Code, Data, Databases

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adversarial attacks

Casper et al. Robust feature-level adversaries are interpretability tools. NeurIPS 2022. PDF

This work introduces targeted, disguised, physically realizable, black-box, and universal adversarial attacks. The methodology shows that adversarial attacks can help better understand reprsentations in machine learning and also illustrates how adversarial attacks have been discovered by biology in natural settings.

face neurons

Bardon et al. Face neurons encode non-semantic features. PNAS 2022. PDF

There has been extensive discussion about neurons that respond more strongly to faces than to other objects like houses or chairs. Here we show that so-called face neurons respond to complex visual features that are present in faces but also in many other faces and do not encode semantic information about faces.

return fixations

Zhang et al. Human or Machine? Turing Tests for Vision and Language. arXiv 2022. PDF

As AI algorithms become increasingly better at multiple tasks, there are many real-world problems where it is imperative to understand whether an agent is human or not. Here we perform extensive Turing tests for vision and language tasks and characterize the state-of-the-art in how well machines can imitate humans.

how to get a match

Sanchez Lopezet al. How to make a match: Neural representation of memories in the human brain during a memory card game. Submitted. PDF coming soon

Here we investigate the mechanisms of memory formation during a realistic game that involves matching images. Invasive neurophysiological recordings from the human brain reveal the spatiotemporal dynamics underlying the processes of encoding, retrieval and matching.          

return fixations

Zhang et al. Look Twice: A Generalist Computational Model Predicts Return Fixations across Tasks and Species.. PLoS Computational Biology 2022. PDF

We move our eyes several times a second, bringing the center of gaze into focus and high resolution. While we typically assume that we can rapidly recognize the contents at each fixation, recent observations cast a doubt on this assumption. Instead, we show that monkeys and humans frequently return to previously visited locations. Zhang and colleagues provide a computational model that can capture these eye movements and return fixations across a wide variety of tasks and conditions.


Dellaferrera et al. Error-driven input modulation: Solving the credit assignment problem without a backward pass. ICML 2022. PDF

Supervised learning in artificial neural networks typically relies on backpropagation (BP). Here we replace the backward pass with a second forward pass in which the input signal is modulated by the network error. This novel learning rule addresses key concerns about the plausibility of BP and can be applied to both fully connected and convolutional models. These results help incorporate biological principles into machine learning.

human cognitive boundaries

Zheng et al. Neurons detect cognitive boundaries to structure episodic memories in humans. Nature Neuroscience 2022. PDF

While experience is continuous, memories are organized as discrete events. Cognitive boundaries are thought to segment experience and structure memory, but how this process is implemented remains unclear. Here we show that neurons responded to abstract cognitive boundaries between different episodes.

cognitive control

Xiao et al. Cross-Task Specificity and Within-Task Invariance of Cognitive Control Processes. Cell Reports 2022. PDF

Everyday decisions require integrating sensory cues and task demands while resolving conflict in goals and cues (e.g., “should I go for a run or stay home and watch a movie?”). Theories of cognitive control posit universal mechanisms of conflict resolution. The results of the current study challenge this dogma by demonstrating that the neural circuits involved in cognitive control are specific to the combination of inputs and outputs in each task.

human functional interactome

Wang et al. Mesoscopic functional interactions in the human brain reveal small-world properties. Cell Reports 2021. PDF

Cognition relies on rapid and robust communication between brain areas. Wang et al. leverage multi-day intracranial field potential recordings to characterize the human mesoscopic functional interactome. The methods are validated using monkey anatomical and physiological data. The human interactome reveals small-world properties and is modulated by sleep versus awake state.

asymmetry in visual search

Gupta et al. Visual Search Asymmetry: Deep Nets and Humans Share Similar Inherent Biases. NeurIPS 2021. PDF

Despite major progress in development of artificial vision systems, humans still outperform computers in most complex visual tasks. To gain better understanding of the similarities and differences between biological and computer vision, here we examined the enigmatic asymmetries in visual search. Sometimes, humans find it much easier to find a certain object A among distractors B than the reverse. Here Gupta et al. demonstrate that an eccentricity-dependent model of visual search can capture these forms of asymmetries and that these asymmetries are dependent on the diet of visual inputs that the networks see during training.

when pigs fly ICCV 2021

Bomatter et al. When Pigs Fly: Contextual Reasoning in Synthetic and Natural Scenes. International Conference on Computer Vision (ICCV) 2021. PDF

Scene understanding requires the integration of contextual cues. In this study, Bomatter et al. study contextual reasoning in humans and machines by creating a novel dataset consisting of synthetic images based on state-of-the-art computer graphics. In this new dataset, they use violations on contextual common sense rules to investigate the impact on visual recognition. Furthermore, the authors propose a new neural network architecture that provides an approximation to human behavior in rapid contextual reasoning tasks.

hamn hypothesis based augmented memory network

Zhang et al. Hypothesis-driven stream learning with augmented memory. arXiv 2104.02206. PDF

This study proposes a new algorithm to avoid catastrophic forgetting in stream learning settings. The model efficiently consolidates previous knowledge with a limited number of hypotheses in an augmented memory and replays relevant hypotheses. The algorithm performs comparably well or better than state-of-the-art methods, while moffering more efficient memory usage.

hopfield networks

Shaham et al. Stochastic consolidation of lifelong memory. bioRxiv 2021. PDF

This study introduces a model for continual leanring based in an attractor-based recurrent neural network that combines Hebbian plasticity, forgettting via synaptic decay, and a replay-based consolidation mechanism.

the role of context in visual recognition

Zhang et al. Putting visual recognition in context. CVPR 2020. PDF

This study systematically investigates where, when, and how contextual information modulates visual object recognition. The work introduces a computational model (CATNet, context-aware two-stream network) that approximates human visual behavior in the incorporation of contextual cues for visual recognition.

Controlled datasets for action recognition

Jacquot et al. Can deep learning recognize subtle human activities?CVPR 2020. PDF

Success in many computer vision efforts capitalizes on confounding factors and biases introduced by poorly controlled datasets. Here we introduce a procedure to create more controlled datasets, and we exemplify the process by creating a challenging dataset to study recognition of everyday actions.

Xiao Kreiman XDream

Xiao et al. Finding Preferred Stimuli for Visual Neurons Using Generative Networks and Gradient-Free Optimization. PLoS Computational Biology 2020. PDF

This study introduces the XDream algorithm to find preferred stimuli for neurons in an unbiased manner. The study shows the robustness of XDream to different architectures, generators, developmental regimes, and noise.

Xiao Kreiman XDream

Vinken et al. Incorporating intrinsic suppression in deep neural networks captures dynamics of adaptation in neurophysiology and perception. Science Advances 2020 PDF

This study introduces a computational model of adaptation in visual cortex. The model relies exclusively on activity-dependent neuronally-intrinsic mechanisms. The deep convolutional neural network architecture can explain a plethora of observations both at the perceptual levels and neurophysiological levels.

violn example

Ben-Yosef et al. Minimal videos: Trade-off between spatial and temporal information in human and machine vision. Cognition 2020. PDF

This study investigates the role of spatiotemporal integration in visual recognition. We introduce "minimal videos", which can be readily recognized by humans but become unrecognizable by a small reduction in the amount of either spatial or temporal information. The stimuli and behavioral results presented here challenge state-of-the-art computer vision models of action recognition.

Zhang et al. What Am I Searching For? EPIC Workshop, CVPR 2020. PDF

Can we infer intentions and goals from a person's actions? As an example of this family of problems, we consider here whether it is possible to decipher what a person is searching for by decoding their eye movement behavior and predicting their behavior using a computational model.

Ponce et al. Evolving Images for Visual Neurons Using a Deep Generative Network Reveals Coding Principles and Neuronal Preferences. Cell 2019. PDF

This study introducs a new algorithm to discover neural tuning properties in visual cortex. The method combines a deep generative network and a genetic algorithm to search for images that elicit high firing rates in real-time in an unbiased manner. The results of applying this algorithm to macaque V1 and IT neurons challenge existing dogmas about how neurons in ventral visual cortex represent information.

Lift the flap Context Reasoning

Zhang et al. Lift-the-flap: what, where and when for context reasoning. arXiv 1902.00163. PDF

This study shows that it is possible to infer the identity of an object purely from contextual cues, without any information about the object itself. The study proposes a computational model of contextual reasoning inference.

Madhavan et al. Neural Interactions Underlying Visuomotor Associations in the Human Brain. Cerebral Cortex, 2019. PDF

This study uncovers plausible neural mechanisms instantiating reinforcement learning rules to associate visual and motor actions by trial-and-error learning via interactions between frontal regions and visual cortex as well as between frontal cortex and motor cortex.

Kreiman. What do neurons really want? The role of semantics in cortical representations Psychology of Learning and Motivation 2019. PDF

This chapter discusses how the field has investigated the neural code for visual features along ventral cortex, how computational models should be used to define neuronal turning preferences and how to think about the role of semantics in the representation of visual information.

Tang et al. Recurrent computations for visual pattern completion. PNAS 2018. PDF

How can we make inferences from partial information? This study combines behavioral, neurophysiological and computational tools to show that recurrent computations can help perform visual pattern completion.

Misra et al. Minimal memory for details in real life events. Scientific Reports 2018. PDF

This study scrutinizes one hour of real life events and shows that humans tend to forget the vast majority of the details. Only a small fraction of events is crystallized in the form of episodic memories.

Zhang et al. Finding any Waldo: zero-shot invariant and efficient visual search. Nature Communications 2018. PDF

This study demonstrates that humans can perform invariant and efficient visual search and introduces a biologically inspired computational model capable of performing zero-shot invariant visual search in complex natural scenes.

Wu et al, Learning scene gist with convolutional neural networks to improve object recognition. IEEE CISS 2018

A deep convolutional architecture with two sub-networks, a fovea and a periphery, to integrate spatial contextual information for visual recognition.

Isik et al Neuroimage 2017 Isik et al. What is changing when: Decoding visual information in movies from human intracranial recordings. Neuroimage 2017. PDF

Detection of temporal transitions directly from field potentials along ventral visual cortex.

Olson et al in preparation Olson et al. Simple learning rules generate complex canonical circuits

This study demonstrates that it is possible to develop a network that resembles the canonical circuit architecture in neocortex starting from a tabula rasa network and implementing simple spike-timing dependent plasticity rules.

Lotter et al ICLR 2016 Lotter et al. Deep predictive coding networks for video prediction and unsupervised learning. International Conferences on Learning Representations (ICLR) 2017 PDF

A deep model including bottom-up and top-down connections to make predictions in video sequences.

Tang et al Scientific Reports 2016 Tang et al. Predicting episodic memory formation for movie events. Scientific Reports 2016. PDF

Machine learning approach to predict whether specific events within a movie will be remembered or not.

Miconi et al Cerebral Cortex 2016 Miconi et al. There's Waldo! A Normalization Model of Visual Search Predicts Single-Trial Human Fixations in an Object Search Task. Cerebral Cortex 2016. PDF

This work presents a biologically inspired computational model for visual search.

Tang et al Stroop effect Tang et al. Cascade of neural processing orchestrates cognitive control in human frontal cortex. eLife 2016. PDF

A dynamic and hierarchical sequence of steps in human frontal cortex orchestrates cognitivie control.

Bansal et al 2014 schematic Bansal et al. Neural dynamics underlying target detection in the human brain. Journal of Neuroscience 2014. PDF

Feature-based attention modulates responses along the human ventral visual stream during a target detection task

Singer et al temporal asynchrony and object recognition Singer and Kreiman. Asynchrony disrupts object recognition. Journal of Vision 2014. PDF

Spatiotemporal integration during recognition breaks down with even small deviations from simultaneity.

Hemberg et al Nucleic Acids Research 2012 Hemberg et al. Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding site. Nucleic Acids Research 2012. PDF

A method to build putative transcripts from high-throughput total RNA-seq data. (HATRIC)

Visual Population Codes MIT Press 2011

Kriegeskorte and Kreiman. Understanding visual population codes MIT PRESS 2011

Towards a common multivariate framework for cell recording and functional imaging. Link to code and other resources.

Kim et al Nature 2010 Kim et al. Widespread transcription at thousands of enhancers during activity-dependent gene expression in neurons. Nature 2010. PDF

Discovery of transcription at enhancers, eRNAs.

Rasch et al Journal of Neuroscience 2009 Rasch et al. From neurons to circuits: linear estimation of local field potentials. Journal of Neuroscience 2009. PDF

Computational model to investigate the relationship between spikes and local field potential signals.

Agam et al Current Biology 2010 Agam et al. Robust selectivity to two-object images in human visual cortex. Current Biology 2010. PDF

The physiological responses at the level of field potentials along ventral visual cortex show robustness to clutter.

Liu et al Neuron 2009 Liu et al. Timing, timing, timing: Fast decoding of object inforrmation from intracranial field potentials in human visual cortex. Neuron 2009. PDF

Rapid selective and tolerant responses along the ventral visual stream in the human can be decoded in single trials.

Hung et al Science 2005 Hung et al. Fast read-out of object identity from macaque inferior temporal cortex. Science 2005. PDF

Single trial rapid decoding of visual information from pseudo-populations of neurons in macaque inferior temporal cortex.

Kreiman et al Neuron 2006 Kreiman et al. Object selectivity of local field potentials and spikes in the macaque inferior temporal cortex. Neuron 2016. PDF

Local field potentials in the macaque inferior temporal cortex show visual selectivity to different objects.

Su et al PNAS 2004 Su et al. A gene atlas of the mouse and human protein-encoding transcriptomes. PNAS 2004. PDF

Microarray based profiling of gene expression across multiple tissues in mice and humans.

Kreiman et al Nucleic Acids Research 2004 Kreiman. Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Research 2004. PDF

A method for de novo discovery of gene regulatory sequences for sets of co-regulated genes. (CISREGUL).

GitHub link.
Zirlinger et al PNAS 2001 Zirlinger et al. Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid sub-nuclei. PNAS 2001. PDF

Microarray technology uncovered gene expression patterns of the different sub-nuclei within the amygdala.

Spike sorting software (spiker) Spike sorting software (Spiker)

Extracellular recordings of spikes often capture the activity of multiple neurons in the vicinity of the microwire electrode. Spiker is an unsupervised algorithm to separate the different putative units.

READ THIS FIRST BEFORE DOWNLOADING FROM THIS WEB SITE: All code is provided as is. You are welcome to send email to the main authors with questions and queries about the code. Note that due to the volume and nature of these emails, in most cases, we will not be able to answer them. Our intent in providing the code is to push the frontiers of science, help people reproduce results and improve upon them. However, we are not a software development company and we lack the resources to provide technical support. Note also that you are responsible for the use and misuse of the code provided here. Downloading any material from this web site implies your agreement with the rules specified here.