I have a corpus with bad sentences and good ones. I need to train a RNN language model to give quality score to every sentence. I tried tensorflow ptb model. It works during training. But the project doesn't give much info about how to use the model. I ran into all sorts of problem when trying to modify it to score sentence.
Is there an example showing how to use.the model?
Also, another project IMDB comment classification caught my eyes. Is it a good idea to use that model to classify good sentences and bad ones?
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This maybe the most beginner question of all :sweat:.
I just started learning about NLP and hugging face. The first thing I'm trying to do is to apply one the bioBERT models on some clinical note data and see what I do, before moving on to the fine-tuning the model. And it looks like "emilyalsentzer/Bio_ClinicalBERT" to be the closest model for my data.
But as I try to use it for any of the analyses I always get this warning.
Some weights of the model checkpoint at emilyalsentzer/Bio_ClinicalBERT were not used when initializing BertForSequenceClassification: ['cls.predictions.transform.dense.bias', 'cls.seq_relationship.bias', 'cls.predictions.transform.dense.weight', 'cls.seq_relationship.weight', 'cls.predictions.bias', 'cls.predictions.transform.LayerNorm.weight', 'cls.predictions.transform.LayerNorm.bias', 'cls.predictions.decoder.weight']
From the hugging face course chapter 2 I understand this meant.
This is because BERT has not been pretrained on classifying pairs of sentences, so the head of the pretrained model has been discarded and a new head suitable for sequence classification has been added instead. The warnings indicate that some weights were not used (the ones corresponding to the dropped pretraining head) and that some others were randomly initialized (the ones for the new head). It concludes by encouraging you to train the model, which is exactly what we are going to do now.
So I went on to test which NLP task I can use "emilyalsentzer/Bio_ClinicalBERT" for, out of the box.
from transformers import pipeline, AutoModel
checkpoint = "emilyalsentzer/Bio_ClinicalBERT"
nlp_task = ['conversational', 'feature-extraction', 'fill-mask', 'ner',
'question-answering', 'sentiment-analysis', 'text-classification',
'token-classification',
'zero-shot-classification' ]
for task in nlp_task:
print(task)
process = pipeline(task=task, model = checkpoint)
And I got the same warning message for all the NLP tasks, so it appears to me that I shouldn't/advised not to use the model for any of the tasks. This really confuses me. The original bio_clinicalBERT model paper stated that they had good results on a few different tasks. So certainly the model was trained for those tasks. I also have similar issue with other models as well, i.e. the blog or research papers said a model obtained good results with a specific task but when I tried to apply with pipeline it gives the warning message. Is there any reason why the head layers were not included in the model?
I only have a few hundreds clinical notes (also unannotated :frowning_face:), so it doesn't look like it's big enough for training. Is there any way I could use the model on my data without training?
Thank you for your time.
This Bio_ClinicalBERT model is trained for Masked Language Model (MLM) task. This task basically used for learning the semantic relation of the token in the language/domain. For downstream tasks, you can fine-tune the model's header with your small dataset, or you can use a fine-tuned model like Bio_ClinicalBERT-finetuned-medicalcondition which is the fine-tuned version of the same model. You can find all the fine-tuned models in HuggingFace by searching 'bio-clinicalBERT' as in the link.
I want to fine tune BERT on a specific domain. I have texts of that domain in text files. How can I use these to fine tune BERT?
I am looking here currently.
My main objective is to get sentence embeddings using BERT.
The important distinction to make here is whether you want to fine-tune your model, or whether you want to expose it to additional pretraining.
The former is simply a way to train BERT to adapt to a specific supervised task, for which you generally need in the order of 1000 or more samples including labels.
Pretraining, on the other hand, is basically trying to help BERT better "understand" data from a certain domain, by basically continuing its unsupervised training objective ([MASK]ing specific words and trying to predict what word should be there), for which you do not need labeled data.
If your ultimate objective is sentence embeddings, however, I would strongly suggest you to have a look at Sentence Transformers, which is based on a slightly outdated version of Huggingface's transformers library, but primarily tries to generate high-quality embeddings. Note that there are ways to train with surrogate losses, where you try to emulate some form ofloss that is relevant for embeddings.
Edit: The author of Sentence-Transformers recently joined Huggingface, so I expect support to greatly improve over the upcoming months!
#dennlinger gave an exhaustive answer. Additional pretraining is also referred as "post-training", "domain adaptation" and "language modeling fine-tuning". here you will find an example how to do it.
But, since you want to have good sentence embeddings, you better use Sentence Transformers. Moreover, they provide fine-tuned models, which already capable of understanding semantic similarity between sentences. "Continue Training on Other Data" section is what you want to further fine-tune the model on your domain. You do have to prepare training dataset, according to one of available loss functions. E.g. ContrastLoss requires a pair of texts and a label, whether this pair is similar.
I believe transfer learning is useful to train the model on a specific domain. First you load the pretrained base model and freeze its weights, then you add another layer on top of the base model and train that layer based on your own training data. However, the data would need to be labelled.
Tensorflow has some useful guide on transfer learning.
You are talking about pre-training. Fine-tuning on unlabeled data is called pre-training and for getting started, you can take a look over here.
BERT pre-training of the base-model is done by a language modeling approach, where we mask certain percent of tokens in a sentence, and we make the model learn those missing mask. Then, I think in order to do downstream tasks, we add a newly initialized layer and we fine-tune the model.
However, suppose we have a gigantic dataset for sentence classification. Theoretically, can we initialize the BERT base architecture from scratch, train both the additional downstream task specific layer + the base model weights form scratch with this sentence classification dataset only, and still achieve a good result?
Thanks.
BERT can be viewed as a language encoder, which is trained on a humongous amount of data to learn the language well. As we know, the original BERT model was trained on the entire English Wikipedia and Book corpus, which sums to 3,300M words. BERT-base has 109M model parameters. So, if you think you have large enough data to train BERT, then the answer to your question is yes.
However, when you said "still achieve a good result", I assume you are comparing against the original BERT model. In that case, the answer lies in the size of the training data.
I am wondering why do you prefer to train BERT from scratch instead of fine-tuning it? Is it because you are afraid of the domain adaptation issue? If not, pre-trained BERT is perhaps a better starting point.
Please note, if you want to train BERT from scratch, you may consider a smaller architecture. You may find the following papers useful.
Well-Read Students Learn Better: On the Importance of Pre-training Compact Models
ALBERT: A Lite BERT for Self-supervised Learning of Language Representations
I can give help.
First of all, MLM and NSP (which are the original pre-training objectives from NAACL 2019) are meant to train language encoders with prior language knowledge. Like a primary school student who read many books in the general domain. Before BERT, many neural networks would be trained from scratch, from a clean slate where the model doesn't know anything. This is like a newborn baby.
So my question is, "is it a good idea to start teaching a newborn baby when you can begin with a primary school student?" My answer is no. This is supported by numerous State-of-The-Arts achieved by the pre-trained models, compared to the old methods of training a neural network from scratch.
As someone who works in the field, I can assure you that it is a much better idea to fine-tune a pre-trained model. It doesn't matter if you have a 200k dataset or a 1mil datapoints. In fact, more fine-tuning data will only make the downstream results better if you use the right hyperparameters.
Though I recommend the learning rate between 2e-6 ~ 5e-5 for sentence classification tasks, you can explore. If your dataset is very, very domain-specific, it's up to you to fine-tune with a higher learning rate, which will deviate the model further away from its "pre-trained" knowledge.
And also, regarding your question on
can we initialize the BERT base architecture from scratch, train both the additional downstream task specific layer + the base model weights form scratch with this sentence classification dataset only, and still achieve a good result?
I'm negative about this idea. Even though you have a dataset with 200k instances, BERT is pre-trained on 3300mil words. BERT is too inefficient to be trained with 200k instances (both size-wise and architecture-wise). If you want to train a neural network from scratch, I'd recommend you look into LSTMs or RNNs.
I'm not saying I recommend LSTMs. Just fine-tune BERT. 200k is not even too big anyways.
All the best luck with your NLP studies :)
I have been attempting to classify an author using multiple texts written by this author, which I would then use to find similarities in other texts to identify that author in the test group.
I have been successful with some of the predictions, however I am still getting results where it failed to predict the author.
I have done pre-processing the texts beforehand with stemming, tokenizing, stop words, removing punctuation etc. in an attempt to make it more accurate.
I am unfamiliar with how exactly the OneClassSVM parameters work. What parameters could I use to best suit my problem and how could I make my model more accurate in it's predictions?
Here is what I have so far:
vectorizer = TfidfVectorizer()
author_corpus = self.pre_process(author_corpus)
test_corpus = self.pre_process(test_corpus)
train = author_corpus
test = test_corpus
train_vectors = vectorizer.fit_transform(train)
test_vectors = vectorizer.transform(test)
model = OneClassSVM(kernel='linear', gamma='auto', nu=0.01)
model.fit(train_vectors)
test_predictions = model.predict(test_vectors)
print(test_predictions[:10])
print(model.score_samples(test_vectors)[:10])
You can use a SVM, but deep learning is really well-suited for this. I did a Kaggle competition with classifying documents that was amazing for this.
If you don't think you have a big enough dataset, you might want to just take a text classifier model and re-train the last layer on your author, then fine-tune the rest of the model.
I’ve heard positive things about Andrew Ng’s deep learning class on Coursera. I learned all I know about AI using the Microsoft Professional Certification in AI on edx.
Good day, fellow humans (?).
I have a methodological question that is confused by a deep research in a tiny amount of time.
The question arises from the following problem(s): I need to apply semi-supervised or unsupervised clustering on documents. I have ~300 documents classified with multi-labels and approximately 3400 documents not classified. The number of unsupervised documents could become ~10'000 in the next days.
The main idea is that of applying semi-supervised clustering based on the labels at hands. Alternatively, that of going fully unsupervised for soft clustering.
We thought of creating embeddings for the whole documents, but here lies the confusion: which library is the best for such a task?
I guess the utmost importance needs to lie in the context of the whole document. As far as I know, BERT and FastText provide context-dependent word embedding, but not whole document embedding. On the other hand, Gensim's Doc2Vec is context-agnostic, right?
I think I saw a way to train sentence embeddings with BERT, via the HuggingFace API, and was wondering whether it could be useful to consider the whole document as a single sentence.
Do you have any suggestion? I'm probably exposing my utter ignorance and confusion on the matter, but my brain is melted.
Thank you very much for your time.
Viva!
Edit to answer to #gojomo:
My documents are on average ~180 words. The original task was that of multi-label text classification, i.e. each document can have from 1 to N labels, with the number of labels now being N=18. They are highly imbalanced.
Having only 330 labeled documents so far due to several issues, we asked the documents' provider to give also unlabeled data, that should reach the order of the 10k.
I used FastText classification mode, but the result is obviously atrocious. I also run a K-NN with Doc2Vec document embedding, but the result is obviously still atrocious.
I was going to use biomedical BERT-based models (like BioBERT and SciBERT) to produce a NER tagging (trained on domain-specific datasets) on the documents to later apply a classifier.
Now that we have unlabeled documents at disposal, we wanted to adventure into semi-supervised classification or unsupervised clustering, just to explore possibilities. I have to say that this is just a master thesis.