Add summary module

.gitignore

@@ -1,2 +1,2 @@
 *__pycache__*
-*pyc
+*.pyc

app.py

@@ -1,8 +1,10 @@
+from logging import PlaceHolder
 import gradio as gr
 import os
 from npc_bert_models.gradio_demo import *
 from npc_bert_models.mlm_module import NpcBertMLM
 from npc_bert_models.cls_module import NpcBertCLS
+from npc_bert_models.summary_module import NpcBertGPT2
 import json
 
 
@@ -72,6 +74,43 @@ class main_window():
             btn.click(fn=self.npc_cls.__call__, inputs=inp, outputs=out)
             inp.submit(fn=self.npc_cls.__call__, inputs=inp, outputs=out)
         
+        #! Initialize report conclusion generation
+        self.npc_summary = NpcBertGPT2()
+        self.npc_summary.load()
+        
+        with gr.Blocks() as self.summary_interface:
+            gr.Markdown("""
+                        # Report conclusion generation
+                        
+                        In this example we explored how the fine-tunned BERT can aid summarizing the reported items and 
+                        generates a conclusion, which includes providing stages of the written reports. 
+                        
+                        # Disclaimer
+                        
+                        Again, similar to the last experiement, the examples we list here are mock reports that are created
+                        with reference to authentic reports and they do not represent any real patients. We essentiall used
+                        the same reports as the last tab, but cropped away the "conclusion" part which we trian the network 
+                        to generate.
+                        
+                        """)
+        
+            with gr.Row():
+                with gr.Column():
+                    inp = gr.TextArea(placeholder="Use examples at the bottom to load example text reports.")
+                    inf = gr.File(file_types=['.txt'], label="Report file (plaintext)", show_label=True, interactive=True)
+                    inf.upload(fn=self._set_report_file_helper, inputs=inf, outputs=inp)
+                    inf.change(fn=self._set_report_file_helper, inputs=inf, outputs=inp)
+                    btn = gr.Button("Run", variant='primary')
+                    
+
+                with gr.Column():
+                    out = gr.TextArea(placeholder="Conclusion is generated here", interactive=False)
+        
+            gr.Examples(examples="./report_examples_summary", inputs=inf)
+            btn.click(fn=self.npc_summary.__call__, inputs=inp, outputs=out)
+            inp.submit(fn=self.npc_summary.__call__, inputs=inp, outputs=out)
+            
+        #! Create tab interface
         with gr.Blocks() as self.interface:
             gr.Markdown("""
                         # Introduction 
@@ -94,7 +133,8 @@ class main_window():
                         This software is provided as is and it is not a clinically validated software. The authors disclaim any responsibility
                         arising as a consequence from using this demo. 
                         """)
-            tabs = gr.TabbedInterface([self.mlm_interface, self.cls_interface], tab_names=["Masked Language Model", "Report classification"])
+            tabs = gr.TabbedInterface([self.mlm_interface, self.cls_interface, self.summary_interface], 
+                                      tab_names=["Masked Language Model", "Report classification", "Report conclusion generation"])     
 
     def lauch(self):
         self.interface.launch()

models/npc-bert-gpt2-best/added_tokens.json

@@ -0,0 +1,3 @@
+{
+  "[BOS]": 5744
+}

models/npc-bert-gpt2-best/config copy.json

@@ -0,0 +1,186 @@
+{
+  "architectures": [
+    "EncoderDecoderModel"
+  ],
+  "decoder": {
+    "_name_or_path": "openai-community/gpt2",
+    "activation_function": "gelu_new",
+    "add_cross_attention": true,
+    "architectures": [
+      "GPT2LMHeadModel"
+    ],
+    "attn_pdrop": 0.1,
+    "bad_words_ids": null,
+    "begin_suppress_tokens": null,
+    "bos_token_id": 50256,
+    "chunk_size_feed_forward": 0,
+    "cross_attention_hidden_size": null,
+    "decoder_start_token_id": 5744,
+    "diversity_penalty": 0.0,
+    "do_sample": false,
+    "early_stopping": false,
+    "embd_pdrop": 0.1,
+    "encoder_no_repeat_ngram_size": 0,
+    "eos_token_id": 50256,
+    "exponential_decay_length_penalty": null,
+    "finetuning_task": null,
+    "forced_bos_token_id": null,
+    "forced_eos_token_id": null,
+    "id2label": {
+      "0": "LABEL_0",
+      "1": "LABEL_1"
+    },
+    "initializer_range": 0.02,
+    "is_decoder": true,
+    "is_encoder_decoder": false,
+    "label2id": {
+      "LABEL_0": 0,
+      "LABEL_1": 1
+    },
+    "layer_norm_epsilon": 1e-05,
+    "length_penalty": 1.0,
+    "max_length": 20,
+    "min_length": 0,
+    "model_type": "gpt2",
+    "n_ctx": 1024,
+    "n_embd": 768,
+    "n_head": 12,
+    "n_inner": null,
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+    "no_repeat_ngram_size": 0,
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+    "output_attentions": false,
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+    "output_scores": false,
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+    "prefix": null,
+    "problem_type": null,
+    "pruned_heads": {},
+    "remove_invalid_values": false,
+    "reorder_and_upcast_attn": false,
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+    "return_dict": true,
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+    "summary_activation": null,
+    "summary_first_dropout": 0.1,
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+    "summary_type": "cls_index",
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+    "task_specific_params": {
+      "text-generation": {
+        "do_sample": true,
+        "max_length": 50
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+    },
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+    "typical_p": 1.0,
+    "use_bfloat16": false,
+    "use_cache": true,
+    "vocab_size": 50257
+  },
+  "decoder_start_token_id": 2,
+  "encoder": {
+    "_name_or_path": "gradio_demo/models/npc-bert-cls",
+    "add_cross_attention": false,
+    "architectures": [
+      "BertForSequenceClassification"
+    ],
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+    "hidden_act": "gelu",
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+    "hidden_size": 768,
+    "id2label": {
+      "0": "Benign/Healthy",
+      "1": "NPC",
+      "2": "Unknown/Out of Domain"
+    },
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+    "is_decoder": false,
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+      "NPC": 1,
+      "Unknown/Out of Domain": 2
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+    "length_penalty": 1.0,
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+    "max_position_embeddings": 512,
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+    "model_type": "bert-generation",
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+    "num_attention_heads": 12,
+    "num_beam_groups": 1,
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+    "num_hidden_layers": 12,
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+    "problem_type": "single_label_classification",
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+  "torch_dtype": "float32",
+  "transformers_version": "4.37.2",
+  "vocab_size": 50257
+}

models/npc-bert-gpt2-best/config.json

@@ -0,0 +1,186 @@
+{
+  "architectures": [
+    "EncoderDecoderModel"
+  ],
+  "decoder": {
+    "_name_or_path": "openai-community/gpt2",
+    "activation_function": "gelu_new",
+    "add_cross_attention": true,
+    "architectures": [
+      "GPT2LMHeadModel"
+    ],
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+    "early_stopping": false,
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+    "eos_token_id": 50256,
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+    "finetuning_task": null,
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+    "id2label": {
+      "0": "LABEL_0",
+      "1": "LABEL_1"
+    },
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+    "is_decoder": true,
+    "is_encoder_decoder": false,
+    "label2id": {
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+    "layer_norm_epsilon": 1e-05,
+    "length_penalty": 1.0,
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+    "min_length": 0,
+    "model_type": "gpt2",
+    "n_ctx": 1024,
+    "n_embd": 768,
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+  },
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+  "encoder": {
+    "_name_or_path": "gradio_demo/models/npc-bert-cls",
+    "add_cross_attention": false,
+    "architectures": [
+      "BertForSequenceClassification"
+    ],
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+    "model_type": "bert-generation",
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+    "problem_type": "single_label_classification",
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+}

models/npc-bert-gpt2-best/generation_config copy.json

@@ -0,0 +1,7 @@
+{
+  "_from_model_config": true,
+  "bos_token_id": 50256,
+  "decoder_start_token_id": 5744,
+  "eos_token_id": 50256,
+  "transformers_version": "4.37.2"
+}

models/npc-bert-gpt2-best/generation_config.json

@@ -0,0 +1,7 @@
+{
+  "_from_model_config": true,
+  "bos_token_id": 50256,
+  "decoder_start_token_id": 5744,
+  "eos_token_id": 50256,
+  "transformers_version": "4.37.2"
+}

models/npc-bert-gpt2-best/model copy.safetensors

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models/npc-bert-gpt2-best/model.safetensors

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models/npc-bert-gpt2-best/special_tokens_map.json

@@ -0,0 +1,51 @@
+{
+  "bos_token": {
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+    "lstrip": false,
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+}

models/npc-bert-gpt2-best/tokenizer_config.json

@@ -0,0 +1,67 @@
+{
+  "added_tokens_decoder": {
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+  "unk_token": "[UNK]"
+}

models/npc-bert-gpt2-best/vocab.txt

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+[PAD]
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+%
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++
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+##x16x18mm
+turcica
+difficulty
+postero
+posteromedial
+##ternoon
+undisrup
+prof
+proves
+proximity
+continue
+continues
+shortly
+pls
+platysm
+placed
+jugulodiag
+relativ
+retains
+tin0m0
+tinnit
+tin1tumour
+evaluated
+conglomerations
+occurs
+contained
+discussion
+discontinuity
+moderately
+10cm
+10x2
+1001
+10x11mm
+event
+striations
+strands
+##x24mm
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+##x23x26mm
+##x26x1
+##x28x3
+incidenal
+incidentally
+pharyngo
+perforation
+1201
+12x11mm
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+12x13x1
+formation
+formamina
+scfs
+icas
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+mottling
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+mechan
+ace
+acessory
+compare
+comparing
+comparatively
+compartment
+equivocally
+inside
+insuff
+insinuate
+##×25×3
+##×20×1
+##regate
+obstrcuted
+3n2
+##×37×2
+cords
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+11cm
+11x10mm
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+raised
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+13cm
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+denervated
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+grade
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+t4n3dis
+checked
+##×15
+##×17×2
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+4n1m0
+4n3m
+goiter
+meninges
+mastication
+replaces
+##omalacic
+developed
+development
+1801
+18x24mm
+mets
+anterosuperior
+anteroinferior
+anterolisthesis
+anteriosuperior
+encroaching
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+##ephalic
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+cisternal
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+structure
+structural
+22x12x2
+22×37×2
+20x26mm
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+2005
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+coexisting
+emphy
+ijc
+osteoma
+osteopenia
+osteometal
+separating
+lns1
+sellae
+basion
+basis
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+ostium
+##artment
+prelaryngeal
+antra
+confirmation
+2n1
+2n3m0
+colli
+later
+ser13
+##×45×3
+pathway
+pathological
+combination
+tracheoes
+tracheostomy
+questioned
+aforem
+afternoon
+block
+bloom
+required
+deviating
+prolapses
+effaces
+effacing
+attachment
+attached
+indicates
+removal
+chemo
+chemort
+valleculae
+14cm
+14x10mm
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+9x7mm
+hamper
+macrosc
+molars
+osterior
+ossification
+wider
+widely
+widened
+##neys
+##tsxcc
+##pressive
+encephalomalacic
+ulcerative
+benefit
+17cm
+1704
+1998
+7x5
+7x4
+7x5mm
+7x8mm
+8x15mm
+epistax
+joints
+pulse
+##ixon
+##omedullary
+depending
+dependent
+department
+adds
+comments
+t2n12m0
+10x6mm
+10x7mm
+10x9x10mm
+needle
+insertions
+inserted
+destroy
+intermingled
+tracheaa
+dysprax
+pneumatised
+pneumatisation
+convincingly
+25x18mm
+25x26x1
+2x1x1
+9x1cm
+9x15mm
+buy
+forearm
+radical
+radiation
+rays
+meati
+##isions
+thalami
+t2bn3
+determined
+contours
+contouring
+obscures
+tsxapxcc
+##ologically
+16x11mm
+16x18mm
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+16x16x18mm
+6x4
+6x4mm
+6x7mm
+6x9mm
+6x5cm
+breaches
+breached
+esrf
+odes
+pedicle
+##aky
+referring
+retrophx
+retropharngeal
+retrophayr
+retrophargye
+retrophayngeal
+define
+accountable
+indeterminent
+t1n3m1
+contents
+favors
+laryngo
+coalesce
+coalescing
+ballooned
+obscured
+penetration
+transependymal
+1x0
+1x4
+1x6
+270
+27x22x2
+27×17×3
+5x6
+5x5mm
+5x6mm
+6x2mm
+6x3mm
+8x5mm
+aorta
+boundary
+csi
+csae
+calvar
+creeping
+ocular
+occluded
+occlude
+occluder
+synch
+systemic
+team
+teeth
+times
+×21
+##ched
+##5×35
+leptomeninges
+propensity
+apxtsxcc
+paranasopharynx
+shadow
+histologically
+fronds
+impinge
+aggregate
+erode
+eroded
+weeks
+blurred
+radiating
+radiata
+homogenously
+essential
+pedunculated
+centering
+34×17×2
+bifrontal
+eyeball
+herniation
+morphologically
+nuclei
+ptergopalatine
+sockets
+tapering
+visible
+injury
+nasopharngeal
+nasophayr
+nasopharyx
+relevance
+concavity
+scalp
+streaky
+abscess
+lymphoadenopathy
+setting
+settled
+fragments
+fragmented
+superolaterally
+rectum
+repeated
+projections
+plaques
+12x8mm
+t4n3bm
+t4n3bm1
+2021
+covering
+micropap
+microhaem
+protrusions
+engulfing
+decrease
+decreased
+decreasing
+coalescent
+calcification
+variable
+protuberans
+hypermetabolism
+outpouchings
+0x0
+0x4
+1n1m0
+1n3m0
+15x11mm
+23x13mm
+23x11x2
+41x28x3
+5×5×4
+aug13
+coli
+colon
+foarm
+foreman
+fasica
+fashion
+filed
+films
+know
+knife
+ome
+premedullary
+premaxillary
+pocket
+pockets
+passes
+passing
+quite
+query
+##iocephalic
+interna
+internatal
+congested
+congestive
+choroidal
+stenosis
+stenosed
+prevent
+channels
+arrange
+arranged
+probabale
+probabaly
+comprised
+compromises
+supraclinoid
+supraclaviv
+##sema
+##seminated
+brachial
+brachiocephalic
+intracanalicular
+undergo
+undergone
+13x10x1
+13x19x2
+avidly
+replacement
+3mmx4mm
+3mmx6mm
+coiling
+courses
+coursing
+limbs
+attenuated
+attenuation
+intermuscular
+intermusclar
+homogeneously
+decompression
+decompressive
+elevated
+elevates
+elements
+apxlrxcc
+scalene
+scalenus
+stretches
+stretched
+cervicoth
+cervicomedullary
+myelopathy
+myelomalacia
+zygoma
+zygomatic
+investigations
+communicate
+communication
+26×15
+28x15mm
+3x0
+4x5
+42×25×3
+40×20×1
+5tesla
+55×35×35
+6×8
+60×45×3
+7mar201
+ahnh
+aspiration
+averaging
+besides
+bialteral
+bows
+burr
+buccinator
+baptist
+cataract
+cribriform
+canthus
+cuts
+crescent
+curvil
+creatinine
+catheter
+dsseminated
+divisions
+document
+easily
+eraly
+establis
+fdg
+falx
+ferry
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+first
+frail
+filtrated
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+granuloma
+hkhc
+higher
+hanson
+ideally
+japan
+kyphosis
+kidneys
+layer
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+nevertheless
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+summary
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+septate
+treated
+tests
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+viral
+vasculature
+vestibules
+waldey
+##nhancement
+##gional
+##ronous
+##tenoid
+##082
+themselves
+##onpc082
+initial
+inspection
+inspected
+innumerable
+##iciency
+levei
+leaving
+nasogastric
+metastataic
+oramen
+necessary
+exotropic
+experienced
+uptake
+t1rhonpc082
+unavailable
+unrelated
+unsharpness
+unbreakable
+conspicuous
+concha
+spills
+spontaneously
+spiculated
+paracentral
+chunks
+cholesterol
+alternatively
+altogether
+smoking
+cortices
+information
+onset
+oncologist
+scaphoid
+pterygomaxillay
+retrobulbar
+retropharyngx
+midjugular
+earlier
+delphian
+dehiscence
+paraesthesia
+paraphyyngeal
+parafalcine
+styloid
+enucleation
+ensuing
+progress
+postsurgical
+pretracheal
+precaval
+believed
+hyperenhancement
+accesorry
+accumulation
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+sphenoethmoidal
+craniofacial
+nonetheless
+subsiding
+appointment
+inderterminate
+seems
+se1001
+hyperostosis
+inferoanteriorly
+inferolaterally
+extracranial
+suppressed
+frozen
+disruption
+centimetre
+cricoarytenoid
+persistently
+encircle
+reconstruction
+remodelling
+response
+locoregional
+longitudinal
+extramedullary
+extramucosal
+undisrupted
+platysma
+jugulodiagastric
+relatives
+tinnitus
+10x20mm
+12aug2013
+12x13x16mm
+mechanical
+insufficiency
+aerodigestive
+descends
+subcentimeter
+presumabaly
+interspersed
+interhemispheric
+gangliocapsular
+nasoendoscopy
+t4n3disease
+anteroinferiorly
+22x12x20mm
+22×37×26
+20x8x16mm
+emphysema
+tracheoesophageal
+aforementioned
+blooming
+macroscopic
+epistaxis
+destroyed
+dyspraxia
+25x26x19mm
+retrophayrngeal
+retrophargyeal
+27x22x23mm
+27×17×31
+calvarial
+synchronous
+impingement
+34×17×25
+nasophayrnx
+micropapillary
+microhaemorrhages
+23x11x23mm
+41x28x36mm
+foarmen
+supraclavivular
+13x10x15mm
+13x19x22mm
+cervicothoracic
+42×25×30
+40×20×14
+60×45×33
+7mar2012
+curvilinear
+documented
+established
+mteastases
+rudimentary
+waldeyers

npc_bert_models/summary_module.py

@@ -0,0 +1,65 @@
+from transformers import AutoTokenizer, EncoderDecoderModel
+from transformers import pipeline as hf_pipeline
+from pathlib import Path
+
+
+class NpcBertGPT2():
+    
+    def __init__(self):
+        self.model = None
+        self.tokenizer = None
+        self.pipeline = None
+        # relative to app.py
+        self.pretrained_model = "./models/npc-bert-gpt2-best"
+    
+    def load(self):
+        """Loads the fine-tuned EncoderDecoder model and related components.
+
+        This method initializes the model, tokenizer, and pipeline for the
+        report conclusion generation task using the pre-trained weights from the
+        specified directory.
+
+        Raises:
+            FileNotFoundError: If the pretrained model directory is not found.
+        """
+        if not Path(self.pretrained_model).is_dir():
+            raise FileNotFoundError(f"Cannot found pretrained model at: {self.pretrained_model}")
+        
+        self.model = EncoderDecoderModel.from_pretrained(self.pretrained_model)
+        self.tokenizer = AutoTokenizer.from_pretrained(self.pretrained_model)
+        self.pipeline = hf_pipeline("text2text-generation", 
+                                    model=self.model, 
+                                    tokenizer=self.tokenizer, 
+                                    device='cpu', 
+                                    num_beams=4,
+                                    do_sample=True,
+                                    top_p = 0.92,
+                                    top_k = 0,
+                                    early_stopping=True,
+                                    no_repeat_ngram_size=2, 
+                                    max_new_tokens=60)
+    
+    def __call__(self, *args):
+        """Performs masked language modeling prediction.
+
+        This method should be called only after the `load` method has been executed
+        to ensure that the model and pipeline are properly initialized. It accepts
+        arguments to pass to the Hugging Face fill-mask pipeline.
+
+        Args:
+            *args: Variable length argument list to pass to the pipeline.
+
+        Returns:
+            The output of the fill-mask pipeline.
+
+        Raises:
+            BrokenPipeError: If the model has not been loaded before calling this method.
+        """
+        if self.pipeline is None:
+            msg = "Model was not initialized, have you run load()?"
+            raise BrokenPipeError(msg)
+        pipe_out, = self.pipeline(*args)
+            
+        pipe_out = pipe_out['generated_text']
+        return pipe_out
+        

report_examples_summary/NPC-report-1.txt

@@ -0,0 +1,22 @@
+History
+NPC for screening MRI
+
+MRI Nasopharynx and Neck.
+A full staging scan was performed in view of preliminary findings
+Axial T1W
+Coronal T2W
+Axial T2 SPIR
+Axial and coronal T1W post contrast
+Axial T1W FS post contrast
+
+REPORT:
+
+Primary Tumour
+There is a small primary nasopharyngeal carcinoma involving all walls, but predominantly the right side, of the nasopharynx.
+The nasal cavity, oropharynx and parapharyngeal regions are unremarkable. There are small bilateral otomastoid effusions.
+The skull base is unremarkable, except for a very small area of abnormal signal in the superior aspect of the clivus which is of uncertain significance. The paranasal sinuses are unremarkable. 
+The cavernous sinus and sections of the cranium included on the scan are unremarkable.
+
+Nodal Metastases
+There are a few metastatic right retropharyngeal nodes measuring up to 8mm in diameter as well as a couple of smaller left retropharyngeal nodes that are non specific. Shotty small nodes are seen in the remainder of the neck, which are not suspicious by MRI criteria.
+

report_examples_summary/NPC-report-2.txt

@@ -0,0 +1,25 @@
+MRI Nasopharynx and Neck.
+
+Axial T1W
+Coronal T2W
+Axial T2 SPIR
+Axial and coronal T1W post contrast
+
+REPORT:
+
+Primary Tumour
+There is a nasopharyngeal carcinoma involving predominantly the right side   of the nasopharynx.
+There is tumour extension into the right sided preclival muscles and early extension into the right parapharyngeal region. No tumour extension into the nasal cavity or oropharynx.
+Early skull base invasion into the right pterygoid process is present and tumour involves the right pterygopalatine fossa and abuts the right foramen lacerum. There are minor mucosal inflammatory changes in the paranasal sinuses.
+The cavernous sinus and sections of the cranium included on the scan are unremarkable.
+There is a right middle ear and mastoid effusion.
+
+Findings:
+The nasal cavity and oropharynx are not involved.
+The parapharyngeal regions are unremarkable and there are no middle ear or mastoid effusions.
+The skull base is unremarkable.
+The cavernous sinus and sections of the cranium included on the scan are unremarkable.
+
+Distant metastases 
+No distant metastases or second primary tumours are identified in the head and neck, upper thorax or bones.
+

report_examples_summary/benign-report-1.txt

@@ -0,0 +1,9 @@
+MRI Nasopharynx
+Technique
+Axial T1W and T2SPIR
+Axial and coronal T1W post contrast
+
+Report
+A small focal area of mucosal thickening (depth approximately 8 mm) is present in the central portion of the superior roof of the nasopharynx which is only present on one slice and lies immediately below the skull base. In addition at this site there appears to be a defect just the right of the midline and it is uncertain whether this could be the site of a biopsy, please correlate clinically. The parapharyngeal regions are normal.
+Several small unremarkable upper cervical lymph nodes are noted.
+

report_examples_summary/benign-report-2.txt

@@ -0,0 +1,15 @@
+MRI Nasopharynx
+
+Technique
+Screening protocol
+Axial T1W and T2SPIR
+Axial and coronal T1W post contrast
+
+Report
+There is very mild generalized thickening of the walls of the nasopharynx suggesting lymphoid hyperplasia.No nasopharyngeal carcinoma is identified.
+The parapharyngeal regions are normal.
+No cervical lymphadenopathy.
+In addition there is greater thickening in the central roof in the region of the adenoid, which is mildly asymmetrical, but no definite nasopharyngeal carcinoma is identified.
+Inflammatory mucosal thickening in the right maxillary sinus.
+There is a borderline enlarged left retropharyngeal node and very small right retropharyngeal and upper cervical nodes but no nodes with any definite metastatic features are identified.
+The remainder of the scan is unremarkable