相关论文: Synthesis Cost-Optimal Targeted Mutant Protein Lib…

Distributed storage systems support failures of individual devices by the use of replication or erasure correcting codes. While erasure correcting codes offer a better storage efficiency than replication for similar fault tolerance, they…

Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…

Content distribution over networks is often achieved by using mirror sites that hold copies of files or portions thereof to avoid congestion and delay issues arising from excessive demands to a single location. Accordingly, there are…

Protein structure prediction is a core challenge in computational biology, particularly for fragments within ligand-binding regions, where accurate modeling is still difficult. Quantum computing offers a novel first-principles modeling…

Writing high-performance code requires significant expertise in the programming language, compiler optimizations, and hardware knowledge. This often leads to poor productivity and portability and is inconvenient for a non-programmer…

Prototyping robotic systems is a time consuming process. Computer aided design, however, might speed up the process significantly. Quality-diversity evolutionary approaches optimise for novelty as well as performance, and can be used to…

Codon usage bias has a crucial impact on the translation efficiency and co-translational folding of proteins, necessitating the algorithmic development of codon optimization/harmonization methods, particularly for heterologous recombinant…

This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of…

The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more…

In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…

In this paper, a library-based synthesis methodology for reversible circuits is proposed where a reversible specification is considered as a permutation comprising a set of cycles. To this end, a pre-synthesis optimization step is…

Despite recent advances, goal-directed generation of structured discrete data remains challenging. For problems such as program synthesis (generating source code) and materials design (generating molecules), finding examples which satisfy…

We study the problem of structured prediction under test-time budget constraints. We propose a novel approach applicable to a wide range of structured prediction problems in computer vision and natural language processing. Our approach…

The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…

Modern software deployment process produces software that is uniform, and hence vulnerable to large-scale code-reuse attacks. Compiler-based diversification improves the resilience and security of software systems by automatically…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

The problem-solving performance of many evolutionary algorithms, including genetic programming systems used for program synthesis, depends on the values of hyperparameters including mutation rates. The mutation method used to produce some…

Designing proteins with desired functions or properties represents a core goal in synthetic biology and drug discovery. Recent advances in protein language models (PLMs) have enabled the generation of highly designable protein sequences,…

This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…

Combinatorial optimization problems are prevalent across a wide variety of domains. These problems are often nuanced, their optimal solutions might not be efficiently obtainable, and they may require lots of time and compute resources to…