Experiment-2: Models for Data Discovery Scalability Evaluation

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Exp-2/models/CMDL/README.md

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+# CMDL Model Checkpoints
+
+Place the following files here (from `CMDL/output_cmdl_mimic/models/`):
+
+- `text_enet_best.pt` — Trained text EncoderNet
+- `col_enet_best.pt` — Trained column EncoderNet

Exp-2/models/CMDL/col_enet_best.pt

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Exp-2/models/LOKI/args.json

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+{
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+  "use_flash_attention": false,
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+  "row_sent_annotation_file": "/run/media/crusnic/OTHER/LOKI_Git_VLDB/Datasets/pharma_flipped_structured/Annotated_Test.json",
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+  "model_name": "sentence-transformers/embeddinggemma-300m-medical",
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+}

Exp-2/models/LOKI/sentence-transformers/embeddinggemma-300m-medical/best_model_epoch_9/model.pt

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Exp-2/models/LOKI/test_metrics.json

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Exp-2/models/LOKI/training_config.json

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Exp-2/models/LOKI/visualizations/diagnostics_example_1/validation_report_example_1.txt

@@ -0,0 +1,158 @@
+=== DIAGNOSTIC VALIDATION REPORT ===
+Example: 1
+Model Type: Bidirectional
+Rows: 10, Sentences: 50
+Generated: 2026-09-04 12:32:35.902049
+
+=== ATTENTION NORMALIZATION CHECKS ===
+Forward attention row sums (should be ~1.0):
+  Row 1: 0.999023
+  Row 2: 1.000000
+  Row 3: 1.000000
+  Row 4: 0.999023
+  Row 5: 1.000000
+  Row 6: 1.000977
+  Row 7: 0.999023
+  Row 8: 0.999023
+  Row 9: 1.000000
+  Row 10: 1.000000
+
+Reverse attention column sums (should be ~1.0):
+  Sentence 1: 5.178711
+  Sentence 2: 7.611328
+  Sentence 3: 2.596680
+  Sentence 4: 8.611328
+  Sentence 5: 8.000977
+  Sentence 6: 1.599609
+  Sentence 7: 2.393555
+  Sentence 8: 8.627930
+  Sentence 9: 2.987305
+  Sentence 10: 2.405273
+
+=== SCORE RANGE VALIDATION ===
+Raw similarities: [-0.021973, 0.566406]
+Forward attention: [0.000000, 0.209961]
+Reverse attention: [0.000000, 0.202148]
+Final pair scores: [-0.068848, 0.161133]
+
+=== TOP 3 PAIRS ANALYSIS ===
+
+Top 3 by Raw Similarities:
+  1. Row 10 - Sentence 8 (Score: 0.566406)
+     Row: ATP Binding Cassette Transporter, Subfamily B, Member 1
+Animals
+Anion Transport Proteins
+Biological ...
+     Sentence: id: BE0001067; name: ATP-binding cassette sub-family G member 2; organism: Humans; known_action: unk...
+
+  2. Row 5 - Sentence 10 (Score: 0.554688)
+     Row: P-glycoprotein (P-gp) was identified as a fexofenadine efflux transporter, using the LLC-PK1 cell, a...
+     Sentence: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: no; position: 6; parent_key: ...
+
+  3. Row 5 - Sentence 24 (Score: 0.546875)
+     Row: P-glycoprotein (P-gp) was identified as a fexofenadine efflux transporter, using the LLC-PK1 cell, a...
+     Sentence: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: unknown; position: 5; parent_...
+
+Top 3 by Final Model Scores:
+  1. Row 10 - Sentence 8 (Score: 0.161133)
+     Row: ATP Binding Cassette Transporter, Subfamily B, Member 1
+Animals
+Anion Transport Proteins
+Biological ...
+     Sentence: id: BE0001067; name: ATP-binding cassette sub-family G member 2; organism: Humans; known_action: unk...
+
+  2. Row 4 - Sentence 9 (Score: 0.147461)
+     Row: On the other hand, the bile acid transporter human sodium taurocholate cotransporting polypeptide (N...
+     Sentence: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; positi...
+
+  3. Row 4 - Sentence 37 (Score: 0.146484)
+     Row: On the other hand, the bile acid transporter human sodium taurocholate cotransporting polypeptide (N...
+     Sentence: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; positi...
+
+=== MATRIX STATISTICS ===
+Raw similarities - Mean: 0.212502, Std: 0.129748
+Final scores - Mean: 0.023606, Std: 0.049349
+Learning effect (Final - Raw) - Mean: -0.188896
+Correlation between raw and final scores: 0.885004
+
+=== ACTUAL CONTENT ===
+Table Rows:
+  Row 1: Fexofenadine, a nonsedating antihistamine, does not undergo significant metabolic biotransformation.
+  Row 2: Accordingly, it was hypothesized that uptake and efflux transporters could be importantly involved in the drug's disposition.
+  Row 3: Utilizing a recombinant vaccinia expression system, members of the organic anion transporting polypeptide family, such as the human organic anion transporting polypeptide (OATP) and rat organic anion transporting polypeptides 1 and 2 (Oatp1 and Oatp2), were found to mediate [(14)C]fexofenadine cellular uptake.
+  Row 4: On the other hand, the bile acid transporter human sodium taurocholate cotransporting polypeptide (NTCP) and the rat organic cation transporter rOCT1 did not exhibit such activity.
+  Row 5: P-glycoprotein (P-gp) was identified as a fexofenadine efflux transporter, using the LLC-PK1 cell, a polarized epithelial cell line lacking P-gp, and the derivative cell line (L-MDR1), which overexpresses P-gp.
+  Row 6: In addition, oral and i.v.
+  Row 7: administration of [(14)C]fexofenadine to mice lacking mdr1a-encoded P-gp resulted in 5- and 9-fold increases in the drug's plasma and brain levels, respectively, compared with wild-type mice.
+  Row 8: Also, a number of drug inhibitors of P-gp were found to be effective inhibitors of OATP.
+  Row 9: Because OATP transporters and P-gp colocalize in organs of importance to drug disposition such as the liver, their activity provides an explanation for the heretofore unknown mechanism(s) responsible for fexofenadine's disposition and suggests potentially similar roles in the disposition of other xenobiotics.
+  Row 10: ATP Binding Cassette Transporter, Subfamily B, Member 1
+Animals
+Anion Transport Proteins
+Biological Transport, Active
+Caco-2 Cells
+Carrier Proteins
+Genes, MDR
+HeLa Cells
+Histamine H1 Antagonists
+Humans
+LLC-PK1 Cells
+Mice
+Rats
+Swine
+Terfenadine
+Tissue Distribution
+Transfection
+Vaccinia virus
+
+Sentences:
+  Sentence 1: id: BE0003664; name: Copper-transporting ATPase 2; organism: Humans; known_action: unknown; position: 4; parent_key: DB00958.
+  Sentence 2: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 23; parent_key: DB04348.
+  Sentence 3: id: BE0004769; name: Y+L amino acid transporter 1; organism: Humans; known_action: unknown; position: 6; parent_key: DB00130.
+  Sentence 4: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 9; parent_key: DB09100.
+  Sentence 5: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 7; parent_key: DB00091.
+  Sentence 6: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 12; parent_key: DB00795.
+  Sentence 7: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 11; parent_key: DB14761.
+  Sentence 8: id: BE0001067; name: ATP-binding cassette sub-family G member 2; organism: Humans; known_action: unknown; position: 16; parent_key: DB13943.
+  Sentence 9: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 13; parent_key: DB13944.
+  Sentence 10: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: no; position: 6; parent_key: DB01117.
+  Sentence 11: id: BE0003666; name: Copper-transporting ATPase 1; organism: Humans; known_action: no; position: 10; parent_key: DB09130.
+  Sentence 12: id: BE0003664; name: Copper-transporting ATPase 2; organism: Humans; known_action: no; position: 11; parent_key: DB09130.
+  Sentence 13: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 5; parent_key: DB01586.
+  Sentence 14: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 3; parent_key: DB01098.
+  Sentence 15: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 3; parent_key: DB02123.
+  Sentence 16: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 1; parent_key: DB13153.
+  Sentence 17: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 1; parent_key: DB00887.
+  Sentence 18: id: BE0004769; name: Y+L amino acid transporter 1; organism: Humans; known_action: unknown; position: 11; parent_key: DB08838.
+  Sentence 19: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 6; parent_key: DB01586.
+  Sentence 20: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 4; parent_key: DB02123.
+  Sentence 21: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: unknown; position: 5; parent_key: DB00945.
+  Sentence 22: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 20; parent_key: DB00328.
+  Sentence 23: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 12; parent_key: DB01098.
+  Sentence 24: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: unknown; position: 5; parent_key: DB01244.
+  Sentence 25: id: BE0003666; name: Copper-transporting ATPase 1; organism: Humans; known_action: unknown; position: 15; parent_key: DB00526.
+  Sentence 26: id: BE0000106; name: Solute carrier family 22 member 5; organism: Humans; known_action: unknown; position: 1; parent_key: DB01208.
+  Sentence 27: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 5; parent_key: DB08912.
+  Sentence 28: id: BE0001134; name: Solute carrier family 15 member 2; organism: Humans; known_action: unknown; position: 2; parent_key: DB01140.
+  Sentence 29: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 11; parent_key: DB06290.
+  Sentence 30: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 13; parent_key: DB13946.
+  Sentence 31: id: BE0003645; name: Solute carrier family 22 member 8; organism: Humans; known_action: unknown; position: 11; parent_key: DB02659.
+  Sentence 32: id: BE0009872; name: Y+L amino acid transporter 2; organism: Humans; known_action: unknown; position: 7; parent_key: DB00130.
+  Sentence 33: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 8; parent_key: DB01583.
+  Sentence 34: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 5; parent_key: DB00451.
+  Sentence 35: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 9; parent_key: DB08860.
+  Sentence 36: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 12; parent_key: DB01032.
+  Sentence 37: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 13; parent_key: DB13943.
+  Sentence 38: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 5; parent_key: DB00286.
+  Sentence 39: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 4; parent_key: DB00787.
+  Sentence 40: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 2; parent_key: DB00646.
+  Sentence 41: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 7; parent_key: DB04348.
+  Sentence 42: id: BE0009680; name: B-cell antigen receptor complex-associated protein beta chain; organism: Humans; known_action: unknown; position: 2; parent_key: DB12240.
+  Sentence 43: id: BE0000106; name: Solute carrier family 22 member 5; organism: Humans; known_action: unknown; position: 3; parent_key: DB14754.
+  Sentence 44: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 7; parent_key: DB09102.
+  Sentence 45: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 6; parent_key: DB00091.
+  Sentence 46: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 5; parent_key: DB00279.
+  Sentence 47: id: BE0003642; name: Solute carrier organic anion transporter family member 1A2; organism: Humans; known_action: unknown; position: 2; parent_key: DB00635.
+  Sentence 48: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 7; parent_key: DB00396.
+  Sentence 49: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 2; parent_key: DB00977.
+  Sentence 50: id: BE0000732; name: Sodium/potassium-transporting ATPase subunit alpha-1; organism: Humans; known_action: unknown; position: 2; parent_key: DB14500.

Exp-2/models/LOKI/visualizations/example_1_similarity_analysis.txt

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+=== Comprehensive Similarity Analysis - Example 1 ===
+Model Type: Bidirectional
+Aggregation Method: top_k_pairs
+Pair Score Method: cosine
+
+TABLE ROWS:
+Row 1: Fexofenadine, a nonsedating antihistamine, does not undergo significant metabolic biotransformation.
+Row 2: Accordingly, it was hypothesized that uptake and efflux transporters could be importantly involved in the drug's disposition.
+Row 3: Utilizing a recombinant vaccinia expression system, members of the organic anion transporting polypeptide family, such as the human organic anion transporting polypeptide (OATP) and rat organic anion transporting polypeptides 1 and 2 (Oatp1 and Oatp2), were found to mediate [(14)C]fexofenadine cellular uptake.
+Row 4: On the other hand, the bile acid transporter human sodium taurocholate cotransporting polypeptide (NTCP) and the rat organic cation transporter rOCT1 did not exhibit such activity.
+Row 5: P-glycoprotein (P-gp) was identified as a fexofenadine efflux transporter, using the LLC-PK1 cell, a polarized epithelial cell line lacking P-gp, and the derivative cell line (L-MDR1), which overexpresses P-gp.
+Row 6: In addition, oral and i.v.
+Row 7: administration of [(14)C]fexofenadine to mice lacking mdr1a-encoded P-gp resulted in 5- and 9-fold increases in the drug's plasma and brain levels, respectively, compared with wild-type mice.
+Row 8: Also, a number of drug inhibitors of P-gp were found to be effective inhibitors of OATP.
+Row 9: Because OATP transporters and P-gp colocalize in organs of importance to drug disposition such as the liver, their activity provides an explanation for the heretofore unknown mechanism(s) responsible for fexofenadine's disposition and suggests potentially similar roles in the disposition of other xenobiotics.
+Row 10: ATP Binding Cassette Transporter, Subfamily B, Member 1
+Animals
+Anion Transport Proteins
+Biological Transport, Active
+Caco-2 Cells
+Carrier Proteins
+Genes, MDR
+HeLa Cells
+Histamine H1 Antagonists
+Humans
+LLC-PK1 Cells
+Mice
+Rats
+Swine
+Terfenadine
+Tissue Distribution
+Transfection
+Vaccinia virus
+
+CONTEXT SENTENCES:
+Sent 1: id: BE0003664; name: Copper-transporting ATPase 2; organism: Humans; known_action: unknown; position: 4; parent_key: DB00958.
+Sent 2: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 23; parent_key: DB04348.
+Sent 3: id: BE0004769; name: Y+L amino acid transporter 1; organism: Humans; known_action: unknown; position: 6; parent_key: DB00130.
+Sent 4: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 9; parent_key: DB09100.
+Sent 5: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 7; parent_key: DB00091.
+Sent 6: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 12; parent_key: DB00795.
+Sent 7: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 11; parent_key: DB14761.
+Sent 8: id: BE0001067; name: ATP-binding cassette sub-family G member 2; organism: Humans; known_action: unknown; position: 16; parent_key: DB13943.
+Sent 9: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 13; parent_key: DB13944.
+Sent 10: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: no; position: 6; parent_key: DB01117.
+Sent 11: id: BE0003666; name: Copper-transporting ATPase 1; organism: Humans; known_action: no; position: 10; parent_key: DB09130.
+Sent 12: id: BE0003664; name: Copper-transporting ATPase 2; organism: Humans; known_action: no; position: 11; parent_key: DB09130.
+Sent 13: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 5; parent_key: DB01586.
+Sent 14: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 3; parent_key: DB01098.
+Sent 15: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 3; parent_key: DB02123.
+Sent 16: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 1; parent_key: DB13153.
+Sent 17: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 1; parent_key: DB00887.
+Sent 18: id: BE0004769; name: Y+L amino acid transporter 1; organism: Humans; known_action: unknown; position: 11; parent_key: DB08838.
+Sent 19: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 6; parent_key: DB01586.
+Sent 20: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 4; parent_key: DB02123.
+Sent 21: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: unknown; position: 5; parent_key: DB00945.
+Sent 22: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 20; parent_key: DB00328.
+Sent 23: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 12; parent_key: DB01098.
+Sent 24: id: BE0001032; name: P-glycoprotein 1; organism: Humans; known_action: unknown; position: 5; parent_key: DB01244.
+Sent 25: id: BE0003666; name: Copper-transporting ATPase 1; organism: Humans; known_action: unknown; position: 15; parent_key: DB00526.
+Sent 26: id: BE0000106; name: Solute carrier family 22 member 5; organism: Humans; known_action: unknown; position: 1; parent_key: DB01208.
+Sent 27: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 5; parent_key: DB08912.
+Sent 28: id: BE0001134; name: Solute carrier family 15 member 2; organism: Humans; known_action: unknown; position: 2; parent_key: DB01140.
+Sent 29: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 11; parent_key: DB06290.
+Sent 30: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 13; parent_key: DB13946.
+Sent 31: id: BE0003645; name: Solute carrier family 22 member 8; organism: Humans; known_action: unknown; position: 11; parent_key: DB02659.
+Sent 32: id: BE0009872; name: Y+L amino acid transporter 2; organism: Humans; known_action: unknown; position: 7; parent_key: DB00130.
+Sent 33: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 8; parent_key: DB01583.
+Sent 34: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 5; parent_key: DB00451.
+Sent 35: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 9; parent_key: DB08860.
+Sent 36: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 12; parent_key: DB01032.
+Sent 37: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 13; parent_key: DB13943.
+Sent 38: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 5; parent_key: DB00286.
+Sent 39: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 4; parent_key: DB00787.
+Sent 40: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 2; parent_key: DB00646.
+Sent 41: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 7; parent_key: DB04348.
+Sent 42: id: BE0009680; name: B-cell antigen receptor complex-associated protein beta chain; organism: Humans; known_action: unknown; position: 2; parent_key: DB12240.
+Sent 43: id: BE0000106; name: Solute carrier family 22 member 5; organism: Humans; known_action: unknown; position: 3; parent_key: DB14754.
+Sent 44: id: BE0001004; name: Solute carrier organic anion transporter family member 1B1; organism: Humans; known_action: unknown; position: 7; parent_key: DB09102.
+Sent 45: id: BE0003643; name: Ileal sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 6; parent_key: DB00091.
+Sent 46: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 5; parent_key: DB00279.
+Sent 47: id: BE0003642; name: Solute carrier organic anion transporter family member 1A2; organism: Humans; known_action: unknown; position: 2; parent_key: DB00635.
+Sent 48: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 7; parent_key: DB00396.
+Sent 49: id: BE0003644; name: Sodium/bile acid cotransporter; organism: Humans; known_action: unknown; position: 2; parent_key: DB00977.
+Sent 50: id: BE0000732; name: Sodium/potassium-transporting ATPase subunit alpha-1; organism: Humans; known_action: unknown; position: 2; parent_key: DB14500.
+
+=== SIMILARITY MATRICES ===
+
+RAW EMBEDDINGS (Sentence Encoder):
+[[ 4.58984375e-02  8.44726562e-02  7.66601562e-02  8.69140625e-02
+   8.15429688e-02  7.47070312e-02  7.37304688e-02 -1.31607056e-04
+   7.71484375e-02  1.46484375e-01  3.75976562e-02  4.88281250e-02
+   7.95898438e-02  7.95898438e-02  8.30078125e-02  8.25195312e-02
+   8.83789062e-02  7.32421875e-02  8.54492188e-02  8.98437500e-02
+   1.45507812e-01  8.83789062e-02  8.20312500e-02  1.48437500e-01
+   3.10058594e-02 -9.09423828e-03  8.15429688e-02  1.96695328e-05
+   8.39843750e-02  7.42187500e-02 -2.19726562e-02  9.76562500e-02
+   8.88671875e-02  8.25195312e-02  8.54492188e-02  8.34960938e-02
+   7.95898438e-02  8.69140625e-02  7.51953125e-02  7.66601562e-02
+   7.56835938e-02  9.76562500e-02 -1.95312500e-02  7.81250000e-02
+   8.10546875e-02  8.93554688e-02  6.07910156e-02  8.15429688e-02
+   8.69140625e-02  2.57873535e-03]
+ [ 2.27539062e-01  2.55859375e-01  3.10546875e-01  2.59765625e-01
+   2.53906250e-01  3.33984375e-01  2.51953125e-01  1.55273438e-01
+   2.42187500e-01  1.66992188e-01  2.15820312e-01  2.21679688e-01
+   2.51953125e-01  3.33984375e-01  2.51953125e-01  3.18359375e-01
+   2.63671875e-01  3.14453125e-01  2.55859375e-01  2.59765625e-01
+   1.61132812e-01  2.59765625e-01  2.59765625e-01  1.59179688e-01
+   2.18750000e-01  2.49023438e-01  3.35937500e-01  2.44140625e-01
+   2.57812500e-01  2.44140625e-01  2.41210938e-01  3.22265625e-01
+   2.57812500e-01  3.33984375e-01  2.63671875e-01  2.55859375e-01
+   2.45117188e-01  2.57812500e-01  2.57812500e-01  3.33984375e-01
+   2.51953125e-01  1.37695312e-01  2.45117188e-01  3.33984375e-01
+   2.51953125e-01  2.59765625e-01  3.16406250e-01  2.51953125e-01
+   2.61718750e-01  1.82617188e-01]
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+   1.27929688e-01  1.17675781e-01  1.58203125e-01  1.28906250e-01
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+   5.24902344e-02  1.25976562e-01  4.73632812e-02  5.29785156e-02
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+   5.71289062e-02  1.29882812e-01  5.02929688e-02  5.00488281e-02
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+   5.71289062e-02  1.57226562e-01  4.80957031e-02  4.49218750e-02
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+   2.08007812e-01  3.86718750e-01  2.57812500e-01  2.71484375e-01
+   2.14843750e-01  3.00781250e-01  2.14843750e-01  2.91015625e-01
+   2.29492188e-01  2.44140625e-01  2.21679688e-01  2.25585938e-01
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+   2.57812500e-01  2.03125000e-01  3.00781250e-01  1.97265625e-01
+   2.20703125e-01  2.10937500e-01  1.83593750e-01  2.81250000e-01
+   2.24609375e-01  2.96875000e-01  2.26562500e-01  2.18750000e-01
+   2.14843750e-01  2.22656250e-01  2.16796875e-01  2.96875000e-01
+   2.08984375e-01  1.17675781e-01  1.93359375e-01  3.00781250e-01
+   2.13867188e-01  2.22656250e-01  3.00781250e-01  2.14843750e-01
+   2.26562500e-01  1.80664062e-01]
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+   3.02734375e-01  2.67578125e-01  4.57031250e-01  4.43359375e-01
+   3.08593750e-01  5.27343750e-01  3.04687500e-01  5.03906250e-01
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+   4.51171875e-01  4.68750000e-01  5.31250000e-01  4.70703125e-01
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+   3.24218750e-01  5.27343750e-01  3.26171875e-01  3.18359375e-01
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+   3.28125000e-01  4.39453125e-01]]
+
+CONTEXTUALIZED SIMILARITIES (After Attention):
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+  0.64453125 0.7578125  0.68359375 0.65625    0.6796875  0.6796875
+  0.68359375 0.68359375 0.61328125 0.65625    0.609375   0.65625
+  0.65625    0.6484375  0.6171875  0.6875     0.671875   0.6171875
+  0.68359375 0.6796875 ]
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+  0.66015625 0.7109375  0.57421875 0.54296875 0.64453125 0.54296875
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+  0.62109375 0.734375   0.640625   0.63671875 0.83203125 0.6328125
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+  0.87109375 0.8046875  0.6015625  0.58984375 0.73828125 0.59765625
+  0.58984375 0.66015625]]
+
+FINAL MODEL SIMILARITIES (After Training):
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+  -0.01782227 -0.02026367 -0.00933838 -0.02868652 -0.04833984 -0.04711914
+  -0.01092529 -0.02575684 -0.00805664 -0.01025391 -0.01855469 -0.0625
+  -0.0168457  -0.015625   -0.02636719 -0.01831055 -0.01879883 -0.02416992
+  -0.04614258 -0.05834961 -0.02807617 -0.05395508 -0.01538086 -0.01116943
+  -0.06884766 -0.04321289 -0.01544189 -0.02172852 -0.02087402 -0.0168457
+  -0.00836182 -0.01733398 -0.0168457  -0.02233887 -0.01623535  0.0088501
+  -0.05932617 -0.02233887 -0.01147461 -0.0177002  -0.03759766 -0.0213623
+  -0.01831055 -0.02600098]
+ [ 0.04321289  0.04907227  0.06079102  0.05175781  0.04956055  0.08789062
+   0.0534668   0.05566406  0.05688477 -0.01556396  0.03759766  0.03881836
+   0.05810547  0.08935547  0.0612793   0.09570312  0.05175781  0.05395508
+   0.05175781  0.05273438 -0.01513672  0.04956055  0.05249023 -0.01477051
+   0.04443359  0.0625      0.08691406  0.06225586  0.05517578  0.05688477
+   0.05517578  0.06787109  0.05151367  0.09082031  0.05126953  0.05297852
+   0.05712891  0.05078125  0.05810547  0.09277344  0.0559082   0.02990723
+   0.06445312  0.09326172  0.05786133  0.04931641  0.07763672  0.0480957
+   0.05224609  0.05932617]
+ [ 0.00683594 -0.00527954 -0.01574707 -0.00285339 -0.00317383  0.05444336
+   0.00549316  0.06591797  0.00723267 -0.03613281  0.00759888  0.00549316
+  -0.00331116  0.06079102 -0.00043106  0.06835938 -0.00202942 -0.0246582
+  -0.00288391 -0.00195312 -0.0324707  -0.0055542  -0.00250244 -0.02954102
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Exp-2/models/TaBERT/tabert_large_k3/model.bin

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