Related papers: Diversifying Design of Nucleic Acid Aptamers Using…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made…
The storage and computation requirements of Convolutional Neural Networks (CNNs) can be prohibitive for exploiting these models over low-power or embedded devices. This paper reduces the computational complexity of the CNNs by minimizing an…
The exploration of selected single nucleotide polymorphisms (SNPs) to identify genetic diversity between different sequencing population pools (Pool-seq) is a fundamental task in genetic research. As underlying sequence reads and their…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
In machine learning and molecular design, there exist two approaches: discriminative and generative. In the discriminative approach dubbed forward design, the goal is to map a set of features/molecules to their respective electronics…
Often the development of novel functional peptides is not amenable to high throughput or purely computational screening methods. Peptides must be synthesized one at a time in a process that does not generate large amounts of data. One way…
Photonic Crystal Surface Emitting Lasers (PCSEL)'s inverse design demands expert knowledge in physics, materials science, and quantum mechanics which is prohibitively labor-intensive. Advanced AI technologies, especially reinforcement…
The synthesis of complex materials through the self-assembly of particles at the nanoscale provides opportunities for the realization of novel material properties. However, the inverse design process to create experimentally feasible…
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from…
Singlet fission has emerged as one of the most exciting phenomena known to improve the efficiencies of different types of solar cells and has found uses in diverse optoelectronic applications. The range of available singlet fission…
Quantifying the effects of amino acid mutations in proteins presents a significant challenge due to the vast combinations of residue sites and amino acid types, making experimental approaches costly and time-consuming. The Potts model has…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
We apply a replica inference based Potts model method to unsupervised image segmentation on multiple scales. This approach was inspired by the statistical mechanics problem of "community detection" and its phase diagram. Specifically, the…