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Generative modeling has become a central paradigm in protein research, extending machine learning beyond structure prediction toward sequence design, backbone generation, inverse folding, and biomolecular interaction modeling. However, the…

Protein engineering seeks to identify protein sequences with optimized properties. When guided by machine learning, protein sequence generation methods can draw on prior knowledge and experimental efforts to improve this process. In this…

Metastructured auxetic patches, characterized by negative Poisson's ratios, offer unique mechanical properties that closely resemble the behavior of human tissues and organs. As a result, these patches have gained significant attention for…

The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…

Sequence generative models are transforming protein engineering. However, no principled framework exists for conditioning these models on auxiliary information, such as experimental data, without additional training of a generative model.…

Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We…

The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…

Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…

Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…

Deep learning has transformed protein design, enabling accurate structure prediction, sequence optimization, and de novo protein generation. Advances in single-chain protein structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and…

Generative models emerge as promising candidates for novel sequence-data driven approaches to protein design, and for the extraction of structural and functional information about proteins deeply hidden in rapidly growing sequence…

The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent…

We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where…

We analyse a simple discrete-time stochastic process for the theoretical modeling of the evolution of protein lengths. At every step of the process a new protein is produced as a modification of one of the proteins already existing and its…

Generative models of macromolecules carry abundant and impactful implications for industrial and biomedical efforts in protein engineering. However, existing methods are currently limited to modeling protein structures or sequences,…

Sequential recommendation (SR) aims to predict the next purchasing item according to users' dynamic preference learned from their historical user-item interactions. To improve the performance of recommendation, learning dynamic…

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g.,…

Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…

The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…

Genome sequencing projects are rapidly increasing the number of high-dimensional protein sequence datasets. Clustering a high-dimensional protein sequence dataset using traditional machine learning approaches poses many challenges. Many…