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One of the central challenges in the computational analysis of liquid chromatography-tandem mass spectrometry (LC-MS/MS) data is to identify the compounds underlying the output spectra. In recent years, this problem is increasingly tackled…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Unlike covalent two-dimensional (2D) materials like graphene, 2D metals have non-layered structures due to their non-directional, metallic bonding. While experiments on 2D metals are still scarce and challenging, density-functional theory…
We introduce a composition-weighted symbolic regression framework for interpretable prediction of materials properties directly from chemical composition. The method jointly learns analytical functional forms and task-dependent elemental…
A non-vector-based dissimilarity measure is proposed by combining vector-based distance metrics and set operations. This proposed compound dissimilarity measure (CDM) is applicable to quantify similarity of collections of attribute/feature…
With the ever-increasing quantity and variety of data worldwide, the Web has become a rich repository of mathematical formulae. This necessitates the creation of robust and scalable systems for Mathematical Information Retrieval, where…
Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine…
Modern text retrieval systems often provide a similarity search utility, that allows the user to find efficiently a fixed number k of documents in the data set that are most similar to a given query (here a query is either a simple sequence…
Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial…
Functional properties of nanomaterials strongly depend on their surface atomic structure, but they often become largely different from their bulk structure, exhibiting surface reconstructions and relaxations. However, most of the surface…
We introduce a differential visual similarity metric to train deep neural networks for 3D reconstruction, aimed at improving reconstruction quality. The metric compares two 3D shapes by measuring distances between multi-view images…
Measurements of nuclear spin-dependent parity-violating (NSD-PV) effects provide an excellent opportunity to test nuclear models and to search for physics beyond the Standard Model. Molecules possess closely-spaced states with opposite…
Finding groups of similar image blocks within an ample search area is often necessary in different applications, such as video compression, image clustering, vector quantization, and nonlocal noise reduction. A block-matching algorithm that…
In pharmaceutical R&D, predicting the efficacy of a pharmaceutical in treating a particular disease prior to clinical testing or any real-world use has been challenging. In this paper, we propose a flexible and modular machine…
Similarity search in math is to find mathematical expressions that are similar to a user's query. We conceptualized the similarity factors between mathematical expressions, and proposed an approach to math similarity search (MSS) by…
This paper develops a theory of clustering and coding which combines a geometric model with a probabilistic model in a principled way. The geometric model is a Riemannian manifold with a Riemannian metric, ${g}_{ij}({\bf x})$, which we…
Finding process pathways in molecular simulations such as the unbinding paths of small molecule ligands from their binding sites at protein targets in a set of trajectories via unsupervised learning approaches requires the definition of a…
Determining the structure and following the structural evolution of molecules undergoing chemical reactions is one of the key goals of ultrafast molecular physics and chemistry. Recently, Coulomb explosion imaging has emerged as a promising…
Similarity search is a popular technique for seismic signal processing, with template matching, matched filters and subspace detectors being utilized for a wide variety of tasks, including both signal detection and source discrimination.…
Edge-to-edge interprecipitate distance distributions are critical for predicting precipitation strengthening of alloys and other physical phenomena. A method to calculate this 3D distance and the 2D interplanar distance from atom-probe…