How to make the most of your masked language model for protein engineering
Calvin McCarterNick BhattacharyaSebastian W. OberHunter Elliott
Aug 2026
Machine Learning
Abstract
A plethora of protein language models have been released in recent years. Yet comparatively little work has addressed how to best sample from them to optimize desired biological properties. We fill this gap by proposing a flexible, effective sampling method for masked language models (MLMs), and by systematically evaluating models and methods both in silico and in vitro on actual antibody therapeutics campaigns. Firstly, we propose sampling with stochastic beam search, exploiting the fact that MLMs are remarkably efficient at evaluating the pseudo-perplexity of the entire 1-edit neighborhood of a sequence. Reframing generation in terms of entire-sequence evaluation enables flexible guidance with multiple optimization objectives. Secondly, we report results from our extensive in vitro head-to-head evaluation for the antibody engineering setting. This reveals that the choice of sampling method can have a substantial impact, motivating future research into this under-explored area.
This work introduces a pioneering exploration of Self-Supervised Learning (SSL) within the SNN, and proposes a novel Spiking Self-Attention (SSA) and Spiking Transformer (Spikformer) that achieves 80+% accuracy on ImageNet.
Zhaokun Zhou, Kaiwei Che, Wei Fang et al.· arXiv.org· 69 citations· ⚡10
EquiPocket is proposed, an E(3)-equivariant Graph Neural Network for binding site prediction, which comprises three modules: the first one to extract local geometric information for each surface atom, the second one to model both the chemical and spatial structure of protein and the last one to capture the geometry of the surface via equivariant message passing over the surface atoms.
Yang Zhang, Wenbing Huang, Zhewei Wei et al.· International Conference on...· 43 citations· ⚡4
It is shown that the maximum hypergraph density of any multiclass hypothesis class is upper-bounded by its DS dimension, which proves a longstanding conjecture of Daniely and Shalev-Shwartz (2014) and determines the optimal dependence of the sample complexity on the DS dimension for multiclass as well as list learning.
Quantum measurements are the means by which we recover messages encoded into quantum states. They are at the forefront of quantum hypothesis testing, wherein the goal is to perform an optimal measurement for arriving at a correct conclusion. Mathematically, a measurement operator is Hermitian with eigenvalues in [0,1]. By noticing that this constraint on each eigenvalue is the same as that imposed on fermions by the Pauli exclusion principle, we interpret every eigenmode of a measurement operator as an independent effective fermionic mode. Under this perspective, various objective functions in quantum hypothesis testing can be viewed as the total expected energy associated with these fermionic occupation numbers. By instead fixing a temperature and minimizing the total expected fermionic free energy, we find that optimal measurements for these modified objective functions are Fermi-Dirac thermal measurements, wherein their eigenvalues are specified by Fermi-Dirac distributions. In the low-temperature limit, their performance closely approximates that of optimal measurements for quantum hypothesis testing, and we show that their parameters can be learned by classical or hybrid quantum-classical optimization algorithms. This leads to a new quantum machine-learning model, termed Fermi-Dirac machines, consisting of parameterized Fermi-Dirac thermal measurements-an alternative to quantum Boltzmann machines based on thermal states. Beyond hypothesis testing, we show how general semidefinite optimization problems can be solved using this approach, leading to a novel paradigm for semidefinite optimization on quantum computers, in which the goal is to implement thermal measurements rather than prepare thermal states. Finally, we propose quantum algorithms for implementing Fermi-Dirac thermal measurements, and we also propose second-order hybrid quantum-classical optimization algorithms.
This systematic review evaluates 55 studies from 2017 to 2023 on the application of machine learning techniques to ASD, highlighting key challenges and opportunities, particularly the need for models that can integrate complex data to improve diagnostic accuracy and treatment outcomes.
Rafael Muñoz-Terol, Jesús Peral, Sandra Amador et al.· Heliyon· 4 citations· ⚡1
SimulRAG, a simulator-based RAG framework with a generalized retrieval interface that translates between text and simulator parameters/outputs, is proposed, which improves informativeness and factuality over the strongest adapted RAG baselines, while UE+SBA enhances claim-level efficiency and quality.
Haozhou Xu, D. Wu, M. Chinazzi et al.· arXiv.org· 3 citations
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