tmnt 0.7.54b20240817__py3-none-any.whl → 0.7.56__py3-none-any.whl

tmnt/data_loading.py

@@ -41,13 +41,14 @@ llm_catalog = {
     'allenai/scibert_scivocab_uncased': (AutoTokenizer.from_pretrained, AutoModel.from_pretrained),
     'johngiorgi/declutr-sci-base': (AutoTokenizer.from_pretrained, AutoModel.from_pretrained),
     'BAAI/bge-base-en-v1.5': (AutoTokenizer.from_pretrained, AutoModel.from_pretrained),
-    'pritamdeka/BioBERT-mnli-snli-scinli-scitail-mednli-stsb': (AutoTokenizer.from_pretrained, AutoModel.from_pretrained)
-    ## add more model options here if desired
+    'pritamdeka/BioBERT-mnli-snli-scinli-scitail-mednli-stsb': (AutoTokenizer.from_pretrained, AutoModel.from_pretrained),
+    'Alibaba-NLP/gte-base-en-v1.5': (AutoTokenizer.from_pretrained, AutoModel.from_pretrained)
+    ## add more model options here ...
     }
 
 def get_llm(model_name):
     tok_fn, model_fn = llm_catalog.get(model_name, ((AutoTokenizer.from_pretrained, AutoModel.from_pretrained)))
-    return tok_fn(model_name), model_fn(model_name)
+    return tok_fn(model_name), model_fn(model_name, trust_remote_code=True)
 
 def get_llm_tokenizer(model_name):
     tok_fn, model_fn = llm_catalog.get(model_name, ((AutoTokenizer.from_pretrained, AutoModel.from_pretrained)))    
@@ -55,7 +56,7 @@ def get_llm_tokenizer(model_name):
 
 def get_llm_model(model_name):
     tok_fn, model_fn = llm_catalog.get(model_name, ((AutoTokenizer.from_pretrained, AutoModel.from_pretrained)))        
-    return model_fn(model_name)
+    return model_fn(model_name, trust_remote_code=True)
 
 def get_unwrapped_llm_dataloader(data, bow_vectorizer, llm_name, label_map, batch_size, max_len, shuffle=False, device='cpu'):
     label_pipeline = lambda x: label_map.get(x, 0)

tmnt/estimator.py

@@ -285,16 +285,11 @@ class BaseBowEstimator(BaseEstimator):
                 logging.error("File {} does not appear to be a valid vocabulary file".format(vocabulary))
                 raise Exception("Invalid Json Configuration File")            
             vocabulary = torchtext.vocab.vocab(voc_js)
-        #if vocabulary['embedding'] is not None:
-        if False:
-            raise Exception("Pre-trained embeddings not yet (re-)supported")
-            #emb_size = vocabulary['embedding'].idx_to_vec[0].size
-        else:
-            emb_size = config['embedding'].get('size')
-            if not emb_size:
-                emb_size = config['derived_info'].get('embedding_size')
-            if not emb_size:
-                raise Exception("Embedding size must be provided as the 'size' attribute of 'embedding' or as 'derived_info.embedding_size'")
+        emb_size = config['embedding'].get('size')
+        if not emb_size:
+            emb_size = config['derived_info'].get('embedding_size')
+        if not emb_size:
+            raise Exception("Embedding size must be provided as the 'size' attribute of 'embedding' or as 'derived_info.embedding_size'")
         gamma = config.get('gamma', 1.0)
         multilabel = config.get('multilabel', False)
         lr = config['lr']
@@ -781,12 +776,6 @@ class BowMetricEstimator(BowEstimator):
     def _get_model(self, bow_size=-1):
         if self.embedding_source != 'random':
             e_type, e_name = tuple(self.embedding_source.split(':'))
-            #pt_embedding = nlp.embedding.create(e_type, source=e_name)
-            #self.vocabulary.set_embedding(pt_embedding)
-            #emb_size = len(self.vocabulary.embedding.idx_to_vec[0])
-            #for word in self.vocabulary.embedding._idx_to_token:
-            #    if (self.vocabulary.embedding[word] == mx.nd.zeros(emb_size)).sum() == emb_size:
-            #        self.vocabulary.embedding[word] = mx.nd.random.normal(0, 0.1, emb_size)
         else:
             emb_size = self.embedding_size
         model = \
@@ -1030,7 +1019,6 @@ class SeqBowEstimator(BaseEstimator):
         tr_bow_counts = self._get_bow_wd_counts(train_data)
         model.initialize_bias_terms(tr_bow_counts)
         if self.npmi_matrix is not None:
-            print("****** INITIALIZING NPMI LOSS FUNCTION *******")
             model.initialize_npmi_loss(self.npmi_matrix)
         return model
         
@@ -1057,7 +1045,6 @@ class SeqBowEstimator(BaseEstimator):
         else:
             config['latent_distribution'] = {'dist_type':'gaussian'}
         config['epochs'] = self.epochs
-        #config['embedding_source'] = self.embedding_source
         config['gamma'] = self.gamma
         config['warmup_ratio'] = self.warmup_ratio
         config['llm_model_name'] = self.llm_model_name
@@ -1091,9 +1078,6 @@ class SeqBowEstimator(BaseEstimator):
                   log_interval, epoch_id, learning_rate):
         """Generate and print out the log message for training. """
         if self.has_classifier:
-            #metric_nm, metric_val = self.metric.compute()
-            #if not isinstance(metric_nm, list):
-            #    metric_nm, metric_val = [metric_nm], [metric_val]
             metric_nm = "AUPRC"
             try:
                 metric_val = self.metric.compute()
@@ -1126,7 +1110,6 @@ class SeqBowEstimator(BaseEstimator):
         rows = 0
         for i, data in enumerate(dataloader):
             seqs, = data
-            #bow_batch = list(seqs[3].squeeze(axis=1))
             bow_batch = list(seqs[3])
             rows += len(bow_batch)
             if i >= max_rows:
@@ -1170,10 +1153,7 @@ class SeqBowEstimator(BaseEstimator):
             label_ls = label_ls.mean()
             total_ls = (self.gamma * label_ls) + elbo_ls.mean()
             if not self.multilabel:
-                #label_ind = label.argmax(dim=0)
-                #self.metric.update([out], [label_ind])
                 self.metric.update(torch.tensor(out), torch.tensor(label))
-                #self.metric.update(torch.Tensor([out]), torch.Tensor([label_ind]))
             else:
                 self.metric.update([out], [label])
         else:
@@ -1214,7 +1194,6 @@ class SeqBowEstimator(BaseEstimator):
         joint_loader = PairedDataLoader(train_data, aux_data)
         num_train_steps = len(joint_loader) * self.epochs
 
-        ## The following from HuggingFace trainer.py lines 1047 to 1063
         decay_parameters = get_parameter_names(model.llm, ALL_LAYERNORM_LAYERS)
         decay_parameters = [name for name in decay_parameters if "bias" not in name]
         non_llm_parameters = [name for name,_ in model.named_parameters() if not name.startswith("llm")]
@@ -1288,10 +1267,8 @@ class SeqBowEstimator(BaseEstimator):
                 if aux_batch is not None:
                     update_loss_details(total_ls_2, elbo_ls_2, red_ls_2, None)
                     
-                #debug
-
                 if not accumulate or (batch_id + 1) % accumulate == 0:
-                    #torch.nn.utils.clip_grad.clip_grad_value_(model.llm.parameters(), 1.0)
+                    torch.nn.utils.clip_grad.clip_grad_value_(model.llm.parameters(), 1.0)
                     optimizer.step()
                     dec_optimizer.step()
                     lr_scheduler.step()

tmnt/eval_npmi.py

@@ -115,6 +115,25 @@ class EvaluateNPMI(object):
                 npmi = (log10(n_docs) + log10(bigram_cnt) - log10(unigram_1) - log10(unigram_2)) / (log10(n_docs) - log10(bigram_cnt) + 1e-4)
             npmi_matrix[w1, w2] = npmi
         return npmi_matrix
+    
+class EvaluateNPMIUmass(object):
+
+    def __init__(self, npmi_matrix: np.array, vectorizer: TMNTVectorizer):
+        self.vectorizer = vectorizer
+        self.npmi_matrix = npmi_matrix # by convention this will be lower-triangular
+        dim = npmi_matrix.shape[0]
+        for mc in range(self.npmi_matrix.shape[0]):
+            for i in range(mc+1,dim):
+                self.npmi_matrix[mc,i] = self.npmi_matrix[i,mc]
+    
+    def evaluate_topics(self, topic_ids):
+        npmi_score = 0.0
+        total_size = len(topic_ids) * len(topic_ids[0])
+        for topic in topic_ids:
+            for (w1, w2) in combinations(topic):
+                npmi_score += self.npmi_matrix[w1, w2]
+        return npmi_score / total_size
+
 
 
 class FullNPMI(object):

{tmnt-0.7.54b20240817.dist-info → tmnt-0.7.56.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tmnt
-Version: 0.7.54b20240817
+Version: 0.7.56
 Summary: Topic modeling neural toolkit
 Home-page: https://github.com/mitre/tmnt.git
 Author: The MITRE Corporation

{tmnt-0.7.54b20240817.dist-info → tmnt-0.7.56.dist-info}/RECORD

@@ -1,9 +1,9 @@
 tmnt/__init__.py,sha256=EPNq1H7UMyMewWT_zTGBaC7ZouvCywX_gMX4G1dtmvw,250
 tmnt/configuration.py,sha256=P8PEhzVPKO5xG0FrdTLRQ60OYWigbzPY-OSx_hzQlrY,10054
-tmnt/data_loading.py,sha256=A0tsM6x61BGhYBV6rAYdryz2NwbR__8EAYj_Q4Z-DCs,18736
+tmnt/data_loading.py,sha256=vsAMyHGi3fuOFDmqo_zenNKOtVQiuqMHA-iPYWYpGKE,18873
 tmnt/distribution.py,sha256=Pmyc5gwDd_-jP7vLVb0vdNQaSSvF1EuiTZEWg3KfmI8,10866
-tmnt/estimator.py,sha256=bPyLx4rmVe4mC9ciEq7uluONTD2y1enUluAkmw-TPBI,69095
-tmnt/eval_npmi.py,sha256=DTW9dNHVe6H57gndQIZ4gX9EghuBstwznA3YBqILJk0,5820
+tmnt/estimator.py,sha256=htQ_JeUedEYWLPIBDbDhEL5deWtHiVNRKQN1528SybY,67751
+tmnt/eval_npmi.py,sha256=8S-IE-bEhtQofF6oKeXs7oaUeu-7yDlaEqjMj52gmNQ,6549
 tmnt/inference.py,sha256=da8qAnjTDTuWQfPEOQewOfgikqE00XT1xGMiO2mckI4,15679
 tmnt/modeling.py,sha256=O1V7ppU7J6pvESTvdEoV9BXbEF4Z-J1OHnRtszuagaA,29956
 tmnt/preprocess/__init__.py,sha256=gwMejkQrnqKS05i0JVsUru2hDUR5jE1hKC10dL934GU,170
@@ -17,9 +17,9 @@ tmnt/utils/ngram_helpers.py,sha256=VrIzou2oQHCLBLSWODDeikN3PYat1NqqvEeYQj_GhbA,1
 tmnt/utils/pubmed_utils.py,sha256=3sHwoun7vxb0GV-arhpXLMUbAZne0huAh9xQNy6H40E,1274
 tmnt/utils/random.py,sha256=qY75WG3peWoMh9pUyCPBEo6q8IvkF6VRjeb5CqJOBF8,327
 tmnt/utils/recalibrate.py,sha256=TmpB8An8bslICZ13UTJfIvr8VoqiSedtpHxec4n8CHk,1439
-tmnt-0.7.54b20240817.dist-info/LICENSE,sha256=qFZJrfJ7Zi4IXDiyiGVrHWic_l1h2tc36tI8Z7rK9bs,11356
-tmnt-0.7.54b20240817.dist-info/METADATA,sha256=zhqLOFFBySECnzwDqy9n-QrmJNxWqUk8IPCGqJkK3RY,1445
-tmnt-0.7.54b20240817.dist-info/NOTICE,sha256=p0kYIVAkReTFaGb4C-qPa7h5ztze6hGzOpjCMMbOipU,425
-tmnt-0.7.54b20240817.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-tmnt-0.7.54b20240817.dist-info/top_level.txt,sha256=RpYgUl187sXnqmiwKjZZdcDlHz2AALs6bGdUcukyd_E,5
-tmnt-0.7.54b20240817.dist-info/RECORD,,
+tmnt-0.7.56.dist-info/LICENSE,sha256=qFZJrfJ7Zi4IXDiyiGVrHWic_l1h2tc36tI8Z7rK9bs,11356
+tmnt-0.7.56.dist-info/METADATA,sha256=jk7-JlrqxLTACr0LsMoLGXT0nq0VVQIkWFoFNqYlEPE,1436
+tmnt-0.7.56.dist-info/NOTICE,sha256=p0kYIVAkReTFaGb4C-qPa7h5ztze6hGzOpjCMMbOipU,425
+tmnt-0.7.56.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+tmnt-0.7.56.dist-info/top_level.txt,sha256=RpYgUl187sXnqmiwKjZZdcDlHz2AALs6bGdUcukyd_E,5
+tmnt-0.7.56.dist-info/RECORD,,

{tmnt-0.7.54b20240817.dist-info → tmnt-0.7.56.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.2.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any