Fix bibtex definition for arxiv papers

src/thesis/bibliography.bib

@@ -13,13 +13,14 @@
 	pages = {416--418},
 }
 
-@article{huang_improved_2023,
+@misc{huang_improved_2023,
 	title = {Improved {Noisy} {Syndrome} {Decoding} of {Quantum} {LDPC} {Codes} with {Sliding} {Window}},
 	doi = {10.48550/arXiv.2311.03307},
 	publisher = {arXiv},
 	author = {Huang, Shilin and Puri, Shruti},
 	month = nov,
 	year = {2023},
+	howpublished = {arXiv:2311.03307},
 }
 
 @article{huang_increasing_2024,
@@ -35,13 +36,14 @@
 	pages = {012453},
 }
 
-@article{xu_batched_2025,
+@misc{xu_batched_2025,
 	title = {Batched high-rate logical operations for quantum {LDPC} codes},
 	doi = {10.48550/arXiv.2510.06159},
 	publisher = {arXiv},
 	author = {Xu, Qian and Zhou, Hengyun and Bluvstein, Dolev and Cain, Madelyn and Kalinowski, Marcin and Preskill, John and Lukin, Mikhail D. and Maskara, Nishad},
 	month = oct,
 	year = {2025},
+	howpublished = {arXiv:2510.06159},
 }
 
 @article{gidney_stability_2022,
@@ -57,13 +59,14 @@
 	pages = {786},
 }
 
-@article{koutsioumpas_colour_2025,
+@misc{koutsioumpas_colour_2025,
 	title = {Colour {Codes} {Reach} {Surface} {Code} {Performance} using {Vibe} {Decoding}},
 	doi = {10.48550/arXiv.2508.15743},
 	publisher = {arXiv},
 	author = {Koutsioumpas, Stergios and Noszko, Tamas and Sayginel, Hasan and Webster, Mark and Roffe, Joschka},
 	month = aug,
 	year = {2025},
+	howpublished = {arXiv:2508.15743},
 }
 
 @article{koutsioumpas_automorphism_2025,
@@ -74,13 +77,14 @@
 	year = {2025},
 }
 
-@article{gottesman_heisenberg_1998,
+@misc{gottesman_heisenberg_1998,
 	title = {The {Heisenberg} {Representation} of {Quantum} {Computers}},
 	doi = {10.48550/arXiv.quant-ph/9807006},
 	publisher = {arXiv},
 	author = {Gottesman, Daniel},
 	month = jul,
 	year = {1998},
+	howpublished = {arXiv:quant-ph/9807006},
 }
 
 @article{gidney_stim_2021,
@@ -199,13 +203,14 @@
 	pages = {6424--6438},
 }
 
-@article{derks_designing_2025,
+@misc{derks_designing_2025,
 	title = {Designing fault-tolerant circuits using detector error models},
 	doi = {10.48550/arXiv.2407.13826},
 	publisher = {arXiv},
 	author = {Derks, Peter-Jan H. S. and Townsend-Teague, Alex and Burchards, Ansgar G. and Eisert, Jens},
 	month = oct,
 	year = {2025},
+	howpublished = {arXiv:2407.13826},
 }
 
 @phdthesis{klinke_neural_2025,
@@ -219,7 +224,7 @@
 	year = {2025},
 }
 
-@article{camps-moreno_toward_2024,
+@misc{camps-moreno_toward_2024,
 	title = {Toward {Quantum} {CSS}-{T} {Codes} from {Sparse} {Matrices}},
 	doi = {10.48550/arXiv.2406.00425},
 	abstract = {CSS-T codes were recently introduced as quantum error-correcting codes that respect a transversal gate. A CSS-T code depends on a pair \$(C\_1, C\_2)\$ of binary linear codes \$C\_1\$ and \$C\_2\$ that satisfy certain conditions. We prove that \$C\_1\$ and \$C\_2\$ form a CSS-T pair if and only if \$C\_2 {\textbackslash}subset {\textbackslash}operatorname\{Hull\}(C\_1) {\textbackslash}cap {\textbackslash}operatorname\{Hull\}(C\_1{\textasciicircum}2)\$, where the hull of a code is the intersection of the code with its dual. We show that if \$(C\_1,C\_2)\$ is a CSS-T pair, and the code \$C\_2\$ is degenerated on \${\textbackslash}\{i{\textbackslash}\}\$, meaning that the \$i{\textasciicircum}\{th\}\$-entry is zero for all the elements in \$C\_2\$, then the pair of punctured codes \$(C\_1{\textbar}\_i,C\_2{\textbar}\_i)\$ is also a CSS-T pair. Finally, we provide Magma code based on our results and quasi-cyclic codes as a step toward finding quantum LDPC or LDGM CSS-T codes computationally.},
@@ -227,6 +232,7 @@
 	author = {Camps-Moreno, Eduardo and López, Hiram H. and Matthews, Gretchen L. and McMillon, Emily},
 	month = jun,
 	year = {2024},
+	howpublished = {arXiv:2406.00425},
 }
 
 @article{roffe_quantum_2019,
@@ -244,13 +250,14 @@
 	pages = {226--245},
 }
 
-@article{gottesman_introduction_2009,
+@misc{gottesman_introduction_2009,
 	title = {An {Introduction} to {Quantum} {Error} {Correction} and {Fault}-{Tolerant} {Quantum} {Computation}},
 	doi = {10.48550/arXiv.0904.2557},
 	publisher = {arXiv},
 	author = {Gottesman, Daniel},
 	month = apr,
 	year = {2009},
+	howpublished = {arXiv:0904.2557},
 }
 
 @article{gottesman_theory_1998,
@@ -266,31 +273,34 @@
 	pages = {127--137},
 }
 
-@article{calderbank_quantum_1997,
+@misc{calderbank_quantum_1997,
 	title = {Quantum {Error} {Correction} via {Codes} over {GF}(4)},
 	doi = {10.48550/arXiv.quant-ph/9608006},
 	publisher = {arXiv},
 	author = {Calderbank, A. R. and Rains, E. M. and Shor, P. W. and Sloane, N. J. A.},
 	month = sep,
 	year = {1997},
+	howpublished = {arXiv:quant-ph/9608006},
 }
 
-@article{gottesman_stabilizer_1997,
+@misc{gottesman_stabilizer_1997,
 	title = {Stabilizer {Codes} and {Quantum} {Error} {Correction}},
 	doi = {10.48550/arXiv.quant-ph/9705052},
 	publisher = {arXiv},
 	author = {Gottesman, Daniel},
 	month = may,
 	year = {1997},
+	howpublished = {arXiv:quant-ph/9705052},
 }
 
-@article{shor_fault-tolerant_1997,
+@misc{shor_fault-tolerant_1997,
 	title = {Fault-tolerant quantum computation},
 	doi = {10.48550/arXiv.quant-ph/9605011},
 	publisher = {arXiv},
 	author = {Shor, Peter W.},
 	month = mar,
 	year = {1997},
+	howpublished = {arXiv:quant-ph/9605011},
 }
 
 @article{divincenzo_fault-tolerant_1996,
@@ -374,13 +384,14 @@
 	pages = {83--84},
 }
 
-@article{blume-kohout_estimating_2025,
+@misc{blume-kohout_estimating_2025,
 	title = {Estimating detector error models from syndrome data},
 	doi = {10.48550/arXiv.2504.14643},
 	publisher = {arXiv},
 	author = {Blume-Kohout, Robin and Young, Kevin},
 	month = apr,
 	year = {2025},
+	howpublished = {arXiv:2504.14643},
 }
 
 @inproceedings{chatterjee_quantum_2023,
@@ -438,6 +449,7 @@
 	author = {Beni, Laleh Aghababaie and Higgott, Oscar and Shutty, Noah},
 	month = aug,
 	year = {2025},
+	howpublished = {arXiv:2503.10988},
 }
 
 @article{bausch_learning_2024,
@@ -463,6 +475,7 @@
 	author = {Bhardwaj, Devansh and Takou, Evangelia and Lin, Yingjia and Brown, Kenneth R.},
 	month = nov,
 	year = {2025},
+	howpublished = {arXiv:2511.09491},
 }
 
 @article{roffe_decoding_2020,
@@ -511,6 +524,7 @@
 	author = {Lin, Hsiang-Ku and Lim, Pak Kau and Kovalev, Alexey A. and Pryadko, Leonid P.},
 	month = aug,
 	year = {2025},
+	howpublished = {arXiv:2506.16910},
 }
 
 @misc{fan_accelerating_2025,
@@ -520,6 +534,7 @@
 	author = {Fan, Wenxuan and Suzuki, Yasunari and Ravi, Gokul Subramanian and Ueno, Yosuke and Inoue, Koji and Tanimoto, Teruo},
 	month = sep,
 	year = {2025},
+	howpublished = {arXiv:2509.01892},
 }
 
 @misc{senior_scalable_2025,
@@ -529,6 +544,7 @@
 	author = {Senior, Andrew W. and Edlich, Thomas and Heras, Francisco J. H. and Zhang, Lei M. and Higgott, Oscar and Spencer, James S. and Applebaum, Taylor and Blackwell, Sam and Ledford, Justin and Žemgulytė, Akvilė and Žídek, Augustin and Shutty, Noah and Cowie, Andrew and Li, Yin and Holland, George and Brooks, Peter and Beattie, Charlie and Newman, Michael and Davies, Alex and Jones, Cody and Boixo, Sergio and Neven, Hartmut and Kohli, Pushmeet and Bausch, Johannes},
 	month = dec,
 	year = {2025},
+	howpublished = {arXiv:2512.07737},
 }
 
 @misc{wang_fully_2025,
@@ -585,6 +601,7 @@
 	author = {Tsubouchi, Kento and Yamasaki, Hayata and Tamiya, Shiro},
 	month = oct,
 	year = {2025},
+	howpublished = {arXiv:2510.08695},
 }
 
 @misc{lee_scalable_2025,
@@ -594,6 +611,7 @@
 	author = {Lee, Changwon and Hur, Tak and Park, Daniel K.},
 	month = oct,
 	year = {2025},
+	howpublished = {arXiv:2510.22724},
 }
 
 @misc{maan_decoding_2025,
@@ -603,6 +621,7 @@
 	author = {Maan, Arshpreet Singh and Herrero, Francisco-Garcia and Paler, Alexandru and Savin, Valentin},
 	month = oct,
 	year = {2025},
+	howpublished = {arXiv:2510.14060},
 }
 
 @article{skoric_parallel_2023,
@@ -667,6 +686,7 @@
 	author = {{\'S}wierkowska, Aleksandra and Pflieger, Jannik and Giortamis, Emmanouil and Bhatotia, Pramod},
 	month = nov,
 	year = {2025},
+	howpublished = {arXiv:2511.01062},
 }
 
 @phdthesis{guernut_fault-tolerant_2025,
@@ -741,6 +761,7 @@
 	author = {Kuo, Kao-Yueh and Lai, Ching-Yi},
 	month = sep,
 	year = {2024},
+	howpublished = {arXiv:2409.18689},
 }
 
 @misc{poor_ultra_2025,
@@ -750,6 +771,7 @@
 	author = {Poór, Boldizsár and Rodatz, Benjamin and Kissinger, Aleks},
 	month = nov,
 	year = {2025},
+	howpublished = {arXiv:2511.13700},
 }
 
 @article{feynman_simulating_1982,
@@ -829,6 +851,7 @@
 	author = {Caune, Laura and Skoric, Luka and Blunt, Nick S. and Ruban, Archibald and McDaniel, Jimmy and Valery, Joseph A. and Patterson, Andrew D. and Gramolin, Alexander V. and Majaniemi, Joonas and Barnes, Kenton M. and Bialas, Tomasz and Buğdaycı, Okan and Crawford, Ophelia and Gehér, György P. and Krovi, Hari and Matekole, Elisha and Topal, Canberk and Poletto, Stefano and Bryant, Michael and Snyder, Kalan and Gillespie, Neil I. and Jones, Glenn and Johar, Kauser and Campbell, Earl T. and Hill, Alexander D.},
 	month = oct,
 	year = {2024},
+	howpublished = {arXiv:2410.05202},
 }
 
 @misc{ye_beam_2025-1,
@@ -838,6 +861,7 @@
 	author = {Ye, Min and Wecker, Dave and Delfosse, Nicolas},
 	month = dec,
 	year = {2025},
+	howpublished = {arXiv:2512.07057},
 }
 
 @misc{noauthor_reproducing_nodate,
@@ -914,6 +938,7 @@
 	author = {Yao, Hanwen and Laban, Waleed Abu and Häger, Christian and Amat, Alexandre Graell i and Pfister, Henry D.},
 	month = jun,
 	year = {2024},
+	howpublished = {arXiv:2312.10950},
 }
 
 @article{sharon_efficient_2007,
@@ -1048,6 +1073,7 @@
 	author = {Gottesman, Daniel},
 	month = jul,
 	year = {2014},
+	howpublished = {arXiv:1310.2984},
 }
 
 @misc{gidney_new_2023,
@@ -1057,6 +1083,7 @@
 	author = {Gidney, Craig and Jones, Cody},
 	month = dec,
 	year = {2023},
+	howpublished = {arXiv:2312.08813},
 }
 
 @article{gidney_fault-tolerant_2021,
@@ -1093,7 +1120,7 @@
 	number = {7867},
 	journal = {Nature},
 	publisher = {Nature Publishing Group},
-	author = {Chen, Zijun and Satzinger, Kevin J. and Atalaya, Juan and Korotkov, Alexander N. and Dunsworth, Andrew and Sank, Daniel and Quintana, Chris and McEwen, Matt and Barends, Rami and Klimov, Paul V. and Hong, Sabrina and Jones, Cody and Petukhov, Andre and Kafri, Dvir and Demura, Sean and Burkett, Brian and Gidney, Craig and Fowler, Austin G. and Paler, Alexandru and Putterman, Harald and Aleiner, Igor and Arute, Frank and Arya, Kunal and Babbush, Ryan and Bardin, Joseph C. and Bengtsson, Andreas and Bourassa, Alexandre and Broughton, Michael and Buckley, Bob B. and Buell, David A. and Bushnell, Nicholas and Chiaro, Benjamin and Collins, Roberto and Courtney, William and Derk, Alan R. and Eppens, Daniel and Erickson, Catherine and Farhi, Edward and Foxen, Brooks and Giustina, Marissa and Greene, Ami and Gross, Jonathan A. and Harrigan, Matthew P. and Harrington, Sean D. and Hilton, Jeremy and Ho, Alan and Huang, Trent and Huggins, William J. and Ioffe, L. B. and Isakov, Sergei V. and Jeffrey, Evan and Jiang, Zhang and Kechedzhi, Kostyantyn and Kim, Seon and Kitaev, Alexei and Kostritsa, Fedor and Landhuis, David and Laptev, Pavel and Lucero, Erik and Martin, Orion and McClean, Jarrod R. and McCourt, Trevor and Mi, Xiao and Miao, Kevin C. and Mohseni, Masoud and Montazeri, Shirin and Mruczkiewicz, Wojciech and Mutus, Josh and Naaman, Ofer and Neeley, Matthew and Neill, Charles and Newman, Michael and Niu, Murphy Yuezhen and O’Brien, Thomas E. and Opremcak, Alex and Ostby, Eric and Pató, Bálint and Redd, Nicholas and Roushan, Pedram and Rubin, Nicholas C. and Shvarts, Vladimir and Strain, Doug and Szalay, Marco and Trevithick, Matthew D. and Villalonga, Benjamin and White, Theodore and Yao, Z. Jamie and Yeh, Ping and Yoo, Juhwan and Zalcman, Adam and Neven, Hartmut and Boixo, Sergio and Smelyanskiy, Vadim and Chen, Yu and Megrant, Anthony and Kelly, Julian and {Google Quantum AI}},
+	author = {{Google Quantum AI}},
 	month = jul,
 	year = {2021},
 	pages = {383--387},
@@ -1120,6 +1147,7 @@
 	author = {Bomb{\'i}n, H{\'e}ctor and Dawson, Chris and Liu, Ye-Hua and Nickerson, Naomi and Pastawski, Fernando and Roberts, Sam},
 	month = mar,
 	year = {2023},
+	howpublished = {arXiv:2303.04846},
 }
 
 @misc{leverrier_decoding_2022,
@@ -1129,4 +1157,5 @@
 	author = {Leverrier, Anthony and Z{\'e}mor, Gilles},
 	month = dec,
 	year = {2022},
+	howpublished = {arXiv:2208.05537},
 }

src/thesis/clean_bibliography.sh

@@ -3,3 +3,70 @@ sed -i "s/Héctor/H{\\\\'e}ctor/" bibliography.bib
 sed -i "s/Bombín/Bomb{\\\\'i}n/" bibliography.bib
 sed -i "s/Zémor/Z{\\\\'e}mor/" bibliography.bib
 sed -Ezi "s/\s(abstract|note|urldate|url|keywords|file) = \{[^}]*(\{[^}]*\}[^}]*)*\},?\n//g" bibliography.bib
+
+# Normalize arXiv-only entries to @misc with howpublished = {arXiv:<id>}.
+# Detection: doi matches 10.48550/arXiv.<id>. The IEEEtranSA .bst's @article
+# handler needs a journal field (which preprints lack) and ignores publisher,
+# so for arXiv preprints we coerce the type to @misc and add howpublished
+# (the field the .bst actually prints for @misc).
+python3 - <<'PY'
+import re
+
+path = "bibliography.bib"
+with open(path) as f:
+    text = f.read()
+
+doi_re = re.compile(r"doi\s*=\s*\{10\.48550/arXiv\.([^}]+)\}")
+type_re = re.compile(r"^@([A-Za-z]+)\{", re.MULTILINE)
+howpublished_re = re.compile(r"^\s*howpublished\s*=\s*\{", re.MULTILINE)
+
+# Split into entries by scanning for top-level "@type{...}" blocks. We walk
+# brace depth so that the closing "}" of the entry is matched correctly even
+# if internal fields contain braces.
+def split_entries(s):
+    out, i, n = [], 0, len(s)
+    while i < n:
+        m = type_re.search(s, i)
+        if not m:
+            out.append(("text", s[i:]))
+            break
+        if m.start() > i:
+            out.append(("text", s[i:m.start()]))
+        depth, j = 0, m.start()
+        while j < n:
+            c = s[j]
+            if c == "{":
+                depth += 1
+            elif c == "}":
+                depth -= 1
+                if depth == 0:
+                    j += 1
+                    break
+            j += 1
+        out.append(("entry", s[m.start():j]))
+        i = j
+    return out
+
+def transform(entry):
+    doi_m = doi_re.search(entry)
+    if not doi_m:
+        return entry
+    arxiv_id = doi_m.group(1)
+    entry = type_re.sub("@misc{", entry, count=1)
+    if not howpublished_re.search(entry):
+        # insert howpublished as the last field, before the entry-closing "}"
+        entry = re.sub(
+            r"(,?)(\s*)\}\s*$",
+            lambda m: ("," if m.group(1) != "," else m.group(1))
+                      + m.group(2) + "\thowpublished = {arXiv:" + arxiv_id + "},\n}",
+            entry,
+            count=1,
+        )
+    return entry
+
+parts = split_entries(text)
+new_text = "".join(transform(p) if kind == "entry" else p for kind, p in parts)
+
+with open(path, "w") as f:
+    f.write(new_text)
+PY