Related papers: Eliminating unwanted patterns with minimal interfe…

Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made…

We propose and discuss a novel strategy for protein design. The method is based on recent theoretical advancements which showed the importance to treat carefully the conformational free energy of designed sequences. In this work we show how…

Embedded devices are omnipresent in modern networks including the ones operating inside critical environments. However, due to their constrained nature, novel mechanisms are required to provide external, and non-intrusive anomaly detection.…

Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…

Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…

In recent years, many neural network models have been proposed for pattern classification, function approximation and regression problems. This paper presents an approach for classifying patterns from simplified NNs. Although the predictive…

In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…

Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to…

Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…

In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…

The goal of filter pruning is to search for unimportant filters to remove in order to make convolutional neural networks (CNNs) efficient without sacrificing the performance in the process. The challenge lies in finding information that can…

In product design, a decomposition of the overall product function into a set of smaller, interacting functions is usually considered a crucial first step for any computer-supported design tool. Here, we propose a new approach for the…

Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…

DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…

We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…

Raman spectroscopy can provide insight into the molecular composition of cells and tissue. Consequently, it can be used as a powerful diagnostic tool, e.g. to help identify changes in molecular contents with the onset of disease. But robust…

The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…

Optimization acceleration techniques such as momentum play a key role in state-of-the-art machine learning algorithms. Recently, generic vector sequence extrapolation techniques, such as regularized nonlinear acceleration (RNA) of Scieur et…

Domain-specific constraint patterns are introduced, which form the counterpart to design patterns in software engineering for the constraint programming setting. These patterns describe the expert knowledge and best-practice solution to…

Enzymes are genetically encoded biocatalysts capable of accelerating chemical reactions. How can we automatically design functional enzymes? In this paper, we propose EnzyGen, an approach to learn a unified model to design enzymes across…