Related papers: Theorem Proving Based on Semantics of DNA Strand G…
This work concerns formal descriptions of DNA code properties, and builds on previous work on transducer descriptions of classic code properties and on trajectory descriptions of DNA code properties. This line of research allows us to give…
Researchers have relegated natural language processing tasks to Transformer-type models, particularly generative models, because these models exhibit high versatility when performing generation and classification tasks. As the size of these…
Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…
This paper introduces a differentiable semantic reasoner, where rules are presented as a relevant set of graph transformations. These rules can be written manually or inferred by a set of facts and goals presented as a training set. While…
Advances in logic programming and increasing industrial uptake of Datalog-inspired approaches demonstrate the emerging need to express powerful code analyses more easily. Declarative program analysis frameworks (e.g., using logic…
Using appropriate notation systems for proofs, cut-reduction can often be rendered feasible on these notations, and explicit bounds can be given. Developing a suitable notation system for Bounded Arithmetic, and applying these bounds, all…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
Provenance for database queries or scientific workflows is often motivated as providing explanation, increasing understanding of the underlying data sources and processes used to compute the query, and reproducibility, the capability to…
Document structure analysis, such as zone segmentation and table recognition, is a complex problem in document processing and is an active area of research. The recent success of deep learning in solving various computer vision and machine…
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
Recent research efforts aiming to bridge the Neural-Symbolic gap for RDFS reasoning proved empirically that deep learning techniques can be used to learn RDFS inference rules. However, one of their main deficiencies compared to rule-based…
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…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
Applying machine learning to mathematical terms and formulas requires a suitable representation of formulas that is adequate for AI methods. In this paper, we develop an encoding that allows for logical properties to be preserved and is…
We describe an approach to modelling and reasoning about data-centric business processes and present a form of general model checking. Our technique extends existing approaches, which explore systems only from concrete initial states.…
The paper is devoted to showing how to systematically design a programming language in 'reverse order', i.e. from denotations to syntax. This construction is developed in an algebraic framework consisting of three many-sorted algebras: of…
Knowledge graphs store large numbers of relations efficiently, but they remain weak at representing a quieter difficulty: the meaning of a concept often shifts with the domain in which it is used. A triple such as Apple, instance-of,…
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
This book can be seen either as a text on theorem proving that uses techniques from general algebra, or else as a text on general algebra illustrated and made concrete by practical exercises in theorem proving. The book considers several…