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Identification and characterization of large protein complexes is a mainstay of biochemical toolboxes. Utilization of cross-linking chemicals can facilitate the capture and identification of transient or weak interactions of a transient…
This paper studies the design of mechanisms that are robust to misspecification. We introduce a novel notion of robustness that connects a variety of disparate approaches and study its implications in a wide class of mechanism design…
Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely…
The bulk macroscopic response of a system of particles or inclusions with field-induced forces is studied. The susceptibilities and transport coefficients in such a system are expressed as averages of a multiple scattering expansion. A…
Learning accurate drug representation is essential for tasks such as computational drug repositioning and prediction of drug side-effects. A drug hierarchy is a valuable source that encodes human knowledge of drug relations in a tree-like…
Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior…
Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem…
We initiate the combinatorial study of factorization systems on finite lattices, paying special attention to the role that reflective and coreflective factorization systems play in partitioning the poset of factorization systems on a fixed…
Understanding superconductivity emerging from repulsive fermions remains a major challenge in condensed matter physics. In this paper, we investigate the pairing tendencies in a one-dimensional, three component repulsive Hubbard model,…
Revealing the functional sites of biological sequences, such as evolutionary conserved, structurally interacting or co-evolving protein sites, is a fundamental, and yet challenging task. Different frameworks and models were developed to…
In many application domains, domain-specific languages can allow domain experts to contribute to collaborative projects more correctly and efficiently. To do so, they must be able to understand program structure from reading existing source…
A wide range of complex systems can be modeled as networks with corresponding constraints on the edges and nodes, which have been extensively studied in recent years. Nowadays, with the progress of information technology, systems that…
Background. Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. More than 800 different sequences have been characterized so far, but their biological…
An extended formulation of a polytope is a linear description of this polytope using extra variables besides the variables in which the polytope is defined. The interest of extended formulations is due to the fact that many interesting…
In many networks, including networks of protein-protein interactions, interdisciplinary collaboration networks, and semantic networks, connections are established between nodes with complementary rather than similar properties. While…
Statistical detection of a rare class of objects in a two-class classification problem can pose several challenges. Because the class of interest is rare in the training data, there is relatively little information in the known class…
A new family of polynomials, called cumulant polynomial sequence, and its extensions to the multivariate case is introduced relied on a purely symbolic combinatorial method. The coefficients of these polynomials are cumulants, but depending…
Multicomponent superconductivity is a novel quantum phenomenon in many different superconducting materials, such as multiband ones in which different superconducting gaps open in different Fermi surfaces, films engineered at the atomic…
In Clearing Up Mysteries -- The Original Goal (Maximum Entropy and Bayesian Methods: Cambridge, England, 1988 Springer, pp. 1-27) Jaynes derived Fick's Law for a dilute binary solution from Bayes' Theorem by considering, probabilistically,…
The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…