Related papers: Review on DNA Strand Algebra and its Application
Supercomputers are equipped with an increasingly large number of cores to use computational power as a way of solving problems that are otherwise intractable. Unfortunately, getting serial algorithms to run in parallel to take advantage of…
To cope with the ever-increasing computational demand of the DNN execution, recent neural architecture search (NAS) algorithms consider hardware cost metrics into account, such as GPU latency. To further pursue a fast, efficient execution,…
The term Big Data is usually used to describe huge amount of data that is generated by humans from digital media such as cameras, internet, phones, sensors etc. By building advanced analytics on the top of big data, one can predict many…
The explosive growth of large language models (LLMs) has created a vast but opaque landscape: millions of models exist, yet their evolutionary relationships through fine-tuning, distillation, or adaptation are often undocumented or unclear,…
Transformers have demonstrated remarkable performance in natural language processing and related domains, as they largely focus on sequential, autoregressive next-token prediction tasks. Yet, they struggle in logical reasoning, not…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
An ideal signature material and method, which can be used to prove the authenticity of a physical item and against forgery, should be immune to the fast developments in digital and engineering technologies. Herein, the design of signature…
The main motivation of this work was practical, to offer computationally and theoretical scalable ways to structuring large classes of computation. It started from attempts to optimize R code for machine learning/artificial intelligence…
Qualitative reasoning involves expressing and deriving knowledge based on qualitative terms such as natural language expressions, rather than strict mathematical quantities. Well over 40 qualitative calculi have been proposed so far, mostly…
The growing reliance on digital twins across various industries and domains brings with it semantic interoperability challenges. Ontologies are a well-known strategy for addressing such challenges, though given the complexity of the…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
Parallelization techniques have become ubiquitous for accelerating inference and training of deep neural networks. Despite this, several operations are still performed in a sequential manner. For instance, the forward and backward passes…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
As artificial intelligence becomes increasingly prevalent in scientific research, data-driven methodologies appear to overshadow traditional approaches in resolving scientific problems. In this Perspective, we revisit a classic…
Recently, there has been a surge of interest in combining deep learning models with reasoning in order to handle more sophisticated learning tasks. In many cases, a reasoning task can be solved by an iterative algorithm. This algorithm is…
The concept of linearity plays a central role in both mathematics and computer science, with distinct yet complementary meanings. In mathematics, linearity underpins functions and vector spaces, forming the foundation of linear algebra and…
Many numerical algorithms in scientific computing -- particularly in areas like numerical linear algebra, PDE simulation, and inverse problems -- produce outputs that can be represented by semialgebraic functions; that is, the graph of the…
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…
In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper…