Final paper and small tokenizer fix

.gitignore

@@ -605,3 +605,6 @@ TSWLatexianTemp*
 
 # Other
 /figures/
+
+# Mac
+.DS_Store

paper/references.bib

@@ -87,7 +87,8 @@ @article{weininger1988smiles
 }
 
 @article{krennSELFIESSelfReferencingEmbedded2020,
-  title         = {{SELFIES}: A Robust Molecular String Representation},
+  title         = {Self-Referencing Embedded Strings ({SELFIES}):
+                   A 100\% Robust Molecular String Representation},
   author        = {Krenn, Mario and Häse, Florian and Nigam, AkshatKumar
                    and Friederich, Pascal and Aspuru-Guzik, Alán},
   journal       = {Machine Learning: Science and Technology},
@@ -153,7 +154,7 @@ @article{singhChemBERTa3OpenSource2025
 @article{fabianMolecularRepresentationLearning2020,
   title         = {Molecular Representation Learning with Language Models
                    and Domain-Relevant Auxiliary Tasks},
-  author        = {Fabian, Bernd and Edlich, Thomas and Gaspar, Héléna
+  author        = {Fabian, Benedek and Edlich, Thomas and Gaspar, Héléna
                    and Segler, Marwin and Meyers, Joshua and Fiscato, Marco
                    and Ahmed, Mohamed},
   journal       = {arXiv preprint arXiv:2011.13230},
@@ -218,21 +219,24 @@ @inproceedings{seidlEnhancingActivityPrediction2023
 }
 
 @article{axelrodCOATIMultimodalContrastive2024,
-  title         = {{COATI}: Multi-Modal Contrastive Pre-Training for
+  title         = {{COATI}: Multimodal Contrastive Pretraining for
                    Representing and Traversing Chemical Space},
-  author        = {Axelrod, Simon and Gomez-Bombarelli, Rafael},
-  journal       = {Journal of Chemical Theory and Computation},
-  volume        = {20},
+  author        = {Kaufman, Benjamin and Williams, Edward C.
+                   and Underkoffler, Carl and Pederson, Ryan
+                   and Mardirossian, Narbe and Watson, Ian
+                   and Parkhill, John},
+  journal       = {Journal of Chemical Information and Modeling},
+  volume        = {64},
   number        = {4},
-  pages         = {1457--1472},
+  pages         = {1145--1157},
   year          = {2024},
   publisher     = {ACS Publications},
-  doi           = {10.1021/acs.jctc.3c01015},
+  doi           = {10.1021/acs.jcim.3c01753},
 }
 
 @inproceedings{rongGroverTransformerSelfsupervised2020,
-  title         = {{GROVER}: Transformers for Molecular Graph Self-supervised
-                   Learning},
+  title         = {Self-Supervised Graph Transformer on Large-Scale
+                   Molecular Data},
   author        = {Rong, Yu and Bian, Yatao and Xu, Tingyang
                    and Xie, Weiyang and Wei, Ying and Huang, Wenbing
                    and Huang, Junzhou},
@@ -241,6 +245,7 @@ @inproceedings{rongGroverTransformerSelfsupervised2020
   pages         = {12559--12571},
   year          = {2020},
   url           = {https://proceedings.neurips.cc/paper/2020/hash/94aef38441efa3380a3bed3faf1f9d5d-Abstract.html},
+  note          = {GROVER},
 }
 
 @article{krugerMolEncoderOptimalMasked2025,
@@ -579,14 +584,14 @@ @inproceedings{zhouUniMolUniversal3D2023
                    and Zhang, Linfeng and Ke, Guolin},
   booktitle     = {International Conference on Learning Representations},
   year          = {2023},
-  url           = {https://arxiv.org/abs/2303.16982},
+  url           = {https://openreview.net/forum?id=6K2RM6wVqKu},
 }
 
 @article{yukselSELFormerMolecularRepresentation2023,
   title         = {{SELFormer}: Molecular Representation Learning via
                    {SELFIES} Language Models},
-  author        = {Y{\"u}ksel, Asu and Ulusoy, Erva and Erzincan,
-                   Abdulkadir and {\"O}zt{\"u}rk, Hakime},
+  author        = {Y{\"u}ksel, Atakan and Ulusoy, Erva and {\"U}nl{\"u},
+                   Atabey and Do{\u{g}}an, Tunca},
   journal       = {Machine Learning: Science and Technology},
   volume        = {4},
   number        = {2},
@@ -599,13 +604,14 @@ @article{yukselSELFormerMolecularRepresentation2023
 %  ADDITIONAL — NOT YET CITED (retain for future use)
 % ============================================================
 
-% [TODO] Incomplete stub — verify full bibliographic details before citing.
-@article{darrinWhenEmbedderMore,
+@inproceedings{darrinWhenEmbedderMore,
   title         = {When Is an Embedder More Promising than Another?},
   author        = {Darrin, Maxime and Formont, Philippe and Ayed, Ismail Ben
                    and Cheung, Jackie Chi Kit and Piantanida, Pablo},
-  journal       = {arXiv preprint},
+  booktitle     = {Advances in Neural Information Processing Systems},
+  volume        = {37},
   year          = {2024},
+  url           = {https://arxiv.org/abs/2406.07640},
 }
 
 @article{wangUnderstandingHowDimension,

paper/source_data/Fig_bootstrap_ci.csv

@@ -0,0 +1,5 @@
+model_A,model_B,n,wins,ties,losses,mean_delta_x100,ci_low,ci_high
+MMB-base,SELFormer,23,21,0,2,5.43,3.9,7.1
+MMB-base,ChemBERTa-2,23,17,0,6,4.55,1.6,7.9
+MMB-base,ECFP4,23,7,0,16,-1.02,-2.5,0.5
+MMB-base,MoLFormer,23,4,0,19,-1.67,-2.6,-0.7

paper/writing_style/scientific_writing_reference.md

@@ -1,6 +1,7 @@
 ---
 title: Scientific Writing & Manuscript Preparation — Master Reference
 subtitle: The full arc of a manuscript, distilled for researchers who already know the basics
+source: Synthesised from Nature Masterclasses materials
 context: University of Copenhagen — Practitioner Reference
 audience: Experienced researchers (practitioner-grade synthesis, not novice instruction)
 ---