Related papers: Theorem Proving Based on Semantics of DNA Strand G…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
Deep learning is widely used to uncover hidden patterns in large code corpora. To achieve this, constructing a format that captures the relevant characteristics and features of source code is essential. Graph-based representations have…
Explaining why an answer is (or is not) returned by a query is important for many applications including auditing, debugging data and queries, and answering hypothetical questions about data. In this work, we present the first practical…
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
Proof nets are a syntax for linear logic proofs which gives a coarser notion of proof equivalence with respect to syntactic equality together with an intuitive geometrical representation of proofs. In this paper we give an alternative…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
The analysis of DNA sequences has become critical in numerous fields, from evolutionary biology to understanding gene regulation and disease mechanisms. While deep neural networks can achieve remarkable predictive performance, they…
The aim of this thesis is to present an extension to the string graphs of Dixon, Duncan and Kissinger that allows the finite representation of certain infinite families of graphs and graph rewrite rules, and to demonstrate that a logic can…
We introduce a logical foundation to reason on tree structures with constraints on the number of node occurrences. Related formalisms are limited to express occurrence constraints on particular tree regions, as for instance the children of…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
In the medical domain, the continuous stream of scientific research contains contradictory results supported by arguments and counter-arguments. As medical expertise occurs at different levels, part of the human agents have difficulties to…
Automated mathematical reasoning is a challenging problem that requires an agent to learn algebraic patterns that contain long-range dependencies. Two particular tasks that test this type of reasoning are (1) mathematical equation…
I introduce a formalism for representing the syntax of recursively structured graph-like patterns. It does not use production rules, like a conventional graph grammar, but represents the syntactic structure in a more direct and declarative…
Reasoning, the ability to logically draw conclusions from existing knowledge, is a hallmark of human. Together with perception, they constitute the two major themes of artificial intelligence. While deep learning has pushed the limit of…
We introduce Spectral NSR, a fully spectral neuro-symbolic reasoning framework that embeds logical rules as spectral templates and performs inference directly in the graph spectral domain. By leveraging graph signal processing (GSP) and…
The meaning of a sentence is a function of the relations that hold between its words. We instantiate this relational view of semantics in a series of neural models based on variants of relation networks (RNs) which represent a set of…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
A model checking computation checks whether a given logical sentence is true in a given finite structure. Provenance analysis abstracts from such a computation mathematical information on how the result depends on the atomic data that…