Improving few-and zero-shot reaction template prediction using modern hopfield networks

P Seidl, P Renz, N Dyubankova, P Neves… - Journal of chemical …, 2022 - ACS Publications
Finding synthesis routes for molecules of interest is essential in the discovery of new drugs
and materials. To find such routes, computer-assisted synthesis planning (CASP) methods …

Adaptive immune receptor repertoire analysis

V Mhanna, H Bashour, K Lê Quý, P Barennes… - Nature Reviews …, 2024 - nature.com
B cell and T cell receptor repertoires compose the adaptive immune receptor repertoire
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …

Hopfield networks is all you need

H Ramsauer, B Schäfl, J Lehner, P Seidl… - arxiv preprint arxiv …, 2020 - arxiv.org
We introduce a modern Hopfield network with continuous states and a corresponding
update rule. The new Hopfield network can store exponentially (with the dimension of the …

DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires

JW Sidhom, HB Larman, DM Pardoll… - Nature communications, 2021 - nature.com
Deep learning algorithms have been utilized to achieve enhanced performance in pattern-
recognition tasks. The ability to learn complex patterns in data has tremendous implications …

Cloob: Modern hopfield networks with infoloob outperform clip

A Fürst, E Rumetshofer, J Lehner… - Advances in neural …, 2022 - proceedings.neurips.cc
CLIP yielded impressive results on zero-shot transfer learning tasks and is considered as a
foundation model like BERT or GPT3. CLIP vision models that have a rich representation are …

In silico proof of principle of machine learning-based antibody design at unconstrained scale

R Akbar, PA Robert, CR Weber, M Widrich, R Frank… - MAbs, 2022 - Taylor & Francis
Generative machine learning (ML) has been postulated to become a major driver in the
computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to …

Large associative memory problem in neurobiology and machine learning

D Krotov, J Hopfield - arxiv preprint arxiv:2008.06996, 2020 - arxiv.org
Dense Associative Memories or modern Hopfield networks permit storage and reliable
retrieval of an exponentially large (in the dimension of feature space) number of memories …

On sparse modern hopfield model

JYC Hu, D Yang, D Wu, C Xu… - Advances in Neural …, 2024 - proceedings.neurips.cc
We introduce the sparse modern Hopfield model as a sparse extension of the modern
Hopfield model. Like its dense counterpart, the sparse modern Hopfield model equips a …

[HTML][HTML] CLEVR-XAI: A benchmark dataset for the ground truth evaluation of neural network explanations

L Arras, A Osman, W Samek - Information Fusion, 2022 - Elsevier
The rise of deep learning in today's applications entailed an increasing need in explaining
the model's decisions beyond prediction performances in order to foster trust and …

Conformal prediction for time series with modern hopfield networks

A Auer, M Gauch, D Klotz… - Advances in Neural …, 2023 - proceedings.neurips.cc
To quantify uncertainty, conformal prediction methods are gaining continuously more
interest and have already been successfully applied to various domains. However, they are …