smi_ssed/training/pubchem_encoder.py

import regex as re
import torch
import numpy as np
import random
import collections

class Encoder():

    def __init__(self, max_length=500, add_bos=True, add_eos=True, feature_size=32):
        self.vocab_encoder = torch.load('pubchem_canon_zinc_final_vocab_sorted_curated.pth')

        self.max_length = max_length
        self.min_length = 1
        self.mod_length = 42
        self.mlm_probability = .15
        self.avg_length = 66
        self.tail = 122
        self.b0_cache=collections.deque()
        self.b1_cache=collections.deque()
        self.b2_cache=collections.deque()
        self.b3_cache=collections.deque()
        self.bucket0=collections.deque()
        self.bucket1=collections.deque()
        self.bucket2=collections.deque()
        self.bucket3=collections.deque()
        if feature_size == 32:
            self.b0_max=1100
            self.b1_max=700
            self.b2_max=150
            self.b3_max=50
        else:
            self.b0_max=1382
            self.b1_max=871
            self.b2_max=516
            self.b3_max=311
        values = list(self.vocab_encoder.values())
        num_top = 0
        middle_top = 0
        bottom = 0
        for  count in values:
            if count > 100000:
                num_top += 1
            if count > 50:
                middle_top += 1
        middle_top = middle_top - num_top
        self.cutoffs = [num_top+4, middle_top]
        self.char2id = {"<bos>":0, "<eos>":1, "<pad>":2, "<mask>":3}
        self.id2char = {0:"<bos>", 1:"<eos>", 2:"<pad>", 3:"<mask>"}
        self.pad  = self.char2id['<pad>']
        self.mask = self.char2id['<mask>']
        self.eos  = self.char2id['<eos>']
        self.bos  = self.char2id['<bos>']
        pos = 0
        for key, value in self.vocab_encoder.items():
        #for pos, key in enumerate(self.vocab_encoder.keys()):
            self.char2id[key] = pos+4
            self.id2char[pos+4] = key
            pos += 1
        self.char2id["<unk>"] = pos + 4
        self.id2char[pos+4] = "<unk>"
        self.pattern =  "(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\\\|\/|:|~|@|\?|>|\*|\$|\%[0-9]{2}|[0-9])"
        self.regex = re.compile(self.pattern)
        self.add_bos = add_bos
        self.add_eos = add_eos
        #print(self.char2id)

    def encode(self, char):
        #if len(char) > self.max_length:
        #    char = char[:self.max_length]
        if self.add_bos == True:
            char = ['<bos>'] + char
        if self.add_eos == True:
            char = char + ['<eos>']

        return torch.tensor([self.char2id[word] for word in char])

    def encoder(self, tokens):
        #return *map(lambda x: self.encode(x), tokens)
        return [self.encode(mol) for mol in tokens]

    def process_text(self, text):
        #print(text)
        #random length sequences seems to help training
        mod_length = self.mod_length #+ random.randint(-1, 3)
        avg_length = self.avg_length #+ random.randint(-3, 5)
        for mol in text:
            #fill up buckets and caches
            if '\n' in mol['text']:
                print('carriage return in mol')
            raw_regex = self.regex.findall(mol['text'].strip('\n'))
            length = len(raw_regex)
            if length > self.min_length and length < mod_length:
                if len(self.bucket0) < self.b0_max:
                    self.bucket0.append(raw_regex)
                else:
                    self.b0_cache.append(raw_regex)
            elif length >= mod_length and length < avg_length:
                if len(self.bucket1) < self.b1_max:
                    self.bucket1.append(raw_regex)
                else:
                    self.b1_cache.append(raw_regex)
            elif length >= avg_length and length < self.tail:
                if len(self.bucket2) < self.b2_max:
                   self.bucket2.append(raw_regex)
                else:
                   self.b2_cache.append(raw_regex)
            elif length >= self.tail and length < self.max_length:
                if len(self.bucket3) < self.b3_max:
                   self.bucket3.append(raw_regex)
                else:
                   self.b3_cache.append(raw_regex)
            # elif length >= avg_length and length < self.tail:
            #     self.b2_cache.append(raw_regex)
            #     #if len(bucket2) < self.b2_max:
            #     #    bucket2.append(raw_regex)
            #     #else:
            #     #    self.b2_cache.append(raw_regex)
            # elif length >= self.tail and length < self.max_length:
            #     self.b3_cache.append(raw_regex)
            #     #if len(bucket3) < self.b3_max:
            #     #    bucket3.append(raw_regex)
            #     #else:
            #     #    self.b3_cache.append(raw_regex)

        #print('before Cache size  {} {} {} {}'.format(len(self.b0_cache), len(self.b1_cache), len(self.b2_cache), len(self.b3_cache)))
        #pour cache elements into any open bucket
        if len(self.bucket0) < self.b0_max and len(self.b0_cache) > 0:
            cache_size = len(self.b0_cache)
            max_margin = self.b0_max-len(self.bucket0)
            range0 = min(cache_size, max_margin)
            outbucket0 = [self.bucket0.pop() for item in range(len(self.bucket0))] + [self.b0_cache.pop() for i in range(range0)]
            #self.b0_cache =  collections.deque(self.b0_cache[:self.b0_max-len(bucket0)])
            #print('0 type {}'.format(type(self.b0_cache)))
        else:
            outbucket0 = [self.bucket0.pop() for item in range(len(self.bucket0))]

        if len(self.bucket1) < self.b1_max and len(self.b1_cache) > 0:
            cache_size = len(self.b1_cache)
            max_margin = self.b1_max-len(self.bucket1)
            range1 = min(cache_size, max_margin)
            outbucket1 = [self.bucket1.pop() for item in range(len(self.bucket1))] + [self.b1_cache.pop() for i in range(range1)]
        else:
            outbucket1 = [self.bucket1.pop() for item in range(len(self.bucket1))]

        if len(self.bucket2) < self.b2_max and len(self.b2_cache) > 0:
            cache_size = len(self.b2_cache)
            max_margin = self.b2_max-len(self.bucket2)
            range2 = min(cache_size, max_margin)
            outbucket2 = [self.bucket2.pop() for item in range(len(self.bucket2))] + [self.b2_cache.pop() for i in range(range2)]
        else:
            outbucket2 = [self.bucket2.pop() for item in range(len(self.bucket2))]

        if len(self.bucket3) < self.b3_max and len(self.b3_cache) > 0:
            cache_size = len(self.b3_cache)
            max_margin = self.b3_max-len(self.bucket3)
            range3 = min(cache_size, max_margin)
            outbucket3 = [self.bucket3.pop() for item in range(len(self.bucket3))] + [self.b3_cache.pop() for i in range(range3)]
        else:
            outbucket3 = [self.bucket3.pop() for item in range(len(self.bucket3))]

        # if len(self.b2_cache) > self.b2_max:
        #     cache_size = len(self.b2_cache)
        #     max_margin = self.b2_max
        #     range2 = min(cache_size, max_margin)
        #     outbucket2 =  [self.b2_cache.pop() for i in range(range2)]
        # else:
        #     outbucket2=[]

        # if len(self.b3_cache) > self.b3_max:
        #     cache_size = len(self.b3_cache)
        #     max_margin = self.b3_max
        #     range3 = min(cache_size, max_margin)
        #     outbucket3 =  [self.b3_cache.pop() for i in range(range3)]
        # else:
        #     outbucket3 = []

        return outbucket0, outbucket1, outbucket2, outbucket3

    def mask_tokens( self, inputs, special_tokens_mask= None):
        """
        Prepare masked tokens inputs/labels for masked language modeling: 80% MASK, 10% random, 10% original.
        """
        labels = inputs.clone()
        # We sample a few tokens in each sequence for MLM training (with probability `self.mlm_probability`)
        probability_matrix = torch.full(labels.size(), self.mlm_probability)
        if special_tokens_mask is None:
            special_tokens_mask = [
                self.tokenizer.get_special_tokens_mask(val, already_has_special_tokens=True) for val in labels.tolist()
            ]
            special_tokens_mask = torch.tensor(special_tokens_mask, dtype=torch.bool)
        else:
            special_tokens_mask = torch.tensor(special_tokens_mask, dtype=torch.bool)
            #special_tokens_mask = special_tokens_mask.bool()

        #print(special_tokens_mask.size())
        probability_matrix.masked_fill_(special_tokens_mask, value=0.0)
        masked_indices = torch.bernoulli(probability_matrix).bool()
        labels[~masked_indices] = -100  # We only compute loss on masked tokens

        # 80% of the time, we replace masked input tokens with tokenizer.mask_token ([MASK])
        indices_replaced = torch.bernoulli(torch.full(labels.size(), 0.8)).bool() & masked_indices
        inputs[indices_replaced] = self.mask

        # 10% of the time, we replace masked input tokens with random word
        indices_random = torch.bernoulli(torch.full(labels.size(), 0.5)).bool() & masked_indices & ~indices_replaced
        random_words = torch.randint(len(self.char2id.keys()), labels.size(), dtype=torch.long)
        inputs[indices_random] = random_words[indices_random]

        # The rest of the time (10% of the time) we keep the masked input tokens unchanged
        return inputs, labels
    def pack_tensors(self, tokens):
        array_ids = self.encoder(tokens)
        array =  torch.nn.utils.rnn.pad_sequence(array_ids, batch_first=True, padding_value=self.pad)
        lengths = (array!=self.pad).sum(dim=-1)
        #Bert tokenization
        special_token_mask = [list(map(lambda x: 1 if x in [self.bos, self.eos, self.pad] else 0, stuff)) for stuff in array.tolist()]
        masked_array, masked_labels = self.mask_tokens(array, special_token_mask)
        return masked_array, masked_labels, array_ids, lengths
    def process(self, text):
        arrays = []
        lengths = []
        targets = []
        arrays_ids = []
        for tokens in self.process_text(text):
            if len(tokens) > 0:
                array, target, array_ids, lgt = self.pack_tensors(tokens)
                arrays.append(array)
                targets.append(target)
                arrays_ids.append(array_ids)
                lengths.append(lgt)
        return arrays, targets, arrays_ids, lengths

if __name__ == '__main__':

    text_encoder = Encoder()