Related papers: Reconciling Inconsistent Molecular Structures from…

In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of…

Table structure recognition is necessary for a comprehensive understanding of documents. Tables in unstructured business documents are tough to parse due to the high diversity of layouts, varying alignments of contents, and the presence of…

Information extraction from chemistry literature is vital for constructing up-to-date reaction databases for data-driven chemistry. Complete extraction requires combining information across text, tables, and figures, whereas prior work has…

One of the recent best attempts at Text-to-SQL is the pre-trained language model. Due to the structural property of the SQL queries, the seq2seq model takes the responsibility of parsing both the schema items (i.e., tables and columns) and…

Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…

We report development of a data infrastructure for drug repurposing that takes advantage of two currently available chemical ontologies. The data infrastructure includes a database of compound- target associations augmented with molecular…

Nuclear Magnetic Resonance (NMR) spectroscopy is particularly well-suited to determine the structure of molecules and materials in powdered form. Structure determination usually proceeds by finding the best match between experimentally…

We have developed an end-to-end, retrosynthesis system, named ChemiRise, that can propose complete retrosynthesis routes for organic compounds rapidly and reliably. The system was trained on a processed patent database of over 3 million…

This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our…

The determination of chemical mixture components is vital to a multitude of scientific fields. Oftentimes spectroscopic methods are employed to decipher the composition of these mixtures. However, the sheer density of spectral features…

As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across…

Despite Retrieval-Augmented Generation improving code completion, traditional retrieval methods struggle with information redundancy and a lack of diversity within limited context windows. To solve this, we propose a resource-optimized…

Molecular function is largely determined by structure. Accurately aligning molecular structure with natural language is therefore essential for enabling large language models (LLMs) to reason about downstream chemical tasks. However, the…

In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank…

Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A…

Retrosynthesis analysis is a critical task in organic chemistry central to many important industries. Previously, various machine learning approaches have achieved promising results on this task by representing output molecules as strings…

We consider the evaluation of first-order queries over classes of databases that have bounded degree and low degree. More precisely, given a query and a database, we want to efficiently test whether there is a solution, count how many…

One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation…

With distributed computing and mobile applications, synchronizing diverging replicas of data structures is a more and more common problem. We use algebraic methods to reason about filesystem operations, and introduce a simplified definition…

Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for…