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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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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24 views

Complete digital copy of a brain: What are the main data metrics?

For the field of a theoretical scenario, future scientists map the body of an arthropod which has about 100,000 neurons and duplicate a precise copy of the animal onto SSD, including the dendrite ...
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22 views

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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2 votes
1 answer
24 views

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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3 votes
0 answers
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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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13 views

Integrated Information Theory: research about concrete mechanisms, their emergence and specialization?

I am reading articles about IIT (https://en.wikipedia.org/wiki/Integrated_information_theory) and many accompanying articles, but they talk essentially nothing about the 1) concrete mechanisms; 2) ...
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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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1 vote
1 answer
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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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48 views

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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-1 votes
1 answer
57 views

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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1 answer
91 views

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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3 votes
1 answer
4k views

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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1 vote
1 answer
32 views

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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1 vote
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31 views

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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1 answer
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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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3 votes
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60 views

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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2 votes
1 answer
75 views

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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3 votes
1 answer
151 views

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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2 votes
0 answers
231 views

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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2 votes
2 answers
405 views

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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4 votes
0 answers
77 views

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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2 votes
1 answer
30 views

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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3 votes
1 answer
71 views

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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2 votes
0 answers
10 views

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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  • 171
5 votes
1 answer
179 views

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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2 votes
1 answer
52 views

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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3 votes
2 answers
75 views

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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0 votes
1 answer
55 views

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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2 votes
1 answer
61 views

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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1 vote
0 answers
33 views

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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6 votes
2 answers
266 views

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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3 votes
1 answer
118 views

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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13 votes
2 answers
650 views

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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6 votes
4 answers
986 views

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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2 votes
1 answer
61 views

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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0 votes
1 answer
633 views

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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3 votes
3 answers
815 views

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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5 votes
1 answer
511 views

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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3 votes
1 answer
474 views

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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3 votes
1 answer
172 views

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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4 votes
1 answer
170 views

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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1 vote
0 answers
36 views

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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9 votes
0 answers
404 views

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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1 vote
0 answers
34 views

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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4 votes
0 answers
81 views

Good Resources for Learning Modeling of fMRI Data [closed]

As a neuroscience student who works with fMRI I'm competent at the standard univariate analyses and resting state analysis techniques in AFNI and MATLAB/SPM. However, I want to learn how to use models ...
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3 votes
2 answers
456 views

How often are complex networks and graph theory useful in computational neuroscience?

Complex networks and graph theory seem like they would be important for computational neuroscience, but they don't come up in the literature as often as I would expect. I'm wondering how frequently ...
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1 vote
0 answers
187 views

Which is more important for computational neuroscience: differential equations or linear algebra? [closed]

I know that they are both used in computational neuroscience. However, I am trying to optimize my studying, so it might be useful to know which to focus more time upon, at least in the beginning.
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18 votes
3 answers
5k views

Is back-prop biologically plausible?

One of the common criticisms of Deep Learning is it's training algorithms, back-propagation of error (back-prop), has no biologically plausible implementation, despite evidence of something like it ...
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