Questions tagged [separation]

Separation occurs when some classes of a categorical outcome can be perfectly distinguished by a linear combination of other variables.

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Is it still possible to run a zero-inflated negative binomial model if there is complete separation with some combinations of the response variables? [duplicate]

I am trying to analyze how the number of events Y is influenced by three factors A (4 levels), B (2 levels) and C (2 levels) and the interactions between the three. Initially trying a poisson ...
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Warning: Hauck-Donner effect detected in the following estimate(s): INTERCEPT

This is a quick question because I could not find an answer online. I ran a truncated Poisson model and I got the warning in the title (perfect separation?) affecting my intercept. The output is: <...
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estimating effect with marginaleffect package

I want to estimate ATE. first of all I used MatchIt package for full matching for propensity score and then I used logistic regression with all of variable in propensity score model after that I used ...
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Is G*Power reliable for logistic regression? It does not seem to account for Hauck-Donner

I've just been introduced to G*Power. The only option I could find for analysing logistic regression is described as: Options: Large sample z-Test, Demidenko (2007) with var corr That seems to ...
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What method should be used if the clusters contains different classes?

Assume that you having $N$ clusters. Each cluster have multiple classes. So we know the class ID for every major clusters, but not the class ID for the data points inside the major clusters. Each ...
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glm.fit: fitted probabilities numerically between 0 and 1 warning [duplicate]

I am currently writing my master's thesis and am doing a logistic regression with the following glm formula in R: ...
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Perfect separation, perhaps? In binary outcome and repeated measure (random effect) with multiple independent variables (using R)

(Using R) - this is my first time posting a stats question online, so please let me know if I'm on the wrong forum or haven't provided enough information and I'll do my best to fix it! About the data ...
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DHARMa residuals plot vs. binned residuals using stan_glm object

I am quite a newbie in R and even more so in Bayesian regression. I have fit a stan_glm binomial model with 1689 observations, 12 variables and two interaction ...
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What is the proof that non-linearly separable data can't become linearly separable with the results of PCA?

Give a non-linearly separable dataset $X,$ I want to proof that after performing PCA on it, the resulting dataset is guaranteed to be still non-linearly separable. I think we could argue that we still ...
Saltuk Kezer's user avatar
3 votes
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fitting a gam with constraints on parameters to deal with separation in parametric terms

I am trying to fit a gam using mgcv which has a mix of smooth and parametric terms. The model is for some count data on fish catches. I am modelling variation in location and time, but also ...
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Do neural networks create a separating hyperplane?

https://colah.github.io/posts/2014-03-NN-Manifolds-Topology/ mentions that neural networks learn a representation of the data so as to make the classes linearly separable. What I fail to see is how ...
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How to find a mapping to a higher dimension that separates the data, given a data set

We have the following dataset: $$ \begin{bmatrix} x_1 & x_2 & y\\ +1 & 0 & +1\\ -1 & 0 & +1\\ 0 & +2 & +1\\ 0 & +1 & -1 \end{bmatrix} $$ I was asked to find ...
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Logistic regression difficulty with multi-level factor and many 0 outcomes

My dataset describes the presence/absence of an animal in a number of different plant species. Below is a table of plant species Vs animal presence/absence, i.e each row show the number of animal ...
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Logistic regression - Exp (B) = 0? and sig is 0.999 or 1? [duplicate]

I'm having an issue with binary logistic regression for a project I'm working on. For some of the variables, I'm receiving a significance value of 0.999 and exp(B) of 0. Is this normal?
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Proportion data with number of trials known (and separation?): GLM or beta regression?

I perform a lot of bioassays in which I score mortality not on individuals, but on groups of individuals as a proportion (the denominator, i.e., number of trials, is known): Sample Data: ...
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Unexpected weights in Gradient descent algorithm (linear classification) in python

I am attempting to implement a back propagation algorithm that can efficevley read from a file of features and there targets and predict there outputs correctly, however for sake of testing I am hard ...
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Hauck-Donner effect in ordinal generalized regression

I am running a series of ordinal regressions on a rather large data set (n=3640). With some predictors I had issues with violations of parallel lines assumptions, so I decided to run those with a ...
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Pooling Profile Penalised LTRs in multiple imputation

I am analysizing data from a clinical trial. I used multiple imputation to impute the (binary) outcome variable, which is the only variable with missing data. All of the covariates are categorical and ...
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Binomial (1/0) response, Factor explanatory variable: why can't GLM estimate effect when one factor level has all 1s in response?

I have a dataset with a binomial response variable (1/0) and a single explanatory categorical variable with 2 levels. For one level, the response is all 1s and no 0s (e.g. ...
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For the Logistic model, why is the objective function unbounded below if two sets are linearly seperated?

I am reading Approximate linear discrimination via logistic modeling in the Section 8.6.1 of B & V's Convex Optimization book. On Page 428, $$ \operatorname{minimize} \ -l(a, b) \tag{8.27} $$ ...
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Why PCA is not considered in the taxonomy of blind source separation approaches?

Blind source separation (BSS) approaches are divided in the literature into four methods, including independent component analysis (ICA), sparse component analysis (SCA), and non-negative matrix ...
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Cold Start and First Price Auctions

I have the following contrived scenario... I've participated on various auction platforms where I bid on widgets. Assume that win/loss outcomes on individual platforms are well-separated such that for ...
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Is the sum of 3 bits a linearly separable task?

In other words can a linear classifier learn to correctly assign a class (label 0 to 3) for an input of 3 bits? Intuitively this cannot work, since the half-adder circuit contains an XOR block, which ...
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Hidden vs Firth vs Shen-Gao logistic regression: dealing with the Hauck-Donner effect

In 1993 a version of penalized logistic regression was introduced by Firth in order to reduce the bias due to outliers and/or (quasi-)perfect prediction in logistic regression: Bias Reduction of ...
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On the use of the sampling year as fixed-effect

I have my database in temporal blocks (so I have my occurrence sites into the year of sampling of a few years with maximum 7 years). In order to fix the complete separation problem that I also have, ...
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Is there any impact on the results of random forest if we have perfect separation in the database?

I'm having a perfect separation in my database. One of the solutions is to switch randomly some of the values of the dependent variable to the opposite for the variables that cause the problem this ...
user1988's user avatar
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Dealing with quasi-complete separation in General Additive Model?

I am modelling influence of fire on occurrence of certain bird species (count response variable) in Before/after control/impact experiment design. I've got intact and burned sites and count data both ...
Michał Walesiak's user avatar
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How many percentage to randomize and how many iterations in a "what-if analysis"?

I've got complete separated data as such: ...
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Options when model complexity and separation causes non-convergence in logistic regression

I have created an example data set here My data represent the presence/absence of a particular animal species (data$outcome) and measurements of trees. I would like ...
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Analysis of Danish mask study data by Nassim Nicholas Taleb (binomial GLM with complete separation)

Recently, Nassim Nicholas Taleb made this post about the recent Danish mask study, a randomized controlled trial which concluded that the proportions of newly diagnosed coronavirus infections was not ...
Tom Wenseleers's user avatar
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Are these two 2D datasets the same and can they be separated with the XOR NN?

I'm a very beginner in the neural network topic. So I ran into a problem. I see on the online lectures: Famous example of a simple non-linearly separable data set, the XOR problem (Minsky 1969) in the ...
Maryam Panahi's user avatar
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386 views

Is this logistf approach the right way to deal with complete separation in my logistic regression?

I am performing lots of association tests between genotypes and binary diseases. The genotypes can be very rare, and my tests often have extreme case control imbalance (e.g. 500 controls for every ...
curious's user avatar
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Using Chi-squared test when perfect separation in logistic model?

My dataset is similar to this; it describes the presence/absence of a parasite in six species of animal from two locations. Each row in the dataset represents a different individual animal. I would ...
Pat Taggart's user avatar
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249 views

penalised logistic regression with brglm - warnings

I've built a logistic model to predict a binary response. I've got four categorical predictors. One of them (posicion) has 6 levels, 3 of which occur not too frequently and are ALWAYS (by definition) ...
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Unexpected behaviour of logit regression with glm in R

I recently was puzzled by the behaviour of R's glm when trying to compute a logistic regression ...
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Separation and Correlation

In a logistic regression setting, can there be a relation between the fact that covariates are highly correlated and the problem of perfect(quasi-perfect) separation?
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What is the cause of this very high standard error in my logistic regression model?

I am running a logistic regression model where the outcome variable is Neurologic Complications, and there are various factors who's impact I am examining. One of the factors (HTN_new1), a categorical ...
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3 votes
1 answer
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Probability of linear separation in a dataset with categorical response

I am simulating datasets to which I fit polytomous logistic regression models. The maximum likelihood estimator of this model is undefined when all categories are linearly separated (and it is quite ...
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What does it means getting p-values equal to 1 and complete separation in logistic regression? [duplicate]

I was really confused if I should ask this here or in Stackoverflow, but I'll give a shot here. I ran a logistic regression using statsmodels library in Python. However, two things went wrong here (...
trder's user avatar
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Separating hardly distinguishable classes for easier classification

I apologize for this seemingly basic question, but I was just thrust into this data science role and would like to get some advice from some experts. I have a dataset with a small number of features ...
The Dude's user avatar
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2 votes
1 answer
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Logistic Regression assumption

In Logistic Regression, the assumption is that the data must be linearly separable, but if the data is not linearly separable then we can't apply Logistic Regression?
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1 answer
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Fourier analysis to retrieve components of individual spectra

I have a basic, simple question, I am a physics student, and searching internet gives me a lot of signal processing theory but couldn't find this basic answer, which I plan to implement in my speech ...
Ayan Mitra's user avatar
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607 views

Cumulative explained variance between scaled and unscaled data

I was writing a small piece of code to portray the difference between scaled and unscaled data when doing PCA and (as expected) I found that the separability of classes was better by doing the ...
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instability of logistic regression

I am reading Introduction to Statistical Learning and it is said (as in other websites) that Logistic Regression is unstable compared to Linear Discriminant Analysis in well separated cases. ...
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Doubt on d-separation

In the book: Bayesian Networks With Examples in R, the author shows three examples of d-separation: He cites: Then, just a few lines below, the author uses the dsep function, which returns FALSE for ...
Chicago1988's user avatar
13 votes
1 answer
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Which theorem in Cover's 1965 paper is actually referred to as Cover's Theorem?

Cover's Theorem is stated on Wikipedia (and similarly elsewhere) as A complex pattern-classification problem, cast in a high-dimensional space nonlinearly, is more likely to be linearly separable ...
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likelihood ratio test for logistic regression with a complete separation

Can likelihood ratio test be used for logistic regression in the case of complete separation? I understand that individual parameters can go to infinity so Wald's test is not recommended, but does ...
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1 vote
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Clustering Proof of Equation

Greetings! Could anyone enlighten me about the validity of this equation? I'm trying to prove it without success. $K$ is the number of clusters, $C_i$ is the $i$-th cluster, $m_i$ is the number of ...
Ioannis Tsirovasilis's user avatar
1 vote
1 answer
290 views

Relationship between Cohesion and Separation

Hello! May someone explain to me please how to prove the equation depiicted with the red line? Thank you in advance!
Ioannis Tsirovasilis's user avatar
2 votes
1 answer
110 views

Doesn't separation in data affects Random Forest?

I'd like to know if separation in data points given by a certain variable will affect Random Forest in terms of "being a correct built model"? For example, logistic regression is highly vulnerable in ...
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