A name is different than a label.
Name: a word by which a person or thing is known Label: an identifying or descriptive marker that is attached to an object
So a label might have your name on it, but often it has something else on it, such as a warning, or description, or classification.
A rule of thumb is that names are unique(ish) and labels are not.
In the example question, it looks like the word you want is "name".
Consider this website: the question's name is the question headline itself: "Is the usage of 'labeled' preferred to the usage of 'named'?".
The question's labels are its tags: "usage".
Edit: I just noticed your edit to this question.
The third and fourth sentences carry the same meaning as "named".
You are "called" by your name, usually.
I'd use "named" or go with the fourth option, which just names the method.
There are lots of synonyms for "name" but, importantly, "label" isn't really one of them.
Edit 2:
Google's built-in dictionary defines label as a classifying phrase or name applied to a person or thing, especially one that is inaccurate or restrictive.
This strengthens the notion that while labels are related to names, names are not a subset of labels (though labels might be said to be a subset of names).
english.stackexchange.com/users/380/Mr. Shiny and New 安宇
Named is preferred in your example, since you are formally giving a name to your method.
Labelling (beyond the literal) generally infers that someone else has suggested an alternative name for something.
Microsoft named their browser 'Internet Explorer', but it's often labelled as 'Internet Exploder'!
Edit :Labelling is something you do when you categorise something informally; that is, you are attaching a virtual label to it, some meta-data, if you will.
For example, Critics have labelled Project X a disaster from start to finish http://en.wikipedia.org/wiki/Labelling
english.stackexchange.com/users/2302/CJM
Name is a better choice than label if you are giving a name to something new.
The latter is used when you want to describe or give information about something instead.
For example, we say name the baby but not label the baby , don't label me as stupid but not don't name me as stupid , and label the medication with this sticker but not name the medication with this sticker .
english.stackexchange.com/users/None/
Pardon the brevity of this answer, but I would say "named" is preferred within the context of your example.
Thus: In this paper, we will describe our new method named "KICK".
Better still, you can omit "named" or "labeled" altogether for succinctness:
In this paper, we will describe our new method, "KICK".
The comma before "KICK" is sometimes treated as a matter of preference.
english.stackexchange.com/users/2705/Jimi Oke
You should actually use neither.
The implication is obvious: Here we discuss our new method "Fantastic Method".
To draw a parallel: Here we discuss our child named Thomas.
Or: Here we discuss our child labeled Thomas.
english.stackexchange.com/users/2469/Eric
Considering the description of a method in a research paper, which is the most natural way to express how we refer to the method? Is there a rule about when to use named vs labeled?   In this paper, we will describe our new method  named  "KICK".  In this paper, we will describe our new method  labeled  "KICK".  In this paper, we will describe our new method  called  "KICK".  In this paper, we will describe our new method, "KICK".
Is the usage of "labeled" preferred to the usage of "named"?
english.stackexchange.com
<word-choice>
english.stackexchange.com/questions/6823
english.stackexchange.com/users/1117/xmoleslo
A name is different to a label. A name is a word by which a person or thing is known, whilst a label is an identifying marker that is attached to an object. In the example question, the correct term would be "name". The preference here is for name and not label. There is a distinction between what we name and label. Name identifies the person or object, whereas label is a descriptor. "Name" is also considered the best option here if you are giving a name to something. Google defines "label" as something more restrictive. "Labelling" can also be a form of categorisation. Some suggest using neither "name" nor "label" in this sentence as your intentions are clear.
A name is different to a label. A name is a word by which a person or thing is known, whilst a label is an identifying marker that is attached to an object. In the example question, the correct term would be "name". Not the same. A name refers to a word by which something is known. A label identifies or decribes something.
In the example question, the word you want is "name", since you are formally giving a name to  your  method.  Name: a word by which a person or thing is known.  Label: an identifying or descriptive marker that is attached to an object.  In this example, "name" would be the preferred word to use. A name is the word that something is known by, whereas a label is a description attributed to something. Therefore, a label implies that there might be an alternative. In any case, it may be that you shouldn't use either word in this context.
The comma before "KICK" is sometimes treated as a matter of preference. Edit :Labelling is something you do when you categorise something informally; that is, you are attaching a virtual label to it, some meta-data, if you will.
The comma before "KICK" is sometimes treated as a matter of preference. Edit :Labelling is something you do when you categorise something informally; that is, you are attaching a virtual label to it, some meta-data, if you will.
A name is different to a label. "Name" is used for people whereas "label" is for things. Names are unique, lables are not. The answer is name. The third and fourth sentences have the meaning of "names" There are  lots of synonyms for "name" but it is not "label" Google defines "label" as classifying phrase or name applied to people or things. This determines that labels are related to names, but names are not a subset of labels. "Name" is perferred here. You are giving your method a name. Labelling can also be categorising something as in critics have "labelled Projext X a disaster" Name is the preferred option, but an alternative would be to omit both. Use neither, it is understood what you are discusing.
 A name is different than a label.    Name: a word by which a person or thing is known  Label: an identifying or descriptive marker that is attached to an object    So a label might have your name on it, but often it has something else on it, such as a warning, or description, or classification.    Google's built-in dictionary defines label as   a classifying phrase or name applied to a person or thing, especially one that is inaccurate or restrictive.   
A name is a word by which something is known, where as a label is a description attributed to something. In this example, "name" would be the preferred word to use. It might be the case that you should use neither "name" nor "label". Using "label" implies that there is an alternative name.