Updated publications

Author: Pseudomanifold

content/publications.md

@@ -1,5 +1,13 @@
 ### 2025
 
+- [*Topology Meets Machine Learning: An Introduction Using the Euler Characteristic Transform*](https://dx.doi.org/10.1090/noti3193)<br />
+B.&nbsp;Rieck<br />
+Notices of the American Mathematical Society, Volume 72, Number 7, pp. 719--727, 2025<br />
+        <small>[\[Preprint\]](https://arxiv.org/abs/2410.17760) &bull; [\[Author's copy\]](https://www.ams.org/journals/notices/202507/rnoti-p719.pdf) &bull; [\[BibTeX\]](Rieck25a.bib)</small>
+- [*Molecular Machine Learning Using Euler Characteristic Transforms*](https://arxiv.org/abs/2507.03474)<br />
+V.&nbsp;Toscano-Duran, F.&nbsp;Rottach, and B.&nbsp;Rieck<br />
+Preprint, 2025<br />
+        <small>[\[Preprint\]](https://arxiv.org/abs/2507.03474) &bull; [\[BibTeX\]](Toscano25a.bib)</small>
 - [*Defining and Benchmarking Open Problems in Single-Cell Analysis*](https://dx.doi.org/10.1038/s41587-025-02694-w)<br />
 M.&thinsp;D.&nbsp;Luecken<sup>&dagger;</sup>, S.&nbsp;Gigante<sup>&dagger;</sup>, D.&thinsp;B.&nbsp;Burkhardt<sup>&dagger;</sup>, R.&nbsp;Cannoodt<sup>&dagger;</sup>, D.&thinsp;C.&nbsp;Strobl, N.&thinsp;S.&nbsp;Markov, L.&nbsp;Zappia, G.&nbsp;Palla, W.&nbsp;Lewis, D.&nbsp;Dimitrov, M.&thinsp;E.&nbsp;Vinyard, D.&thinsp;S.&nbsp;Magruder, M.&thinsp;F.&nbsp;Mueller, A.&nbsp;Andersson, E.&nbsp;Dann, Q.&nbsp;Qin, D.&thinsp;J.&nbsp;Otto, M.&nbsp;Klein, O.&thinsp;B.&nbsp;Botvinnik, L.&nbsp;Deconinck, K.&nbsp;Waldrant, S.&thinsp;N.&nbsp;Yasa, A.&nbsp;Szałata, A.&nbsp;Benz, Z.&nbsp;Li, O.&thinsp;P.&nbsp;Members, B.&nbsp;Rieck, C.&nbsp;Ahlmann-Eltze, E.&nbsp;da Veiga Beltrame, C.&thinsp;B.&nbsp;González-Blas, A.&thinsp;T.&nbsp;Chen, B.&nbsp;DeMeo, C.&nbsp;Ergen, S.&nbsp;Floc'hlay, A.&nbsp;Gayoso, S.&nbsp;Hicks, Y.&nbsp;Ji, V.&nbsp;Kleshchevnikov, G.&nbsp;La Manno, M.&thinsp;G.&nbsp;Lombardo, R.&nbsp;Lopez, D.&nbsp;Righelli, H.&nbsp;Sarkar, V.&nbsp;Svensson, A.&nbsp;Tong, G.&nbsp;Xing, C.&nbsp;Xu, J.&thinsp;M.&nbsp;Bloom, A.&thinsp;O.&nbsp;Pisco, J.&nbsp;Saez-Rodriguez, D.&nbsp;Wulsin, L.&nbsp;Pinello, Y.&nbsp;Saeys, F.&thinsp;J.&nbsp;Theis<sup>&Dagger;</sup>, and S.&nbsp;Krishnaswamy<sup>&Dagger;</sup><br />
 Nature Biotechnology, 2025<br />
@@ -24,7 +32,7 @@ Preprint, 2025<br />
 M.&nbsp;Alain, S.&nbsp;Takao, X.&nbsp;Dong, B.&nbsp;Rieck, and E.&nbsp;Noutahi<br />
 Preprint, 2025<br />
         <small>[\[Preprint\]](https://arxiv.org/abs/2505.10877) &bull; [\[BibTeX\]](Alain25a.bib)</small>
-- [*Neurospectrum: A Geometric and Topological Deep Learning Framework for Uncovering Spatiotemporal Signatures in Neural Activity*](https://dx.doi.org/10.1101/2023.03.22.533807)<br />
+- [*Neurospectrum: A Geometric and Topological Deep Learning Framework for Uncovering Spatiotemporal Signatures in Neural Activity*](https://biorxiv.org/content/10.1101/2023.03.22.533807v3)<br />
 D.&nbsp;Bhaskar<sup>&dagger;</sup>, Y.&nbsp;Zhang<sup>&dagger;</sup>, J.&nbsp;Moore, F.&nbsp;Gao, B.&nbsp;Rieck, G.&nbsp;Wolf, F.&nbsp;Khasawneh, E.&nbsp;Munch, J.&thinsp;A.&nbsp;Noah, H.&nbsp;Pushkarskaya, C.&nbsp;Pittenger, V.&nbsp;Greco, and S.&nbsp;Krishnaswamy<br />
 Preprint, 2025<br />
         <small>[\[Preprint\]](https://biorxiv.org/content/10.1101/2023.03.22.533807v3) &bull; [\[BibTeX\]](Bhaskar25a.bib)</small>
@@ -44,7 +52,7 @@ ICLR Workshop 'I Can't Believe It's Not Better: Challenges in Applied Deep Learn
 C.&nbsp;Koke, Y.&nbsp;Shen, A.&nbsp;Saroha, M.&nbsp;Eisenberger, B.&nbsp;Rieck, M.&thinsp;M.&nbsp;Bronstein, and D.&nbsp;Cremers<br />
 ICLR Workshop on Machine Learning Multiscale Processes, 2025<br />
         <small>[\[BibTeX\]](Koke25a.bib)</small>
-- [*Representation of Visual Sequences in the Tuning and Topology of Neuronal Activity in the Human Hippocampus*](https://dx.doi.org/10.1101/2025.03.04.641300)<br />
+- [*Representation of Visual Sequences in the Tuning and Topology of Neuronal Activity in the Human Hippocampus*](https://biorxiv.org/content/10.1101/2025.03.04.641300v1)<br />
 T.&nbsp;John, Y.&nbsp;Zhou, A.&nbsp;Aljishi, B.&nbsp;Rieck, N.&thinsp;B.&nbsp;Turk-Browne, and E.&thinsp;C.&nbsp;Damisah<br />
 Preprint, 2025<br />
         <small>[\[Preprint\]](https://biorxiv.org/content/10.1101/2025.03.04.641300v1) &bull; [\[BibTeX\]](John25a.bib)</small>
@@ -76,10 +84,6 @@ Transactions on Machine Learning Research, 2024<br />
 M.&nbsp;Alain, S.&nbsp;Takao, B.&nbsp;Rieck, X.&nbsp;Dong, and E.&nbsp;Noutahi<br />
 'Bayesian Decision-Making and Uncertainty' Workshop at NeurIPS, 2024<br />
         <small>[\[BibTeX\]](Alain24a.bib)</small>
-- [*Topology Meets Machine Learning: An Introduction Using the Euler Characteristic Transform*](https://arxiv.org/abs/2410.17760)<br />
-B.&nbsp;Rieck<br />
-Preprint, 2024<br />
-        <small>[\[Preprint\]](https://arxiv.org/abs/2410.17760) &bull; [\[BibTeX\]](Rieck24a.bib)</small>
 - [*Detecting and Approximating Redundant Computational Blocks in Neural Networks*](https://arxiv.org/abs/2410.04941)<br />
 I.&nbsp;Cannistraci, E.&nbsp;Rodolà, and B.&nbsp;Rieck<br />
 Preprint, 2024<br />
@@ -191,10 +195,6 @@ Proceedings of the 40th International Conference on Machine Learning, Volume 202
 G.&nbsp;Huguet<sup>&dagger;</sup>, A.&nbsp;Tong<sup>&dagger;</sup>, B.&nbsp;Rieck<sup>&dagger;</sup>, J.&nbsp;Huang<sup>&dagger;</sup>, M.&nbsp;Kuchroo, M.&nbsp;Hirn<sup>&Dagger;</sup>, G.&nbsp;Wolf<sup>&Dagger;</sup>, and S.&nbsp;Krishnaswamy<sup>&Dagger;</sup><br />
 SIAM Journal on Mathematics of Data Science, Volume 5, Number 2, pp. 346--372, 2023<br />
         <small>[\[Preprint\]](https://arxiv.org/abs/2203.14860) &bull; [\[BibTeX\]](Huguet23a.bib)</small>
-- [*Capturing Spatiotemporal Signaling Patterns in Cellular Data With Geometric Scattering Trajectory Homology*](https://dx.doi.org/10.1101/2023.03.22.533807)<br />
-D.&nbsp;Bhaskar<sup>&dagger;</sup>, J.&nbsp;Moore<sup>&dagger;</sup>, F.&nbsp;Gao, B.&nbsp;Rieck, F.&nbsp;Khasawneh, E.&nbsp;Munch, V.&nbsp;Greco<sup>&Dagger;</sup>, and S.&nbsp;Krishnaswamy<sup>&Dagger;</sup><br />
-Preprint, 2023<br />
-        <small>[\[Preprint\]](https://biorxiv.org/content/10.1101/2023.03.22.533807) &bull; [\[BibTeX\]](Bhaskar23a.bib)</small>
 - [*Single-Cell Analysis Reveals Inflammatory Interactions Driving Macular Degeneration*](https://dx.doi.org/10.1038/s41467-023-37025-7)<br />
 M.&nbsp;Kuchroo<sup>&dagger;</sup>, M.&nbsp;DiStasio<sup>&dagger;</sup>, E.&nbsp;Song, E.&nbsp;Calapkulu, L.&nbsp;Zhang, M.&nbsp;Ige, A.&thinsp;H.&nbsp;Sheth, A.&nbsp;Majdoubi, M.&nbsp;Menon, A.&nbsp;Tong, A.&nbsp;Godavarthi, Y.&nbsp;Xing, S.&nbsp;Gigante, H.&nbsp;Steach, J.&nbsp;Huang, G.&nbsp;Huguet, J.&nbsp;Narain, K.&nbsp;You, G.&nbsp;Mourgkos, R.&thinsp;M.&nbsp;Dhodapkar, M.&thinsp;J.&nbsp;Hirn, B.&nbsp;Rieck, G.&nbsp;Wolf, S.&nbsp;Krishnaswamy<sup>&Dagger;</sup>, and B.&thinsp;P.&nbsp;Hafler<sup>&Dagger;</sup><br />
 Nature Communications, Volume 14, Number 1, pp. 2589, 2023<br />
@@ -206,7 +206,7 @@ Journal of Cell Biology, Volume 222, Number 7, pp. e202302095, 2023<br />
 - [*DONUT: Creation, Development, and Opportunities of a Database*](https://dx.doi.org/10.1090/noti2797)<br />
 B.&nbsp;Giunti, J.&nbsp;Lazovskis, and B.&nbsp;Rieck<br />
 Notices of the American Mathematical Society, Volume 70, Number 10, pp. 1640--1644, 2023<br />
-        <small>[\[Preprint\]](https://arxiv.org/abs/2304.12417) &bull; [\[BibTeX\]](Giunti23a.bib)</small>
+        <small>[\[Preprint\]](https://arxiv.org/abs/2304.12417) &bull; [\[Author's copy\]](https://www.ams.org/journals/notices/202310/rnoti-p1640.pdf) &bull; [\[BibTeX\]](Giunti23a.bib)</small>
 - [*A Note on Cherry-Picking in Meta-Analyses*](https://dx.doi.org/10.3390/e25040691)<br />
 D.&nbsp;Yoneoka and B.&nbsp;Rieck<br />
 Entropy, Volume 25, Number 4, 2023<br />
@@ -247,7 +247,7 @@ Proceedings of Topological, Algebraic, and Geometric Learning Workshops 2022, Vo
 D.&nbsp;Bhaskar<sup>&dagger;</sup>, K.&nbsp;MacDonald<sup>&dagger;</sup>, O.&nbsp;Fasina, D.&nbsp;Thomas, B.&nbsp;Rieck, I.&nbsp;Adelstein<sup>&Dagger;</sup>, and S.&nbsp;Krishnaswamy<sup>&Dagger;</sup><br />
 Advances in Neural Information Processing Systems, 2022<br />
         <small>[\[Preprint\]](https://arxiv.org/abs/2206.03977) &bull; [\[BibTeX\]](Bhaskar22a.bib)</small>
-- [*Improved MALDI-TOF MS Based Antimicrobial Resistance Prediction Through Hierarchical Stratification*](https://dx.doi.org/10.1101/2022.04.13.488198)<br />
+- [*Improved MALDI-TOF MS Based Antimicrobial Resistance Prediction Through Hierarchical Stratification*](https://biorxiv.org/content/10.1101/2022.04.13.488198v1)<br />
 C.&nbsp;Weis<sup>&dagger;</sup>, B.&nbsp;Rieck<sup>&dagger;</sup>, S.&nbsp;Balzer<sup>&dagger;</sup>, A.&nbsp;Cuénod, A.&nbsp;Egli, and K.&nbsp;Borgwardt<br />
 Preprint, 2022<br />
         <small>[\[Preprint\]](https://biorxiv.org/content/10.1101/2022.04.13.488198v1) &bull; [\[BibTeX\]](Weis22b.bib)</small>

static/research/Alain25a.bib

@@ -5,6 +5,5 @@ @unpublished{Alain25a
 	eprint = {2505.10877},
 	primaryclass = {cs.LG},
 	title = {Graph and Simplicial Complex Prediction Gaussian Process via the Hodgelet Representations},
-	type = {Preprint},
 	year = {2025},
 }

static/research/Ballester25a.bib

@@ -6,7 +6,7 @@ @inproceedings{Ballester25a
 	eprint = {2410.02392},
 	keywords = {CORE-A*},
 	primaryclass = {cs.LG},
-	title = {MANTRA: The Manifold Triangulations Assemblage},
+	title = {{MANTRA}: The Manifold Triangulations Assemblage},
 	url = {https://openreview.net/forum?id=X6y5CC44HM},
 	year = {2025},
 }

static/research/Bhaskar23a.bib

@@ -1,11 +1,8 @@
 @unpublished{Bhaskar25a,
 	author = {Bhaskar, Dhananjay and Zhang, Yanlei and Moore, Jessica and Gao, Feng and Rieck, Bastian and Wolf, Guy and Khasawneh, Firas and Munch, Elizabeth and Noah, J. Adam and Pushkarskaya, Helen and Pittenger, Christopher and Greco, Valentina and Krishnaswamy, Smita},
 	author+an = {1=first; 2=first; 5=highlight},
-	doi = {10.1101/2023.03.22.533807},
-	elocation-id = {2023.03.22.533807},
 	eprint = {10.1101/2023.03.22.533807v3},
 	eprinttype = {bioRxiv},
 	title = {Neurospectrum: A Geometric and Topological Deep Learning Framework for Uncovering Spatiotemporal Signatures in Neural Activity},
-	type = {Preprint},
 	year = {2025},
 }

static/research/Bhaskar25a.bib

@@ -5,6 +5,5 @@ @unpublished{Cannistraci24a
 	eprint = {2410.04941},
 	primaryclass = {cs.LG},
 	title = {Detecting and Approximating Redundant Computational Blocks in Neural Networks},
-	type = {Preprint},
 	year = {2024},
 }

static/research/Cannistraci24a.bib

@@ -9,6 +9,7 @@ @article{Giunti23a
 	pages = {1640--1644},
 	primaryclass = {cs.DL},
 	title = {DONUT: Creation, Development, and Opportunities of a Database},
+	url = {https://www.ams.org/journals/notices/202310/rnoti-p1640.pdf},
 	volume = {70},
 	year = {2023},
 }

static/research/Giunti23a.bib

@@ -5,6 +5,5 @@ @unpublished{Holmgren24a
 	eprint = {2402.09529},
 	primaryclass = {cs.LG},
 	title = {The Manifold Density Function: An Intrinsic Method for the Validation of Manifold Learning},
-	type = {Preprint},
 	year = {2024},
 }

static/research/Holmgren24a.bib

@@ -1,5 +1,5 @@
 @article{Huguet23a,
-	abstract = {Abstract. Diffusion condensation is a dynamic process
+	abstract = {Diffusion condensation is a dynamic process
 that yields a sequence of multiscale data
 representations that aim to encode meaningful
 abstractions. It has proven effective for manifold

static/research/Huguet23a.bib

@@ -1,11 +1,9 @@
 @unpublished{John25a,
 	author = {John, Tibin and Zhou, Yajun and Aljishi, Ayman and Rieck, Bastian and Turk-Browne, Nicholas B. and Damisah, Eyiyemisi C.},
 	author+an = {4=highlight},
-	doi = {10.1101/2025.03.04.641300},
 	eprint = {10.1101/2025.03.04.641300v1},
 	eprinttype = {bioRxiv},
 	publisher = {Cold Spring Harbor Laboratory},
 	title = {Representation of visual sequences in the tuning and topology of neuronal activity in the human hippocampus},
-	type = {Preprint},
 	year = {2025},
 }