Citation & References
=====================

If you use MaldiDeepKit in academic work, please cite this repository
until the companion paper is available:

   *Citation will be available soon.* A companion benchmark paper
   comparing the four MaldiDeepKit architectures on DRIAMS-derived
   subsets is in preparation.

Alongside the upstream references for the architectures bundled in
the package:

- **ResNet** - He K, Zhang X, Ren S, Sun J (2016). *Deep Residual
  Learning for Image Recognition*. **CVPR**.
  `doi:10.1109/CVPR.2016.90 <https://doi.org/10.1109/CVPR.2016.90>`_
- **Vision Transformer** - Dosovitskiy A, Beyer L, Kolesnikov A,
  *et al.* (2021). *An Image is Worth 16x16 Words: Transformers for
  Image Recognition at Scale*. **ICLR**.
  `arXiv:2010.11929 <https://arxiv.org/abs/2010.11929>`_
- **LayerScale** - Touvron H, Cord M, Sablayrolles A, *et al.* (2021).
  *Going deeper with Image Transformers*. **ICCV**.
  `arXiv:2103.17239 <https://arxiv.org/abs/2103.17239>`_
- **Stochastic Depth** - Huang G, Sun Y, Liu Z, Sedra D, Weinberger K
  (2016). *Deep Networks with Stochastic Depth*. **ECCV**.
  `arXiv:1603.09382 <https://arxiv.org/abs/1603.09382>`_
- **Temperature Scaling** - Guo C, Pleiss G, Sun Y, Weinberger KQ
  (2017). *On Calibration of Modern Neural Networks*. **ICML**.
  `arXiv:1706.04599 <https://arxiv.org/abs/1706.04599>`_
- **Sharpness-Aware Minimization** - Foret P, Kleiner A, Mobahi H,
  Neyshabur B (2021). *Sharpness-Aware Minimization for Efficiently
  Improving Generalization*. **ICLR**.
  `arXiv:2010.01412 <https://arxiv.org/abs/2010.01412>`_

Related publications using the wider MaldiSuite:

- Rocchi, E., Nicitra, E., Calvo, M. et al. *Combining mass spectrometry
  and machine learning models for predicting Klebsiella pneumoniae
  antimicrobial resistance: a multicenter experience from clinical
  isolates in Italy*. **BMC Microbiol** (2026).
  `doi:10.1186/s12866-025-04657-2
  <https://doi.org/10.1186/s12866-025-04657-2>`_