Philippe A. Robert

Sebastian Towers, Aleksandra Kalisz, Philippe A. Robert et al.

Anti-viral therapies are typically designed to target only the current strains of a virus, a myopic response. However, therapy-induced selective pressures drive the emergence of new viral strains, against which the original myopic therapies are no longer effective. This evolutionary response presents an opportunity: our therapies could both defend against and actively influence viral evolution. This motivates our method ADIOS: Antibody Development vIa Opponent Shaping. ADIOS is a meta-learning framework where the process of antibody therapy design, the outer loop, accounts for the virus's adaptive response, the inner loop. With ADIOS, antibodies are not only robust against potential future variants, they also influence, i.e., shape, which future variants emerge. In line with the opponent shaping literature, we refer to our optimised antibodies as shapers. To demonstrate the value of ADIOS, we build a viral evolution simulator using the Absolut! framework, in which shapers successfully target both current and future viral variants, outperforming myopic antibodies. Furthermore, we show that shapers modify the distribution over viral evolutionary trajectories to result in weaker variants. We believe that our ADIOS paradigm will facilitate the discovery of long-lived vaccines and antibody therapies while also generalising to other domains. Specifically, domains such as antimicrobial resistance, cancer treatment, and others with evolutionarily adaptive opponents. Our code is available at https://github.com/olakalisz/adios.

Sebastian Towers, Aleksandra Kalisz, Philippe A. Robert et al.

Anti-viral therapies are typically designed to target only the current strains of a virus, a myopic response. However, therapy-induced selective pressures drive the emergence of new viral strains, against which the original myopic therapies are no longer effective. This evolutionary response presents an opportunity: our therapies could both defend against and actively influence viral evolution. This motivates our method ADIOS: Antibody Development vIa Opponent Shaping. ADIOS is a meta-learning framework where the process of antibody therapy design, the outer loop, accounts for the virus's adaptive response, the inner loop. With ADIOS, antibodies are not only robust against potential future variants, they also influence, i.e., shape, which future variants emerge. In line with the opponent shaping literature, we refer to our optimised antibodies as shapers. To demonstrate the value of ADIOS, we build a viral evolution simulator using the Absolut! framework, in which shapers successfully target both current and future viral variants, outperforming myopic antibodies. Furthermore, we show that shapers modify the distribution over viral evolutionary trajectories to result in weaker variants. We believe that our ADIOS paradigm will facilitate the discovery of long-lived vaccines and antibody therapies while also generalising to other domains. Specifically, domains such as antimicrobial resistance, cancer treatment, and others with evolutionarily adaptive opponents. Our code is available at https://github.com/olakalisz/adios.

Mai Ha Vu, Rahmad Akbar, Philippe A. Robert et al.

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM approaches do not contribute to a fundamental understanding of sequence-function mappings, hindering rule-based biotherapeutic drug development. We argue that guidance drawn from linguistics, a field specialized in analytical rule extraction from natural language data, can aid with building more interpretable protein LMs that are more likely to learn relevant domain-specific rules. Differences between protein sequence data and linguistic sequence data require the integration of more domain-specific knowledge in protein LMs compared to natural language LMs. Here, we provide a linguistics-based roadmap for protein LM pipeline choices with regard to training data, tokenization, token embedding, sequence embedding, and model interpretation. Incorporating linguistic ideas into protein LMs enables the development of next-generation interpretable machine-learning models with the potential of uncovering the biological mechanisms underlying sequence-function relationships.

Mai Ha Vu, Philippe A. Robert, Rahmad Akbar et al.

Apparent parallels between natural language and biological sequence have led to a recent surge in the application of deep language models (LMs) to the analysis of antibody and other biological sequences. However, a lack of a rigorous linguistic formalization of biological sequence languages, which would define basic components, such as lexicon (i.e., the discrete units of the language) and grammar (i.e., the rules that link sequence well-formedness, structure, and meaning) has led to largely domain-unspecific applications of LMs, which do not take into account the underlying structure of the biological sequences studied. A linguistic formalization, on the other hand, establishes linguistically-informed and thus domain-adapted components for LM applications. It would facilitate a better understanding of how differences and similarities between natural language and biological sequences influence the quality of LMs, which is crucial for the design of interpretable models with extractable sequence-functions relationship rules, such as the ones underlying the antibody specificity prediction problem. Deciphering the rules of antibody specificity is crucial to accelerating rational and in silico biotherapeutic drug design. Here, we formalize the properties of the antibody language and thereby establish not only a foundation for the application of linguistic tools in adaptive immune receptor analysis but also for the systematic immunolinguistic studies of immune receptor specificity in general.

Robert Frank, Michael Widrich, Rahmad Akbar et al.

Generative machine learning models offer a powerful framework for therapeutic design by efficiently exploring large spaces of biological sequences enriched for desirable properties. Unlike supervised learning methods, which require both positive and negative labeled data, generative models such as LSTMs can be trained solely on positively labeled sequences, for example, high-affinity antibodies. This is particularly advantageous in biological settings where negative data are scarce, unreliable, or biologically ill-defined. However, the lack of attribution methods for generative models has hindered the ability to extract interpretable biological insights from such models. To address this gap, we developed Generative Attribution Metric Analysis (GAMA), an attribution method for autoregressive generative models based on Integrated Gradients. We assessed GAMA using synthetic datasets with known ground truths to characterize its statistical behavior and validate its ability to recover biologically relevant features. We further demonstrated the utility of GAMA by applying it to experimental antibody-antigen binding data. GAMA enables model interpretability and the validation of generative sequence design strategies without the need for negative training data.

Asif Khan, Alexander I. Cowen-Rivers, Antoine Grosnit et al.

Antibodies are canonically Y-shaped multimeric proteins capable of highly specific molecular recognition. The CDRH3 region located at the tip of variable chains of an antibody dominates antigen-binding specificity. Therefore, it is a priority to design optimal antigen-specific CDRH3 regions to develop therapeutic antibodies. However, the combinatorial nature of CDRH3 sequence space makes it impossible to search for an optimal binding sequence exhaustively and efficiently using computational approaches. Here, we present \texttt{AntBO}: a combinatorial Bayesian optimisation framework enabling efficient \textit{in silico} design of the CDRH3 region. Ideally, antibodies are expected to have high target specificity and developability. We introduce a CDRH3 trust region that restricts the search to sequences with favourable developability scores to achieve this goal. For benchmarking, \texttt{AntBO} uses the \texttt{Absolut!} software suite as a black-box oracle to score the target specificity and affinity of designed antibodies \textit{in silico} in an unconstrained fashion~\citep{robert2021one}. The experiments performed for $159$ discretised antigens used in \texttt{Absolut!} demonstrate the benefit of \texttt{AntBO} in designing CDRH3 regions with diverse biophysical properties. In under $200$ calls to black-box oracle, \texttt{AntBO} can suggest antibody sequences that outperform the best binding sequence drawn from 6.9 million experimentally obtained CDRH3s and a commonly used genetic algorithm baseline. Additionally, \texttt{AntBO} finds very-high affinity CDRH3 sequences in only 38 protein designs whilst requiring no domain knowledge. We conclude \texttt{AntBO} brings automated antibody design methods closer to what is practically viable for in vitro experimentation.