Related papers: A screened automated structural search with semiem…
Cross-modal retrieval aims to search for instances, which are semantically related to the query through the interaction of different modal data. Traditional solutions utilize a single-tower or dual-tower framework to explicitly compute the…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Multi-stage screening pipelines are ubiquitous throughout experimental and computational science. Much of the effort in developing screening pipelines focuses on improving generative methods or surrogate models in an attempt to make each…
We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global…
We present a high-throughput, end-to-end pipeline for organic crystal structure prediction (CSP) -- the problem of identifying the stable crystal structures that will form from a given molecule based only on its molecular composition. Our…
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a…
In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…
Computational models of human language often involve combinatorial problems. For instance, a probabilistic parser may marginalize over exponentially many trees to make predictions. Algorithms for such problems often employ dynamic…
Current popular methods for Magnetic Resonance Fingerprint (MRF) recovery are bottlenecked by the heavy computations of a matched-filtering step due to the growing size and complexity of the fingerprint dictionaries in multi-parametric…
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in…
Molecular simulations have assumed a paramount role in the fields of chemistry, biology, and material sciences, being able to capture the intricate dynamic properties of systems. Within this realm, coarse-grained (CG) techniques have…
We present a multimodal search tool that facilitates retrieval of chemical reactions, molecular structures, and associated text from scientific literature. Queries may combine molecular diagrams, textual descriptions, and reaction data,…
Online augmentation of an oblique aerial image sequence with structural information is an essential aspect in the process of 3D scene interpretation and analysis. One key aspect in this is the efficient dense image matching and depth…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
We study the problem of performing automated experiment design for drug screening through Bayesian inference and optimisation. In particular, we compare and contrast the behaviour of linear-Gaussian models and Gaussian processes, when used…
One-dimensional nuclear magnetic resonance (NMR) spectroscopy is essential for molecular structure elucidation in organic synthesis, drug discovery, natural product characterization, and metabolomics, yet its interpretation remains heavily…
Automated methods for discovering mechanistic simulator models from observational data offer a promising path toward accelerating scientific progress. Such methods often take the form of agentic-style iterative workflows that repeatedly…
Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule. Existing generative…
Since the advent of various pre-trained large language models, extracting structured knowledge from scientific text has experienced a revolutionary change compared with traditional machine learning or natural language processing techniques.…
We designed a fast similarity search engine for large molecular libraries: FPScreen. We downloaded 100 million molecules' structure files in PubChem with SDF extension, then applied a computational chemistry tool RDKit to convert each…