Related
I have the following binomial (probit) gam using mgcv, which includes y (0 or 1), two continuous predictors (xa, xb) plus the ‘ti’ interactions of a third covariate (xc) with these two predictors.
mygam <- gamV(y ~ s(xa, k=10, bs="cr") + s(xb, k=10, bs="cr") +
ti(xc, xa, bs = c("cr", "cr"), k = c(5, 5)) +
ti(xc, xb, bs = c("cr", "cr"), k = c(5, 5)),
data = df, method = "ML", family = binomial(link = "probit"))
Using default k=10 for main effects and k=c(5,5) for interactions, the intercept and 50 coefficients are the following:
terms <- c("Intercept", "s(xa).1", "s(xa).2", "s(xa).3", "s(xa).4", "s(xa).5", "s(xa).6", "s(xa).7", "s(xa).8", "s(xa).9", "s(xb).1", "s(xb).2", "s(xb).3", "s(xb).4", "s(xb).5", "s(xb).6", "s(xb).7", "s(xb).8", "s(xb).9", "ti(xc,xa).1", "ti(xc,xa).2", "ti(xc,xa).3", "ti(xc,xa).4", "ti(xc,xa).5", "ti(xc,xa).6", "ti(xc,xa).7", "ti(xc,xa).8", "ti(xc,xa).9", "ti(xc,xa).10", "ti(xc,xa).11", "ti(xc,xa).12", "ti(xc,xa).13", "ti(xc,xa).14", "ti(xc,xa).15", "ti(xc,xa).16", "ti(xc,xb).1", "ti(xc,xb).2", "ti(xc,xb).3", "ti(xc,xb).4", "ti(xc,xb).5", "ti(xc,xb).6", "ti(xc,xb).7", "ti(xc,xb).8", "ti(xc,xb).9", "ti(xc,xb).10", "ti(xc,xb).11", "ti(xc,xb).12", "ti(xc,xb).13", "ti(xc,xb).14", "ti(xc,xb).15", "ti(xc,xb).16")
coefs <- c(-0.0702421404106311, 0.0768316292916553, 0.210036768213672, 0.409025596435604, 0.516554288252813, 0.314600352165584, -0.271938137725695, -1.1169186662112, -1.44829172827383, -2.39608336269616, 0.445091855160863, 0.119747299507175, -0.73508332280573, -1.3851857008194, -1.84125850675114, -1.77797283303084, -1.45118023146655, -1.56696555281429, -2.55103708393941, 0.0505422263407052, -0.110361707609838, -0.168897589312596, -0.0602318423244818, 0.095385784704545, -0.20818521830706, -0.318650042681766, -0.113613570916751, 0.123559386280642, -0.269467853796075, -0.412476320830133, -0.147039497705579, 0.189416535823022, -0.412990646359733, -0.632158143648671, -0.225344249076957, 0.0237165469278517, 0.0434926950921869, 0.080572361088243, 0.397397459143317, 0.0453636001566695, 0.0831126054198634, 0.153350111096294, 0.75009880522662, 0.0583689328419794, 0.107001374561518, 0.197852239031467, 0.970623037721609, 0.0894562434842868, 0.163989821269297, 0.303175057387294, 1.48718228468607)
df_coefs <- data.frame(terms, coefs)
I would like the mathematical equation of this model, which would allow to determine the probability of y given known covariates. Given as example from my dataset (n > 70000), the predicted probability ‘prob’ (type = “response”) obtained with xa = 7.116, xb = 2.6, and xc = 19 was prob = 0.76444141, which is the result to be determined with the expected mathematical equation.
Is this possible?
Thanks for your help and time.
Below, the summary(mygam)
Parametric coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.07024 0.00709 -9.907 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Approximate significance of smooth terms:
edf Ref.df Chi.sq p-value
s(xa) 8.007 8.548 5602.328 < 2e-16 ***
s(xb) 8.448 8.908 16282.793 < 2e-16 ***
ti(xc,xa) 1.004 1.007 10.278 0.00138 **
ti(xc,xb) 1.021 1.042 7.718 0.00627 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
R-sq.(adj) = 0.52 Deviance explained = 45.6%
-ML = 29379 Scale est. = 1 n = 77870
If you set type="terms" in the predict function, you get the contributions of the individual components to the linear predictor. However, these are not on the scale of outcome probability, but on that of the linear predictor.
Because of the non-linear transformation of the linear predictor -- in your case with the probit link -- attributing the predicted probability to the individual components requires attribution methods that come with additional assumptions.
An example of such an attribution method is Shapley values.
I've been trying to use the HuggingFace nlp library's GLUE metric to check whether a given sentence is a grammatical English sentence. But I'm getting an error and is stuck without being able to proceed.
What I've tried so far;
reference and prediction are 2 text sentences
!pip install transformers
from transformers import BertTokenizer
tokenizer = BertTokenizer.from_pretrained('bert-large-uncased')
reference="Security has been beefed across the country as a 2 day nation wide curfew came into effect."
prediction="Security has been tightened across the country as a 2-day nationwide curfew came into effect."
import nlp
glue_metric = nlp.load_metric('glue',name="cola")
#Using BertTokenizer
encoded_reference=tokenizer.encode(reference, add_special_tokens=False)
encoded_prediction=tokenizer.encode(prediction, add_special_tokens=False)
glue_score = glue_metric.compute(encoded_prediction, encoded_reference)
Error I'm getting;
ValueError Traceback (most recent call last)
<ipython-input-9-4c3a3ce7b583> in <module>()
----> 1 glue_score = glue_metric.compute(encoded_prediction, encoded_reference)
6 frames
/usr/local/lib/python3.6/dist-packages/nlp/metric.py in compute(self, predictions, references, timeout, **metrics_kwargs)
198 predictions = self.data["predictions"]
199 references = self.data["references"]
--> 200 output = self._compute(predictions=predictions, references=references, **metrics_kwargs)
201 return output
202
/usr/local/lib/python3.6/dist-packages/nlp/metrics/glue/27b1bc63e520833054bd0d7a8d0bc7f6aab84cc9eed1b576e98c806f9466d302/glue.py in _compute(self, predictions, references)
101 return pearson_and_spearman(predictions, references)
102 elif self.config_name in ["mrpc", "qqp"]:
--> 103 return acc_and_f1(predictions, references)
104 elif self.config_name in ["sst2", "mnli", "mnli_mismatched", "mnli_matched", "qnli", "rte", "wnli", "hans"]:
105 return {"accuracy": simple_accuracy(predictions, references)}
/usr/local/lib/python3.6/dist-packages/nlp/metrics/glue/27b1bc63e520833054bd0d7a8d0bc7f6aab84cc9eed1b576e98c806f9466d302/glue.py in acc_and_f1(preds, labels)
60 def acc_and_f1(preds, labels):
61 acc = simple_accuracy(preds, labels)
---> 62 f1 = f1_score(y_true=labels, y_pred=preds)
63 return {
64 "accuracy": acc,
/usr/local/lib/python3.6/dist-packages/sklearn/metrics/_classification.py in f1_score(y_true, y_pred, labels, pos_label, average, sample_weight, zero_division)
1097 pos_label=pos_label, average=average,
1098 sample_weight=sample_weight,
-> 1099 zero_division=zero_division)
1100
1101
/usr/local/lib/python3.6/dist-packages/sklearn/metrics/_classification.py in fbeta_score(y_true, y_pred, beta, labels, pos_label, average, sample_weight, zero_division)
1224 warn_for=('f-score',),
1225 sample_weight=sample_weight,
-> 1226 zero_division=zero_division)
1227 return f
1228
/usr/local/lib/python3.6/dist-packages/sklearn/metrics/_classification.py in precision_recall_fscore_support(y_true, y_pred, beta, labels, pos_label, average, warn_for, sample_weight, zero_division)
1482 raise ValueError("beta should be >=0 in the F-beta score")
1483 labels = _check_set_wise_labels(y_true, y_pred, average, labels,
-> 1484 pos_label)
1485
1486 # Calculate tp_sum, pred_sum, true_sum ###
/usr/local/lib/python3.6/dist-packages/sklearn/metrics/_classification.py in _check_set_wise_labels(y_true, y_pred, average, labels, pos_label)
1314 raise ValueError("Target is %s but average='binary'. Please "
1315 "choose another average setting, one of %r."
-> 1316 % (y_type, average_options))
1317 elif pos_label not in (None, 1):
1318 warnings.warn("Note that pos_label (set to %r) is ignored when "
ValueError: Target is multiclass but average='binary'. Please choose another average setting, one of [None, 'micro', 'macro', 'weighted'].
However, I'm able to get results (pearson and spearmanr) for 'stsb' with the same workaround as given above.
Some help and a workaround for(cola) this is really appreciated. Thank you.
In general, if you are seeing this error with HuggingFace, you are trying to use the f-score as a metric on a text classification problem with more than 2 classes. Pick a different metric, like "accuracy".
For this specific question:
Despite what you entered, it is trying to compute the f-score. From the example notebook, you should set the metric name as:
metric_name = "pearson" if task == "stsb" else "matthews_correlation" if task == "cola" else "accuracy"
I'm just starting to learn how to code in Sagemath, I know it's similar to python but I don't have much experience with that either.
I'm trying to add two binary numbers representing fractions. That is, something like
a = '110'
b = '011'
bin(int(a,2) + int(b,2))
But using values representing fractions, such as '1.1'.
Thanks in advance!
If you want to do this in vanilla Python, parsing the binary fractions by hand isn't too bad (the first part being from this answer);
def binstr_to_float(s):
t = s.split('.')
return int(t[0], 2) + int(t[1], 2) / 2.**len(t[1])
def float_to_binstr(f):
i = 0
while int(f) != f:
f *= 2
i += 1
as_str = str(bin(int(f)))
if i == 0:
return as_str[2:]
return as_str[2:-i] + '.' + as_str[-i:]
float_to_binstr(parse_bin('11.1') + parse_bin('0.111')) # is '100.011'
In python you can use the Binary fractions package. With this package you can convert binary-fraction strings into floats and vice-versa. Then, you can perform operations on them.
Example:
>>> from binary_fractions import Binary
>>> sum = Binary("1.1") + Binary("10.01")
>>> str(sum)
'0b11.11'
>>> float(sum)
3.75
>>>
It has many more helper functions to manipulate binary strings such as: shift, add, fill, to_exponential, invert...
PS: Shameless plug, I'm the author of this package.
I get sums of squares and mean sums of squares 10x higher when I use anova on lmerTest:: lmer compared to lme4:: lmer objects. See the R log file below. Note the warning that when I attach the lmerTest package, the stats::sigma function overrides the lme4::sigma function, and I suspect that it is this that leads to the discrepancy. In addition, the anova report now says that it is a Type III anova rather than the expected Type I. Is this a bug in the lmerTest package, or is there something about use of the Kenward-Roger approximation for degrees of freedom that changes the calculation of SumSQ and MSS and specification of the anova Type that I don't understand?
I would append the test file, but it is confidential clinical trial information. If necessary I can see if I can cobble up a test case.
Thanks in advance for any advice you all can provide about this.
> library(lme4)
Loading required package: Matrix
Attaching package: ‘lme4’
The following object is masked from ‘package:stats’:
sigma
> test100 <- lmer(log(value) ~ prepost * lowhi + (1|CID/LotNo/rep),
REML = F, data = GSIRlong, subset = !is.na(value))
> library(lmerTest)
Attaching package: ‘lmerTest’
The following object is masked from ‘package:lme4’:
lmer
The following object is masked from ‘package:stats’:
step
Warning message:
replacing previous import ‘lme4::sigma’ by ‘stats::sigma’ when loading
‘lmerTest’
> test200 <- lmer(log(value) ~ prepost * lowhi + (1|CID/LotNo/rep),
REML = F, data = GSIRlong, subset = !is.na(value))
> anova(test100)
Analysis of Variance Table
Df Sum Sq Mean Sq F value
prepost 1 3.956 3.956 18.4825
lowhi 1 130.647 130.647 610.3836
prepost:lowhi 1 0.038 0.038 0.1758
> anova(test200, ddf = 'Ken')
Analysis of Variance Table of type III with Kenward-Roger
approximation for degrees of freedom
Sum Sq Mean Sq NumDF DenDF F.value Pr(>F)
prepost 37.15 37.15 1 308.04 18.68 2.094e-05 ***
lowhi 1207.97 1207.97 1 376.43 607.33 < 2.2e-16 ***
prepost:lowhi 0.35 0.35 1 376.43 0.17 0.676
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Update: Thanks, Ben. I did a little code archeology on lmerTest to see if I could dope out an explanation for the above anomalies. First, it turns out that lmerTest::lmer just submits the model to lme4::lmer and then relabels the result as an "mermodLmerTest" object. The only effect of this is to invoke versions of summary() and anova() from the lmerTest package rather than the usual defaults from base and stats. (These lmerTest functions are compiled, and I have not yet gone farther to look at the C++ code.) lmerTest::summary just adds three columns to the base::summary result, giving df, t value, and Pr. Note that lmerTest::anova, by default, computes a type III anova rather than a type I as in stats::anova. (Explanation of my second question above.) Not a great choice if one's model includes interactions. One can request a type I, II, or III anova using the type = 1/2/3 option.
However there are other surprises using the nlmeTest versions of summary and anova, as shown in the R console file below. I used lmerTest's included sleepstudy data so that this code should be replicable.
a. Note that "sleepstudy" has 180 records (with 3 variables)
b. The summaries of fm1 and fm1a are identical except for the added Fixed effects columns. But note that in the lmerTest::summary the ddfs for the intercept and Days are 1371 and 1281 respectively; odd given that there are only 180 records in "sleepstudy."
c. Just as in my original model above, the nlm4 anad nlmrTest versions of anova give very different values of Sum Sq and Mean Sq. (30031 and 446.65 respectively).
d: Interestingly, the nlmrTest versions of anova using Satterthwaite and Kenward-Rogers estimates of the DenDF are wildly different (5794080 and 28 respecitvely). The K-R value seems more reasonable.
Given the above issues, I am reluctant at this point to depend on lmerTest to give reliable p-values. Based on your (Doug Bates's) blog entry (https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html), I am using now (and recommending) the method from the posting by Dan Mirman (http://mindingthebrain.blogspot.ch/2014/02/three-ways-to-get-parameter-specific-p.html) in the final bit of code below to estimate a naive t-test p-value (assuming essentially infinite degrees of freedom) and a Kenward-Rogers estimate of df (using the R package 'pbkrtest' -- the same package used by lmerTest). I couldn't find R code to compute the Satterthwaite estimates. The naive t-test p-value is clearly anti-conservative, but the KR estimate is thought to be pretty good. If the two give similar estimates of p, then I think that one can feel comfortable with a p-value in the range of [naive t-test, KR estimate].
> library(lme4); library(lmerTest); library(pbkrtest);
dim(sleepstudy)
[1] 180 3
>
> fm1 <- lme4::lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> fm1a <- lmerTest::lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
>
> summary(fm1)
Linear mixed model fit by REML ['lmerMod']
Formula: Reaction ~ Days + (Days | Subject)
Data: sleepstudy
REML criterion at convergence: 1743.6
Scaled residuals:
Min 1Q Median 3Q Max
-3.9536 -0.4634 0.0231 0.4634 5.1793
Random effects:
Groups Name Variance Std.Dev. Corr
Subject (Intercept) 612.09 24.740
Days 35.07 5.922 0.07
Residual 654.94 25.592
Number of obs: 180, groups: Subject, 18
Fixed effects:
Estimate Std. Error t value
(Intercept) 251.405 6.825 36.84
Days 10.467 1.546 6.77
Correlation of Fixed Effects:
(Intr)
Days -0.138
> summary(fm1a)
Linear mixed model fit by REML t-tests use Satterthwaite approximations to
degrees of freedom [lmerMod]
Formula: Reaction ~ Days + (Days | Subject)
Data: sleepstudy
REML criterion at convergence: 1743.6
Scaled residuals:
Min 1Q Median 3Q Max
-3.9536 -0.4634 0.0231 0.4634 5.1793
Random effects:
Groups Name Variance Std.Dev. Corr
Subject (Intercept) 612.09 24.740
Days 35.07 5.922 0.07
Residual 654.94 25.592
Number of obs: 180, groups: Subject, 18
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) 251.405 6.825 1371.100 302.06 <2e-16 ***
Days 10.467 1.546 1281.700 55.52 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr)
Days -0.138
Warning message:
In deviance.merMod(object, ...) :
deviance() is deprecated for REML fits; use REMLcrit for the REML
criterion or deviance(.,REML=FALSE) for deviance calculated at the REML fit
>
> anova(fm1)
Analysis of Variance Table
Df Sum Sq Mean Sq F value
Days 1 30031 30031 45.853
> anova(fm1a, ddf = 'Sat', type = 1)
Analysis of Variance Table of type I with Satterthwaite
approximation for degrees of freedom
Sum Sq Mean Sq NumDF DenDF F.value Pr(>F)
Days 446.65 446.65 1 5794080 45.853 1.275e-11 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Warning message:
In deviance.merMod(object, ...) :
deviance() is deprecated for REML fits; use REMLcrit for the REML criterion or deviance(.,REML=FALSE) for deviance calculated at the REML fit
> anova(fm1a, ddf = 'Ken', type = 1)
Analysis of Variance Table of type I with Kenward-Roger
approximation for degrees of freedom
Sum Sq Mean Sq NumDF DenDF F.value Pr(>F)
Days 446.65 446.65 1 27.997 45.853 2.359e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Warning message:
In deviance.merMod(object, ...) :
deviance() is deprecated for REML fits; use REMLcrit for the REML criterion or deviance(.,REML=FALSE) for deviance calculated at the REML fit
>
> # t.test
> coefs <- data.frame(coef(summary(fm1)))
> coefs$p.z <- 2 * (1 - pnorm(abs(coefs$t.value)))
> coefs
Estimate Std..Error t.value p.z
(Intercept) 251.40510 6.824556 36.838311 0.000000e+00
Days 10.46729 1.545789 6.771485 1.274669e-11
>
> # Kenward-Rogers
> df.KR <- get_ddf_Lb(fm1, fixef(fm1))
> df.KR
[1] 25.89366
> coefs$p.KR <- 2 * (1 - pt(abs(coefs$t.value), df.KR))
> coefs
Estimate Std..Error t.value p.z p.KR
(Intercept) 251.40510 6.824556 36.838311 0.000000e+00 0.0000e+00
Days 10.46729 1.545789 6.771485 1.274669e-11 3.5447e-07
Many random-number generators return floating numbers between 0 and 1.
What's the best and correct way to get integers between a and b?
Divide the interval [0,1] in B-A+1 bins
Example A=2, B=5
[----+----+----+----]
0 1/4 1/2 3/4 1
Maps to 2 3 4 5
The problem with the formula
Int (Rnd() * (B-A+1)) + A
is that your Rnd() generation interval is closed on both sides, thus the 0 and the 1 are both possible outputs and the formula gives 6 when the Rnd() is exactly 1.
In a real random distribution (not pseudo), the 1 has probability zero. I think it is safe enough to program something like:
r=Rnd()
if r equal 1
MyInt = B
else
MyInt = Int(r * (B-A+1)) + A
endif
Edit
Just a quick test in Mathematica:
Define our function:
f[a_, b_] := If[(r = RandomReal[]) == 1, b, IntegerPart[r (b - a + 1)] + a]
Build a table with 3 10^5 numbers in [1,100]:
table = SortBy[Tally[Table[f[1, 100], {300000}]], First]
Check minimum and maximum:
In[137]:= {Max[First /# table], Min[First /# table]}
Out[137]= {100, 1}
Lets see the distribution:
BarChart[Last /# SortBy[Tally[Table[f[1, 100], {300000}]], First],
ChartStyle -> "DarkRainbow"]
X = (Rand() * (B - A)) + A
Another way to look at it, where r is your random number in the range 0 to 1:
(1-r)a + rb
As for your additional requirement of the result being an integer, maybe (apart from using built in casting) the modulus operator can help you out. Check out this question and the answer:
Expand a random range from 1–5 to 1–7
Well, why not just look at how Python does it itself? Read random.py in your installation's lib directory.
After gutting it to only support the behavior of random.randint() (which is what you want) and removing all error checks for non-integer or out-of-bounds arguments, you get:
import random
def randint(start, stop):
width = stop+1 - start
return start + int(random.random()*width)
Testing:
>>> l = []
>>> for i in range(2000000):
... l.append(randint(3,6))
...
>>> l.count(3)
499593
>>> l.count(4)
499359
>>> l.count(5)
501432
>>> l.count(6)
499616
>>>
Assuming r_a_b is the desired random number between a and b and r_0_1 is a random number between 0 and 1 the following should work just fine:
r_a_b = (r_0_1 * (b-a)) + a