaling plume onset. Plumes with high odor concentration elicited responses at the end of the plume, signaling plume offset. Although cellular level tracking of plume dynamics was observed to be weak, we found that at the population level, OB activity distinguished whiffs and blanks (accurately detected odor presence versus absence) throughout the duration of a plume. Even ~20 OB cells were enough to accurately discern odor presence throughout a plume. Our findings indicate that the full range of odor concentration dynamics and high frequency fluctuations are not encoded by OB spiking activity. Instead, relatively lower-frequency temporal features of plumes, such as plume onset, plume offset, whiffs, and blanks, are represented in the OB.

  PublisherOA PDFDOI

• Dynamics of odor-source localization: Insights from real-time odor plume recordings and head-motion tracking in freely moving mice

  PLoS ONE · 2024-09-26 · 6 citations

  articleOpen accessSenior author

  Animals navigating turbulent odor plumes exhibit a rich variety of behaviors, and employ efficient strategies to locate odor sources. A growing body of literature has started to probe this complex task of localizing airborne odor sources in walking mammals to further our understanding of neural encoding and decoding of naturalistic sensory stimuli. However, correlating the intermittent olfactory information with behavior has remained a long-standing challenge due to the stochastic nature of the odor stimulus. We recently reported a method to record real-time olfactory information available to freely moving mice during odor-guided navigation, hence overcoming that challenge. Here we combine our odor-recording method with head-motion tracking to establish correlations between plume encounters and head movements. We show that mice exhibit robust head-pitch motions in the 5-14Hz range during an odor-guided navigation task, and that these head motions are modulated by plume encounters. Furthermore, mice reduce their angles with respect to the source upon plume contact. Head motions may thus be an important part of the sensorimotor behavioral repertoire during naturalistic odor-source localization.

  PublisherDOI

• Mechanisms of octopus arm search behavior without visual feedback

  Bioinspiration & Biomimetics · 2023-10-04 · 8 citations

  articleOpen accessSenior author

  The octopus coordinates multiple, highly flexible arms with the support of a complex distributed nervous system. The octopus's suckers, staggered along each arm, are employed in a wide range of behaviors. Many of these behaviors, such as foraging in visually occluded spaces, are executed under conditions of limited or absent visual feedback. In coordinating unseen limbs with seemingly infinite degrees of freedom across a variety of adaptive behaviors, the octopus appears to have solved a significant control problem facing the field of soft-bodied robotics. To study the strategies that the octopus uses to find and capture prey within unseen spaces, we designed and 3D printed visually occluded foraging tasks and tracked arm motion as the octopus attempted to find and retrieve a food reward. By varying the location of the food reward within these tasks, we can characterize how the arms and suckers adapt to their environment to find and capture prey. We compared these results to simulated experimental conditions performed by a model octopus arm to isolate the primary mechanisms driving our experimental observations. We found that the octopus relies on a contact-based search strategy that emerges from local sucker coordination to simplify the control of its soft, highly flexible limbs.

  PublisherOA PDFDOI

• Mechanisms of octopus arm search behavior without visual feedback

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-03-14 · 2 citations

  preprintOpen accessSenior author

  Abstract The octopus coordinates multiple, highly flexible arms with the support of a complex distributed nervous system. The octopus’s suckers, staggered along each arm, are employed in a wide range of behaviors. Many of these behaviors, such as foraging in visually occluded spaces, are executed under conditions of limited or absent visual feedback. In coordinating unseen limbs with seemingly infinite degrees of freedom across a variety of adaptive behaviors, the octopus appears to have solved a significant control problem facing the field of soft-bodied robotics. To study the strategies that the octopus uses to find and capture prey within unseen spaces, we designed and 3D printed visually occluded foraging tasks and tracked arm motion as the octopus attempted to find and retrieve a food reward. By varying the location of the food reward within these tasks, we can characterize how the arms and suckers adapt to their environment to find and capture prey. We compared these results to simulated experimental conditions performed by a model octopus arm to isolate the primary mechanisms driving our experimental observations. We found that the octopus relies on a contact-based search strategy that emerges from local sucker coordination to simplify the control of its soft, highly flexible limbs.

  PublisherOA PDFDOI

• Octopus arm search strategies over complex surfaces

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-08-01 · 1 citations

  preprintOpen accessSenior author

  Abstract Despite the extreme flexibility of the octopus’s arms and their resulting near infinite possible configurations, the octopus effectively controls its arms during a wide variety of behaviors, including locomotion, foraging, excavation, exploration, and manipulation. If appropriately characterized, the octopus’s biomechanical properties and control strategies could be implemented in the development of a soft robotic limb with the same range of capabilities. When operating without visual feedback, the octopus must rely on the complex chemotactile sensory system within its suckers, and in these conditions sucker recruitment plays a prominent role in search behavior, causing the arm to conform to surface features in the environment. However, how this mechanism is used to search over the complex and convoluted surfaces in the octopus’s natural habitat is unknown. Here, we investigate the strategies the octopus uses to search for a reward hidden among a row of multiple small openings of a task space, and how it uses multiple arms to search three parallel versions of this task space. We found that when the arm encounters multiple openings in a surface, it performs a distal to proximal search pattern, starting with the farthest openings within reach then working its way proximally with a preference for searching each opening in succession. This strategy would allow the octopus to use its highly flexible limbs to perform an exhaustive search pattern over complex surfaces.

  PublisherOA PDFDOI

• Dynamics of odor-source localization: Insights from real-time odor plume recordings and head-motion tracking in freely moving mice

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-11-13 · 4 citations

  preprintOpen accessSenior author

  Animals navigating turbulent odor plumes exhibit a rich variety of behaviors, and employ efficient strategies to locate odor sources. A growing body of literature has started to probe this complex task of localizing airborne odor sources in walking mammals to further our understanding of neural encoding and decoding of naturalistic sensory stimuli. However, correlating the intermittent olfactory information with behavior has remained a long-standing challenge due to the stochastic nature of the odor stimulus. We recently reported a method to record real-time olfactory information available to freely moving mice during odor-guided navigation, hence overcoming that challenge. Here we combine our odor-recording method with head-motion tracking to establish correlations between plume encounters and head movements. We show that mice exhibit robust head-pitch motions in the 5-14Hz range during an odor-guided navigation task, and that these head motions are modulated by plume encounters. Furthermore, mice reduce their angles with respect to the source upon plume contact. Head motions may thus be an important part of the sensorimotor behavioral repertoire during naturalistic odor-source localization.

  PublisherOA PDFDOI

• Lessons for Robotics From the Control Architecture of the Octopus

  Frontiers in Robotics and AI · 2022-07-18 · 16 citations

  articleOpen accessSenior authorCorresponding

  Biological and artificial agents are faced with many of the same computational and mechanical problems, thus strategies evolved in the biological realm can serve as inspiration for robotic development. The octopus in particular represents an attractive model for biologically-inspired robotic design, as has been recognized for the emerging field of soft robotics. Conventional global planning-based approaches to controlling the large number of degrees of freedom in an octopus arm would be computationally intractable. Instead, the octopus appears to exploit a distributed control architecture that enables effective and computationally efficient arm control. Here we will describe the neuroanatomical organization of the octopus peripheral nervous system and discuss how this distributed neural network is specialized for effectively mediating decisions made by the central brain and the continuous actuation of limbs possessing an extremely large number of degrees of freedom. We propose top-down and bottom-up control strategies that we hypothesize the octopus employs in the control of its soft body. We suggest that these strategies can serve as useful elements in the design and development of soft-bodied robotics.

  PublisherOA PDFDOI

• Natural behavior is the language of the brain

  Current Biology · 2022 · 176 citations

  • Computer Science
  • Artificial Intelligence
  • Cognitive science
  PublisherOA PDFDOI

Recent grants

• Evidence accumulation across large-scale cortical networks during odor tracking by freely moving mice

  NIH · $410k · 2020–2023

• NIH Grant F31DC009118

  NIH · $39k · 2010

• Neural circuit mechanisms of odor localization in mice

  NIH · $230k · 2013–2015

• Neural circuit mechanisms of odor localization in mice

  NIH · $796k · 2013–2019

• NIH Grant F32DC011980

  NIH · $48k · 2012

Frequent coauthors

• Dominic M. Sivitilli

  University of Washington

  18 shared

• Nicola Rigolli

  Laboratoire de Physique de l'ENS

  9 shared

• Nathan E. Schoppa

  University of Colorado Anschutz Medical Campus

  7 shared

• Agnese Seminara

  University of Genoa

  7 shared

• Diego Restrepo

  University of Colorado Anschutz Medical Campus

  7 shared

• Anan Li

  Jiangxi Provincial People's Hospital

  7 shared

• Willem Weertman

  Alaska Pacific University

  6 shared

• Mohammad F. Tariq

  University of Washington

  6 shared

Education

• Ph.D., Astrobiology

  University of Washington

  2009

• M.S., Astronomy

  University of Washington

  2004

• B.S., Astronomy

  University of California, Santa Barbara

  2002