#!/usr/local/bin/python3 # avenir-python: Machine Learning # Author: Pranab Ghosh # # Licensed under the Apache License, Version 2.0 (the "License"); you # may not use this file except in compliance with the License. You may # obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or # implied. See the License for the specific language governing # permissions and limitations under the License. import os import sys from random import randint import random import time from datetime import datetime import re, string, unicodedata import spacy import torch from collections import defaultdict import pickle import numpy as np import re from sentence_transformers import CrossEncoder sys.path.append(os.path.abspath("../lib")) from util import * from mlutil import * """ neural language model """ class NeuralLangModel(object): def __init__(self): """ initialize """ self.dexts = None def loadDocs(self, fpaths): """ loads documents from one file """ fPaths = fpaths.split(",") if len(fPaths) == 1: if os.path.isfile(fPaths[0]): #one file print("got one file from path") dnames = fpaths docStr = getOneFileContent(fPaths[0]) dtexts = [docStr] else: #all files under directory print("got all files under directory from path") dtexts, dnames = getFileContent(fPaths[0]) print("found following files") for dt, dn in zip(dtexts, dnames): print(dn + "\t" + dt[:40]) else: #list of files print("got list of files from path") dnames = fpaths dtexts = list(map(getOneFileContent, fpaths)) ndocs = (dtexts, dnames) return ndocs #Encoded doc class EncodedDoc: def __init__(self, dtext, dname, drank=None): """ initialize """ self.dtext = dtext self.dname = dname self.drank = drank self.denc = None self.score = None def encode(self, nlp): """ encode """ self.denc = nlp(self.dtext) #similarity at token and sentence level for BERT encoding class SemanticSearch: def __init__(self, docs=None): """ initialize """ print("loading BERT transformer model") self.nlp = spacy.load("en_trf_bertbaseuncased_lg") self.docs = docs if docs is not None else list() def docAv(self,qu, doc): """ whole doc similarity """ return qu.similarity(doc) def tokSimAv(self, qu, doc): """ token pair wise average """ qts = simAll(qu, doc) asi = numpy.mean(qts) return asi def tokSimMed(self, qu, doc): """ token pair wise average """ qts = simAll(qu, doc) asi = numpy.median(qts) return asi def tokSimMax(self, qu, doc): """ token pair wise max (tsma) """ qte = self. __getTensor(qu) dte = self. __getTensor(doc) return self.simMax(qte, dte) def tokSimAvMax(self, qu, doc): """ token max then average (tsavm) """ qte = self. __getTensor(qu) dte = self. __getTensor(doc) return self.simAvMax(qte, dte) def tokSimMaxAv(self, qu, doc): """ token average and then max """ qte = self. __getTensor(qu) dte = self. __getTensor(doc) return self.simMaxAv(qte, dte) def sentSimAv(self, qu, doc): """ sentence wise average """ qse, dse = self.__sentEnc(qu, doc) sims = self.simAll(qse, dse) return numpy.mean(sims) def sentSimMed(self, qu, doc): """ sentence wise average (ssma) """ qse, dse = self.__sentEnc(qu, doc) sims = self.simAll(qse, dse) return numpy.median(sims) def sentSimMax(self, qu, doc): """ sentence wise average (ssma) """ qse, dse = self.__sentEnc(qu, doc) sims = self.simAll(qse, dse) return numpy.maximum(sims) def sentSimAvMax(self, qu, doc): """ sentence max then average (tsavm) """ qse, dse = self.__sentEnc(qu, doc) return self.simAvMax(qse, dse) def sentSimMaxAv(self, qu, doc): """ sentence average and then max """ qse, dse = self.__sentEnc(qu, doc) return self.simMaxAv(qse, dse) def simMax(self, qte, dte): """ max similarity between 2 elements """ msi = 0 for qt in qte: for dt in dte: si = cosineSimilarity(qt, dt) if not math.isnan(si) and si > msi: msi = si return msi def simAvMax(self, qte, dte): """ max then average (tsavm) """ qts = list() for qt in qte: msi = 0 for dt in dte: si = cosineSimilarity(qt, dt) if not math.isnan(si) and si > msi: msi = si qts.append(msi) amsi = numpy.mean(numpy.array(qts)) return amsi def simMaxAv(self, lqe, lde): """ average and then max """ masi = 0 for qe in lqe: qes = list() for de in lde: si = cosineSimilarity(qe, de) if not math.isnan(si): qes.append(si) av = numpy.mean(numpy.array(qes)) if av > masi: masi = av return masi def simAll(self, lqe, lde): """ all similarity """ qes = list() for qe in lqe: for de in lde: si = cosineSimilarity(qe, de) if not math.isnan(si): qes.append(si) return numpy.array(qes) def __sentEnc(self, qu, doc): """ sentence encoding for query and doc """ qstr = qu._.trf_word_pieces_ qte = zip(qstr, qu._.trf_last_hidden_state) qse = list() for t, v in qte: if t == "[CLS]": qse.append(v) dstr = doc._.trf_word_pieces_ dte = zip(dstr, doc._.trf_last_hidden_state) dse = list() for t, v in dte: if t == "[CLS]": dse.append(v) enp = (numpy.array(qse), numpy.array(dse)) return enp def __getTensor(self, toks): """ tensors from tokens """ return list(map(lambda t: t.tensor, toks)) def addDocs(self, docs): """ add named doc content """ self.docs.extend(docs) def loadDocs(self, fpaths): """ loads documents from one file """ fPaths = fpaths.split(",") if len(fPaths) == 1: if os.path.isfile(fPaths[0]): #one file print("one file") dnames = fpaths docStr = getOneFileContent(fPaths[0]) dtexts = [docStr] else: #all files under directory print("all files under directory") dtexts, dnames = getFileContent(fPaths[0]) print("found following files") for dt, dn in zip(dtexts, dnames): print(dn + "\t" + dt[:40]) else: #list of files print("list of files") dnames = fpaths dtexts = list(map(getOneFileContent, fpaths)) docs = list(map(lambda dtext, dname : EncodedDoc(dtext, dname), zip(dtexts, dnames))) self.docs.extend(docs) def search(self, qstr, algo, gdranks=None): """ tensors from tokens """ qv = self.nlp(qstr) res = list() for d in self.docs: dn = d.dname if d.denc == None: d.encode(self.nlp) dv = d.denc if algo == "ds": si = self.docAv(qv, dv) elif algo == "tsa": si = self.tokSimAv(qv, dv) elif algo == "tsme": si = self.tokSimMed(qv, dv) elif algo == "tsma": si = self.tokSimMax(qv, dv) elif algo == "tsavm": si = self.tokSimAvMax(qv, dv) elif algo == "tsmav": si = self.tokSimMaxAv(qv, dv) elif algo == "ssa": si = self.sentSimAv(qv, dv) elif algo == "ssme": si = self.sentSimMed(qv, dv) elif algo == "ssma": si = self.sentSimMax(qv, dv) elif algo == "ssavm": si = self.sentSimAvMax(qv, dv) elif algo == "ssmav": si = self.sentSimMaxAv(qv, dv) else: si = -1.0 print("invalid semilarity algo") #print("{} score {:.6f}".format(dn, si)) d.score = si r = (dn, si) res.append(r) #search score for each document res.sort(key=lambda r : r[1], reverse=True) print("\nsorted search result") print("query: {} matching algo: {}".format(qstr, algo)) for r in res: print("{} score {:.3f}".format(r[0], r[1])) #rank order if gold truuth rank provided if gdranks is not None: i = 0 count = 0 for d in gdranks: while i < len(gdranks): if d == res[i][0]: count += 1 i += 1 break; i += 1 ro = count / len(gdranks) print("rank order {:.3f}".format(ro)) #similarity at passage or paragraph level using sbertcross encoder class SemanticSimilaityCrossEnc(NeuralLangModel): def __init__(self, docs=None): self.dparas = None self.scores = None print("loading cross encoder") self.model = CrossEncoder("cross-encoder/ms-marco-TinyBERT-L-2") print("done loading cross encoder") super(NeuralLangModel, self).__init__() def paraSimilarity(self, dtext, fpaths, minParNl=1): """ returns paragarph pair similarity across 2 documents """ dtexts, dnames = self.loadDocs(fpaths) if dtext is None: assertEqual(len(dtexts), 2, "exactly 2 files needed") self.dtexts = dtexts else: assertEqual(len(dtexts), 1, "exactly 1 file needed") self.dtexts = list() self.dtexts.append(dtext) self.dtexts.append(dtexts[0]) self.dparas = list() for text in self.dtexts: regx = "\n+" if minParNl == 1 else "\n{2,}" paras = re.split(regx, text.replace("\r\n", "\n")) print("no of paras {}".format(len(paras))) self.dparas.append(paras) tinp = list() for para1 in self.dparas[0]: inp = list(map(lambda para2: [para1, para2], self.dparas[1])) tinp.extend(inp) print("input shape " + str(np.array(tinp).shape)) scores = self.model.predict(tinp) print("score shape " + str(np.array(scores).shape)) #assertEqual(len(scores), len(self.dparas[0]) * len(self.dparas[1]), "no of scores don't match no of paragraph pairs") print(scores) i = 0 print("text paragraph pair wise similarity") for para1 in self.dparas[0]: for para2 in self.dparas[1]: print("first: {}\t second: {}\t score: {:.6f}".format(para1[:20], para2[:20], scores[i])) i += 1 self.scores = scores def avMaxScore(self): """ """ pass def ner(text, nlp): #nlp = spacy.load("en_core_web_md") doc = nlp(text) for ent in doc.ents: print(ent.text, ent.start_char, ent.end_char, ent.label_)