Questions tagged [computational-modeling]
For questions about modeling processes from cognitive and neurobiological theories via algorithms and computer simulations, and also about confirming experimental results with theoretical/statistical constructs.
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Neuroscience Research in High School [closed]
To preface, I completely understand that expecting to make waves in such a technical field with a high-school level of experience is unreasonable, and I'm asking this question specifically to avoid ...
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Are there open data for long-term potentiation/depression experiments?
The following is Figure 8.2 from Dayan & Abbott (2001), p. 292:
It describes the phenomenon of long-term potentiation/depression (LTP/LTD): Change in synaptic strength (y-axis) is inversely ...
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How to best understand recursive computation within hierarchically cascading neural systems?
Context: The suprachiasmatic nucleus outputs to either the lateral geniculate nucleus (LGN) or the pretectal area. The LGN outputs to either V1, V2, or V3. The V1 goes to V2, V4, V5, and V6. The V2 ...
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Simulating accuracy according to a predictor variable? (R)
I'm trying to illustrate a proof-of-concept by simulating some data in RStudio, but I'm not totally sure how to go about the first part of the simulation -- modelling response accuracy.
Basically: I ...
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is there a way to predict the possible modularizations of the brain?
we know that human brain becomes more and more modular during its development. We see similar places for the similar modules in the brain (probably because of the similar inputs and vasculature around ...
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Are there any standard tools for neuroscience models programming, like for spiking neural networks?
I come from deep learning environment and there is quite a few standard tools and frameworks that you can use in different occasions. I am trying to build a spiking neural network model in Python and ...
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BOLD->functional connectivity->spectral graph theory (e.g. Atasoy 2016) vs BOLD->Fourier Analysis
My read of "Human brain networks function in connectome-specific harmonic waves" (Atasoy 2016) seems to be that you can model brain activity in terms of standing waves of the connectome (...
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What is the best network-based cognitive model to explain and predict political decision-making?
I would like to build a simple human-readable model based on connected concepts that can model how people - very approximately - represent and update their decision-making on a political subject as ...
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Does human biology compute audio fast enough to benefit from phase accurate audio propagation in 3D space?
In nature when people perceive a point source of audio moving in 3D space say when I am stationary and listening to someone talking who is walking around me does my perception of that audio benefit ...
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How to control spike timings and the number of spikes in the Izhikevich model in the context of Rebound burst?
We are using Izhikevich neurons for our study. We want to tweak the parameters to be able to control the number of spikes and spike timing when the negative current is removed. With the parameters ...
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DSM-5 Assessments for App (electronic) use [closed]
I'm a budding entrepreneur building an app in the health and wellness space. As a part of the onboarding and user journey experience, I'm thinking of incorporating all DSM-5 assessments in my app, ...
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What is the actual interpretation of the "correlation of a connection between neurons"?
I am student of Mathematics who is currently studying the utility of Algebraic Topology in the field of Neuroscience. In the paper I am reading (Reimann et al 2017) the authors explain that for ...
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Can't understand the proof of the Time-Rescaling theorem
I was reading the following paper: The time-rescaling theorem and its application to neural spike train data analysis
and I have some difficulties understanding the proof of the time-rescaling-theorem....
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Success rate of computational models in psychology
I come from computer science background. I don't know anything about formal studies of psychology. I intend to know about the success rate of computational models in domain of psychology.
Is it ...
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Why do psychologists often not use mathematical models to express their theories?
I come from an economics background where people often written explicit mathematical models for their theories. To be clear, the vast majority of economic models are not useful quantitatively — the ...
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Confusion about Marr's "computational level" and computational neuroscience
I'm writing my masters thesis in the field of computational neuroscience (using a spiking model). One of my supervisors is a cognitive scientist, who likes to use Marr's 3 levels of analysis.
Marr's '...
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Explaining mathematically why most people chose 7 when asked to chose a number between 1-10
Last day, I watched a video at ‘Numberphile’ which made a strange demand. According to the video, if you ask people to randomly pick any one integer between 1 and 10 (both inclusive), people are more ...
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Why do Na+/K+ ion pumps in neurons have a ratio of 3 to 2
As I understand it the resting potential is maintained due to the different permeabilities of K+ and Na+ and in fact at the resting potential the sum of the Na+ and K+ currents is zero. The pump's job ...
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In Integrate-and-fire models, why can we assume spike arrivals to be random?
I'm reading through some notes on integrate and fire models and it says that we assume that spike arrivals are random.
Why exactly can we make this assumption?
Is it because experiments haven't ...
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Testing Multilayer Perceptron [closed]
The following script is from Trappenberg's Fundamentals of Computational Neuroscience and is used to test a perceptron's robustness against noise.
However, how would one alter it to test the output ...
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Extra-classical receptive fields are surprising, but retinal ganglion receptive fields are not. Why?
Rao and Ballard (1999) start their paper by stating that extra-classical receptive fields, which exhibit the phenomenon of end-stopping are difficult to explain. They show that in an idealized ...
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Understanding the transition from integrated form to ODE form of neuron models
I'm trying to convert a fairly complicated neuron model from integrated form (a form of the spike response model) to ODE form for use in the BRIAN simulator.
The BRIAN simulator requires neuron/...
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Who was the first to use Softmax to model decision making?
Softmax is a mathematical function frequently used to model probabilistic choice between multiple alternatives associated with different values, e.g. two arms in a bandit task; See for example [1] and ...
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How do I find Computer Science-Focused Cognitive Science Labs for Research?
I'm applying for Master's in Computer Science programs with the goal of gaining research experience and moving into the field of Cognitive Science to one day get my PhD.
I'm trying to find labs and ...
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Noise ceiling estimate is lower than model prediction in RSA?
I am using representational similarity analyses (RSA) to compare models to some fMRI data. As part of this analysis I have computed noise ceilings for each of my regions of interest (ROIs). What's ...
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ML/Neuroscience: TensorFlow vs PyTorch vs Keras for bulding NN models of the nervous system?
I would be very grateful to people with experience in using neural network models in neuroscience for advice!
What approach would you recommend for building neural networks?
I am choosing between ...
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The same neuron sometimes released different neurotransmitters, so how does this affect our interpretation of computational models?
Most studies I see compare firing rate with some observed variable (stimuli or behavior). However, they treat all spikes the same. But neurons sometimes release different neurotransmitters depending ...
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Is HTM (Hierarchical Temporarl Model) accepted as credible?
I ran across this article Why Neurons Have Thousands of Synapses, a Theory of Sequence Memory in Neocortex, which leads to Wikipedia and HTM.
To my reading, this provides a credible theory of sensory ...
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How are the outputs of neurons encoded, if at all?
The way I learned it, a neuron fires with a fixed amplitude, and the only information encoded in the output is the frequency at which it fires. 10 spikes per second is in some sense a 'stronger' ...
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What models are there for neuronal sequence memory?
This paper https://www.frontiersin.org/articles/10.3389/fncir.2016.00023/full proposes a neuronal model to learn time-based sequences, referred to as HTM (https://en.wikipedia.org/wiki/...
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What sources of randomness does the brain use for sampling?
As an applied mathematician, I have a growing interest in the mechanisms for uncertainty representation and computation in the human brain. In fact, I recently compiled a list of papers on this ...
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Homogeneous Poisson Process of spike train
In Theoretical Neuroscience by Dayan and Abbott page 25,
the probability $P[t_1, t_2, ..., t_n]$ that a sequence of n spikes occurs with spike $i$ falling between times $t_i$ and $t_i+\Delta t$ ...
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Simulating Hudgkin Huxley neural network
I'm starting work on a computational neuroscience project where I want to create my own model of a spiking Hodgkin-Huxley neuron and connect many instances (about 400) of this model through synapses. ...
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Do people still use ACT-R?
A lot of computational cognitive scientists seem to be working on Neural nets (mostly vision scientists), Reinforcement learning (mostly decision making people) and Bayesian Inferences. I could hardly ...
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Are there animals with only excitatory neurons?
Are there animals with only excitatory neurons?
I am not sure it is possible.
Also, maybe excitation/inhibition can become relative?
I however will be happy to read your opinion..
For example, are ...
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Trying to remember the name of an Agent-Based Model
Out of curiosity- I used to read a Wiki page of a scientist (sadly I don't remember the name) who were the developer of an agent-based model.
Diagram had another entity class named similar to "...
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Parallel arrangement of capacitor and resistor in leaky integrate-and-fire model
I have read from several sources that in the leaky integrate-and-fire model of a single neuron resistor (leakage) and capacitor (membrane potential) are arranged in parallel. Look at the following RC ...
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What extent is non linear dynamics and chaos helpful to study brain function?
Recently I've started reading dynamical systems in neuroscience by izhikevich and was fascinated by the subject. I would like to pursue PhD in computational neuroscience after my masters. Is it worth ...
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The computer model of the brain
I am a computer programmer or computer engineer, and am interested in comparing the brain to a classical computer in some way. How well does this comparison hold up?
This is a general introduction ...
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What are good introductory books on mathematical psychology?
I have a background in physics and has enough knowledge in Fourier analysis, group & representation theory, projective geometry, complexity theory, and dynamical systems theory. What introductory ...
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In TD learning, is the weight function used as a linear filter?
In the Temporal difference learning algorithm (TD-learning), an agent seeks to predict the total value of future rewards that will be received during the current trial. The agent updates the ...
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Is staying with an abusive partner actually indicative of Stockholm syndrome? [duplicate]
For the longest time, I've wondered why it is that people who are physically or mentally abused by their partners stay in these relationships. Further, it seems, admittedly from personal experience, ...
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What are some credible conferences and journals in computational neuroscience?
I have a background in computer science, and I wish to introduce cognitive sciences to myself, particularly from a computational/mathematical perspective. My motivation for doing this artificial ...
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How can I visualize DTI tractography streamlines generated from FSL's probtrackX in 3D?
I currently have track files of diffusion tensor imaging (DTI) data generated from FSL's probtrackX tractography tool. What is the best software to visualize the streamlines from FSL in 3D?
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What is the computational role of the cortical column?
The cortex is supposedly composed of semi uniform cortical columns that are interlinked. Many of the resources on cortical columns I found using a Google search do not discuss what a column computes (...
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Are ACT-R and Spaun the state of the art in cognitive science computational models?
I've been looking for a computational model in cognitive science, and perused Anderson's "How can the human mind occur in the physical universe?".
I've also seen this question comparing ACT-R with a ...
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Why Bayesian Cognitive Modeling?
Recently i read an article on Bayesian Program Synthesis. It says that Bayesian cognitive modelling would help AI systems to learn from few examples in comparison to deep learning. But i was not able ...
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How to connect two networks in NEURON software? [closed]
So my goal is to connect STN and SNc neurons by giving synaptic weights and then see the response. I have already modelled STN and SNc separately and observed their response.
I need help with the ...
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Non-computational models of cognition
There is a question on this site that asks a somewhat related question, whether there are non-physical models for cognition. However, that question still assumes a computational paradigm for the non-...
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Resources/studies on physically describing emotion?
I am wondering if there is an effort to described certain basic and perhaps more complicated emotions through the processes that occur in the brain. For example, when people get angry, certain ...
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