Related papers: Optimal Codeword Construction for DNA-based Finite…
A quantum finite-state automaton (QFA) is a theoretical model designed to simulate the evolution of a quantum system with finite memory in response to sequential input strings. We define the language of a QFA as the set of strings that lead…
Solving math word problems is a challenging task that requires accurate natural language understanding to bridge natural language texts and math expressions. Motivated by the intuition about how human generates the equations given the…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
Quantum computing is a new model of computation, based on quantum physics. Quantum computers can be exponentially faster than conventional computers for problems such as factoring. Besides full-scale quantum computers, more restricted…
Most business process automation is still developed using traditional automation technologies such as workflow engines. These systems provide domain specific languages that require both business knowledge and programming skills to…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…
This thesis proposes an advanced, generic and high-level code rewriting and analysis system in the Julia programming language, providing applied equality saturation in the presence of multiple dispatch and metaprogramming. We show how our…
Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient…
Over the last few decades, researchers have made considerable efforts to make decision support more accessible for small and medium enterprises by reducing the cost of designing, developing and maintaining automated decision support…
Deep Learning (DL) techniques for Natural Language Processing have been evolving remarkably fast. Recently, the DL advances in language modeling, machine translation and paragraph understanding are so prominent that the potential of DL in…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Over the last decades, deep neural networks based-models became the dominant paradigm in machine learning. Further, the use of artificial neural networks in symbolic learning has been seen as increasingly relevant recently. To study the…
There are already many DNA large language models, but most of them still follow traditional uses, such as extracting sequence features for classification tasks. More innovative applications of large language models, such as prompt…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
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…
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…
Numerous computer systems use dynamic control and data structures of unbounded size. These data structures have often the character of trees or they can be encoded as trees with some additional pointers. This is exploited by some currently…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
We consider ways to construct a transducer for a given set of input word to output symbol pairs. This is motivated by the need for representing game playing programs in a low-level mathematical format that can be analyzed by algebraic…