When I use SpaCy NER, SpaCy will recognize 'TodoA' as PERSON. This is obviously unreasonable. Is there any way to verify whether the entity extracted by SpaCy is reasonable? Thanks!
Most of these unreasonable entities are extracted by spacy beam search. The beam search code is:
import spacy
import sys
from collections import defaultdict
nlp = spacy.load('en')
text = u'Will Japan join the European Union? If yes, we should \
move to United States. Fasten your belts, America we are coming'
with nlp.disable_pipes('ner'):
doc = nlp(text)
threshold = 0.2
(beams, somethingelse) = nlp.entity.beam_parse([ doc ], beam_width = 16, beam_density = 0.0001)
entity_scores = defaultdict(float)
for beam in beams:
for score, ents in nlp.entity.moves.get_beam_parses(beam):
for start, end, label in ents:
entity_scores[(start, end, label)] += score
print ('Entities and scores (detected with beam search)')
for key in entity_scores:
start, end, label = key
score = entity_scores[key]
if ( score > threshold):
print ('Label: {}, Text: {}, Score: {}'.format(label, doc[start:end], score))
The "unreasonable" annotation you are seeing is directly linked with the nature of the model that is used to perform the annotation and the process of obtaining it.
In short, the model is an approximation of a very complex function (in mathematical terms) from some characteristics of sequences of words (e.g. presence of particular letters, upper-casing, usage of particular terms, etc.) to a closed set of tags (e.g. PERSON). It is an approximation that is close to best across a large body of text (e.g. a few GBs of ASCII text) but certainly it is not a mapping of particular phrases to tags. Therefore, even though the data which is used for training is accurate, the result of applying the model might be not ideal in some circumstances.
In your case it is likely that the model is clinging on upper-casing of a word, and maybe there was a large number of words used in training that share the prefix that were marked with tag PERSON) - e.g. Toddy, toddler, etc. and a very small number of words with such a prefix that were not PERSONs.
This phenomenon that we observe was not chosen explicitly by person preparing the model, it is only a by-product of the combination of the process of preparing it (training), and the data used.
Related
I am doing a college project where I need to compare a string with list of other strings. I want to know if we have any kind of library which can do this or not.
Suppose I have a table called : DOCTORS_DETAILS
Other Table names are : HOSPITAL_DEPARTMENTS , DOCTOR_APPOINTMENTS, PATIENT_DETAILS,PAYMENTS etc.
Now I want to calculate which one among those are more relevant to DOCTOR_DETAILS ?
Expected output can be,
DOCTOR_APPOINTMENTS - More relevant because of the term doctor matches in both string
PATIENT_DETAILS - The term DETAILS present in both string
HOSPITAL_DEPARTMENTS - least relevant
PAYMENTS - least relevant
Therefore I want to find RELEVENCE based on number of similar terms present on both the strings in question.
Ex : DOCTOR_DETAILS -> DOCTOR_APPOITMENT(1/2) > DOCTOR_ADDRESS_INFORMATION(1/3) > DOCTOR_SPECILIZATION_DEGREE_INFORMATION (1/4) > PATIENT_INFO (0/2)
Semantic similarity is a common NLP problem. There are multiple approaches to look into, but at their core they all are going to boil down to:
Turn each piece of text into a vector
Measure distance between vectors, and call closer vectors more similar
Three possible ways to do step 1 are:
tf-idf
fasttext
bert-as-service
To do step 2, you almost certainly want to use cosine distance. It is pretty straightforward with Python, here is a implementation from a blog post:
import numpy as np
def cos_sim(a, b):
"""Takes 2 vectors a, b and returns the cosine similarity according
to the definition of the dot product
"""
dot_product = np.dot(a, b)
norm_a = np.linalg.norm(a)
norm_b = np.linalg.norm(b)
return dot_product / (norm_a * norm_b)
For your particular use case, my instincts say to use fasttext. So, the official site shows how to download some pretrained word vectors, but you will want to download a pretrained model (see this GH issue, use https://dl.fbaipublicfiles.com/fasttext/vectors-english/wiki-news-300d-1M-subword.bin.zip),
Then you'd then want to do something like:
import fasttext
model = fasttext.load_model("model_filename.bin")
def order_tables_by_name_similarity(main_table, candidate_tables):
'''Note: we use a fasttext model, not just pretrained vectors, so we get subword information
you can modify this to also output the distances if you need them
'''
main_v = model[main_table]
similarity_to_main = lambda w: cos_sim(main_v, model[w])
return sorted(candidate_tables, key=similarity_to_main, reverse=True)
order_tables_by_name_similarity("DOCTORS_DETAILS", ["HOSPITAL_DEPARTMENTS", "DOCTOR_APPOINTMENTS", "PATIENT_DETAILS", "PAYMENTS"])
# outputs: ['PATIENT_DETAILS', 'DOCTOR_APPOINTMENTS', 'HOSPITAL_DEPARTMENTS', 'PAYMENTS']
If you need to put this in production, the giant model size (6.7GB) might be an issue. At that point, you'd want to build your own model, and constrain the model size. You can probably get roughly the same accuracy out of a 6MB model!
I have a ML.net project and as of right now everything has gone great. I have a motor that collects a power reading 256 times around each rotation and I push that into a model. Right now it determines the state of the motor nearly perfectly. The motor itself only has room for 38 values on it at a time so I have been spending several rotations to collect the full 256 samples for my training data.
I would like to cut the sample size down to 38 so every rotation I can determine its state. If I just evenly space the samples down to 38 my model degrades by a lot. I know I am not feeding the model the features it thinks are most important but just making a guess and randomly selecting data for the model.
Is there a way I can see the importance of each value in the array during the training process? I was thinking I could use IDataView for this and I found the below statement about it (link).
Standard ML schema: The IDataView system does not define, nor prescribe, standard ML schema representation. For example, it does not dictate representation of nor distinction between different semantic interpretations of columns, such as label, feature, score, weight, etc. However, the column metadata support, together with conventions, may be used to represent such interpretations.
Does this mean I can print out such things as weight for each column and how would I do that?
I have actually only been working with ML.net for a couple weeks now so I apologize if the question is naive, I assure you I have googled this as many ways as I can think to. Any advice would be appreciated. Thanks in advance.
EDIT:
Thank you for the answer I was going down a completely useless path. I have been trying to get it to work following the example you linked to. I have 260 columns with numbers and one column with the conditions as one of five text strings. This is the condition I am trying to predict.
The first time I tried it threw an error "expecting single but got string". No problem I used .Append(mlContext.Transforms.Conversion.MapValueToKey("Label", "Label")) to convert to key values and it threw the error expected Single, got Key UInt32. any ideas on how to push that into this function?
At any rate thank you for the reply but I guess my upvotes don't count yet sorry. hopefully I can upvote it later or someone else here can upvote it. Below is the code example.
//Create MLContext
MLContext mlContext = new MLContext();
//Load Data
IDataView data = mlContext.Data.LoadFromTextFile<ModelInput>(TRAIN_DATA_FILEPATH, separatorChar: ',', hasHeader: true);
// 1. Get the column name of input features.
string[] featureColumnNames =
data.Schema
.Select(column => column.Name)
.Where(columnName => columnName != "Label").ToArray();
// 2. Define estimator with data pre-processing steps
IEstimator<ITransformer> dataPrepEstimator =
mlContext.Transforms.Concatenate("Features", featureColumnNames)
.Append(mlContext.Transforms.NormalizeMinMax("Features"))
.Append(mlContext.Transforms.Conversion.MapValueToKey("Label", "Label"));
// 3. Create transformer using the data pre-processing estimator
ITransformer dataPrepTransformer = dataPrepEstimator.Fit(data);//error here
// 4. Pre-process the training data
IDataView preprocessedTrainData = dataPrepTransformer.Transform(data);
// 5. Define Stochastic Dual Coordinate Ascent machine learning estimator
var sdcaEstimator = mlContext.Regression.Trainers.Sdca();
// 6. Train machine learning model
var sdcaModel = sdcaEstimator.Fit(preprocessedTrainData);
ImmutableArray<RegressionMetricsStatistics> permutationFeatureImportance =
mlContext
.Regression
.PermutationFeatureImportance(sdcaModel, preprocessedTrainData, permutationCount: 3);
// Order features by importance
var featureImportanceMetrics =
permutationFeatureImportance
.Select((metric, index) => new { index, metric.RSquared })
.OrderByDescending(myFeatures => Math.Abs(myFeatures.RSquared.Mean));
Console.WriteLine("Feature\tPFI");
foreach (var feature in featureImportanceMetrics)
{
Console.WriteLine($"{featureColumnNames[feature.index],-20}|\t{feature.RSquared.Mean:F6}");
}
I believe what you are looking for is called Permutation Feature Importance. This will tell you which features are most important by changing each feature in isolation, and then measuring how much that change affected the model's performance metrics. You can use this to see which features are the most important to the model.
Interpret model predictions using Permutation Feature Importance is the doc that describes how to use this API in ML.NET.
You can also use an open-source set of packages, they are much more sophisticated than what is found in ML.NET. I have an example on my GitHub how-to use R with advanced explainer packages to explain ML.NET models. You can get local instance as well as global model breakdown/details/diagnostics/feature interactions etc.
https://github.com/bartczernicki/BaseballHOFPredictionWithMlrAndDALEX
So i have task in front of me to make a custom ner model for the pharmaceutical industry where in i have a finite list of drugs and over 4000 text files from where NER is supposed to be done. I have also tried entity matching using spacy but it is showing some error. So now i plan on using SKlearn crfsuite but in order to do that my data needs to be in conll format and should be annotated.Would really appreciate if someone could guide me in annotating my text files! is there any way i can initiate automatic annotation on the text files using the drug list i have ? as it is a humongous effort for an individual to achieve the same manually.I also had a look at the question asked in the link mentioned below.
NER model to recognize Indian names
But no one has actually addressed my question.Would really appreciate if someone could help me out
Spacy code:-
import spacy
from spacy.matcher import PhraseMatcher
from spacy.tokens import Span
class EntityMatcher(object):
name = 'entity_matcher'
def __init__(self, nlp, terms, label):
patterns = [nlp(term) for term in terms]
self.matcher = PhraseMatcher(nlp.vocab)
self.matcher.add(label, None, *patterns)
def __call__(self, doc):
matches = self.matcher(doc)
spans = []
for label, start, end in matches:
span = Span(doc, start, end, label=label)
spans.append(span)
doc.ents = spans
return doc
data=pd.read_excel(r'C:\Users\xyz\pname.xlsx')
ld=list(set(data['Product']))
nlp = spacy.load('en')
entity_matcher = EntityMatcher(nlp, ld, 'DRUG')
nlp.add_pipe(entity_matcher)
print(nlp.pipe_names)
doc=nlp('Hi bnbbn, ope all is well. In preparation for the bcbcb is there anything that BGTD requires specifically? We had sent you the US centric Briefing Package to align with our previous discussion on having bkjnsd included in the Wave 1 IMOVAX POLIO submission plan. If you would like, we can set-up a BGTD specific meeting after the June 20th meeting to discuss any jk specific product questions you may have as the product mix is a bit different between countries.')
for ent in doc.ents:
print(ent.text, ent.start_char, ent.end_char, ent.label_)
when i run my script, this is the error i get :-
[T002] Pattern length (11) >= phrase_matcher.max_length (10). Length can be set on initialization, up to 10.
Recently, I am implementing an algorithm from a paper that I will be using in my master's work, but I've come across some problems regarding the time it is taking to perform some operations.
Before I get into details, I just want to add that my data set comprehends roughly 4kk entries of data points.
I have two lists of tuples that I've get from a framework (annoy) that calculates cosine similarity between a vector and every other vector in the dataset. The final format is like this:
[(name1, cosine), (name2, cosine), ...]
Because of the algorithm, I have two of that lists with the same names (first value of the tuple) in it, but two different cosine similarities. What I have to do is to sum the cosines from both lists, and then order the array and get the top-N highest cosine values.
My issue is: is taking too long. My actual code for this implementation is as following:
def topN(self, user, session):
upref = self.m2vTN.get_user_preference(user)
spref = self.sm2vTN.get_user_preference(session)
# list of tuples 1
most_su = self.indexer.most_similar(upref, len(self.m2v.wv.vocab))
# list of tuples 2
most_ss = self.indexer.most_similar(spref, len(self.m2v.wv.vocab))
# concat both lists and add into a dict
d = defaultdict(int)
for l, v in (most_ss + most_su):
d[l] += v
# convert the dict into a list, and then sort it
_list = list(d.items())
_list.sort(key=lambda x: x[1], reverse=True)
return [x[0] for x in _list[:self.N]]
How do I make this code faster? I've tried using threads but I'm not sure if it will make it faster. Getting the lists is not the problem here, but the concatenation and sorting is.
Thanks! English is not my native language, so sorry for any misspelling.
What do you mean by "too long"? How large are the two lists? Is there a chance your model, and interim results, are larger than RAM and thus forcing virtual-memory paging (which would create frustrating slowness)?
If you are in fact getting the cosine-similarity with all vectors in the model, the annoy-indexer isn't helping any. (Its purpose is to get a small subset of nearest-neighbors much faster, at the expense of perfect accuracy. But if you're calculating the similarity to every candidate, there's no speedup or advantage to using ANNOY.
Further, if you're going to combine all of the distances from two such calculation, there's no need for the sorting that most_similar() usually does - it just makes combining the values more complex later. For the gensim vector-models, you can supply a False-ish topn value to just get the unsorted distances to all model vectors, in order. Then you'd have two large arrays of the distances, in the model's same native order, which are easy to add together elementwise. For example:
udists = self.m2v.most_similar(positive=[upref], topn=False)
sdists = self.m2v.most_similar(positive=[spref], topn=False)
combined_dists = udists + sdists
The combined_dists aren't labeled, but will be in the same order as self.m2v.index2entity. You could then sort them, in a manner similar to what the most_similar() method itself does, to find the ranked closest. See for example the gensim source code for that part of most_similar():
https://github.com/RaRe-Technologies/gensim/blob/9819ce828b9ed7952f5d96cbb12fd06bbf5de3a3/gensim/models/keyedvectors.py#L557
Finally, you might not need to be doing this calculation yourself at all. You can provide more-than-one vector to most_similar() as the positive target, and then it will return the vectors closest to the average of both vectors. For example:
sims = self.m2v.most_similar(positive=[upref, spref], topn=len(self.m2v))
This won't be the same value/ranking as your other sum, but may behave very similarly. (If you wanted less-than-all of the similarities, then it might make sense to use the ANNOY indexer this way, as well.)
I have names of employees saved in a text file. I processed the file and compared a name that already exist.
When I checked using most_similar method, I found that it returns totally unrelated name even if the exact same name exist in the corpus.
import gensim
training_file='todel.txt'
mylist=list()
with open(training_file, encoding="iso-8859-1") as f:
for i, line in enumerate(f):
mylist.append(gensim.models.doc2vec.TaggedDocument(gensim.utils.simple_preprocess(line), [i]))
model = gensim.models.doc2vec.Doc2Vec(vector_size=50, min_count=2, epochs=55)
model.build_vocab(mylist)
inferred_vector=model.infer_vector(['aakash', 'prakash', 'patel'])
sims = model.docvecs.most_similar([inferred_vector])
' '.join(mylist[sims[0][0]].words)
How do I correctly train the data to return (closely) matching names?
You define similarity in terms of edit distance, i.e. how similar two strings are.
x2vec models define similarity in terms of semantic closeness, i.e. how similar two meanings are, computed through machine learning and co-occurrence statistics.
In other words, you're using a sledgehammer to kill a fly. Look into tools for computing string distance instead:
from Levenshtein import distance
string1 = 'aakash'
string2 = 'akash'
string3 = 'konstantinos'
print(distance(string1, string2))
1
print(distance(string1, string3))
11