Related papers: How to build a DNA search engine like Google?
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Deep learning has shown promising results on many machine learning tasks but DL models are often complex networks with large number of neurons and layers, and recently, complex layer structures known as building blocks. Finding the best…
In the past few years, Differentiable Neural Architecture Search (DNAS) rapidly imposed itself as the trending approach to automate the discovery of deep neural network architectures. This rise is mainly due to the popularity of DARTS, one…
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…
Neural Architecture Search has achieved state-of-the-art performance in a variety of tasks, out-performing human-designed networks. However, many assumptions, that require human definition, related with the problems being solved or the…
We present a Neural Program Search, an algorithm to generate programs from natural language description and a small number of input/output examples. The algorithm combines methods from Deep Learning and Program Synthesis fields by designing…
Effective search methods are crucial for improving the performance of deep generative models at test time. In this paper, we introduce a novel test-time search method, Neural Genetic Search (NGS), which incorporates the evolutionary…
For complex data types such as multimedia, traditional data management methods are not suitable. Instead of attribute matching approaches, access methods based on object similarity are becoming popular. Recently, this resulted in an…
Deep Neural Networks (DNNs) have achieved great success in many applications. The architectures of DNNs play a crucial role in their performance, which is usually manually designed with rich expertise. However, such a design process is…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
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,…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…
Relation linking is essential to enable question answering over knowledge bases. Although there are various efforts to improve relation linking performance, the current state-of-the-art methods do not achieve optimal results, therefore,…
With the rising popularity of user-generated genealogical family trees, new genealogical information systems have been developed. State-of-the-art natural question answering algorithms use deep neural network (DNN) architecture based on…
This paper describes the realization of the Ontology Web Search Engine. The Ontology Web Search Engine is realizable as independent project and as a part of other projects. The main purpose of this paper is to present the Ontology Web…