相关论文: Bloom filters for molecules

Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…

Frequency modulation (FM) Atomic Force Microscopy (AFM) with metal tips functionalized with a CO molecule at the tip apex has provided access to the internal structure of molecules with totally unprecedented resolution. We propose a model…

Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…

The objective of this work is to propose a novel methodology for the finger knuckle print recognition, which is essentially a digital photo of the finger-knuckle region. We have employed very simple concepts of visual computing such as a…

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network…

Machine learning has been widely verified and applied in chemoinformatics, and have achieved outstanding results in the prediction, modification, and optimization of luminescence, magnetism, and electrode materials. Here, we propose a…

Motivation: ``Molecular signatures'' or ``gene-expression signatures'' are used to predict patients' characteristics using data from coexpressed genes. Signatures can enhance understanding about biological mechanisms and have diagnostic…

We introduce a family of positive definite kernels specifically optimized for the manipulation of 3D structures of molecules with kernel methods. The kernels are based on the comparison of the three-points pharmacophores present in the 3D…

In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…

Classical fingerprinting associates with each string a shorter string (its fingerprint), such that, with high probability, any two distinct strings can be distinguished by comparing their fingerprints alone. The fingerprints can be…

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in…

In this paper we compare two probabilistic data structures for association queries derived from the well-known Bloom filter: the shifting Bloom filter (ShBF), and the spatial Bloom filter (SBF). With respect to the original data structure,…

Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the…

As computers get faster, researchers -- not hardware or algorithms -- become the bottleneck in scientific discovery. Computational study of colloidal self-assembly is one area that is keenly affected: even after computers generate massive…

The popular Biometric used to authenticate a person is Fingerprint which is unique and permanent throughout a person's life. A minutia matching is widely used for fingerprint recognition and can be classified as ridge ending and ridge…

Molecular property prediction is a fundamental task in computational chemistry with critical applications in drug discovery and materials science. While recent works have explored Large Language Models (LLMs) for this task, they primarily…

Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…

Membership (membership query / membership testing) is a fundamental problem across databases, networks and security. However, previous research has primarily focused on either approximate solutions, such as Bloom Filters, or exact methods,…

We consider the hashing of a set $X\subseteq U$ with $|X|=m$ using a simple tabulation hash function $h:U\to [n]=\{0,\dots,n-1\}$ and analyse the number of non-empty bins, that is, the size of $h(X)$. We show that the expected size of…

Wolumes is a fast and stand-alone computer program written in standard C that allows the measure of atom volumes in proteins. Its algorithm is a simple discretization of the space by means of a grid of points at 0.75 Angstroms from each…