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Anatomy of High-Performance 2D Similarity Calculations

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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PAPER—Accelerating parallel evaluations of ROCS
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Molecular similarity and diversity in chemoinformatics: From theory to applications
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Clustering a large number of compounds. 1. Establishing the method on an initial sample
inferredcites →https://doi.org/10.1021/ci010132ropenalex-snapshot
Reoptimization of MDL Keys for Use in Drug Discovery
inferredcites →https://doi.org/10.1021/ci049651vopenalex-snapshot
Small Molecule Shape-Fingerprints
inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
inferredcites →https://doi.org/10.1021/ci0499222openalex-snapshot
Accelerated K-Means Clustering in Metric Spaces
inferredcites →https://doi.org/10.1021/ci100011zopenalex-snapshot
SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs
inferredcites →https://doi.org/10.1021/ci1000136openalex-snapshot
SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities
inferredcites →https://doi.org/10.1021/ci100050topenalex-snapshot
Extended-Connectivity Fingerprints
inferredcites →https://doi.org/10.1021/ci100437eopenalex-snapshot
Using Inverted Indices for Accelerating LINGO Calculations
inferredcites →https://doi.org/10.1021/ci200061popenalex-snapshot
Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs
inferredcites →https://doi.org/10.1021/ci600358fopenalex-snapshot
Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time
inferredcites →https://doi.org/10.1021/ci800325vopenalex-snapshot
Compressed Binary Bit Trees: A New Data Structure For Accelerating Database Searching
inferredcites →https://doi.org/10.1021/ja902302hopenalex-snapshot
970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13
inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot
Database resources of the National Center for Biotechnology Information: update
inferredcites →https://doi.org/10.1093/nar/gkq1172openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/nar/gkr441openalex-snapshot
FFAS server: novel features and applications
inferredcites →https://doi.org/10.1108/13665620910985568openalex-snapshot
Beautiful Code. Leading Programmers Explain How They Think
inferredcites →https://doi.org/10.1109/ispass.2010.5452013openalex-snapshot
Demystifying GPU microarchitecture through microbenchmarking
inferredcites →https://doi.org/10.1109/tpds.2002.1058095openalex-snapshot
Recursive array layouts and fast matrix multiplication
inferredcites →https://doi.org/10.2174/156802606775193310openalex-snapshot
Diversity in Medicinal Chemistry Space
inferredcites →https://doi.org/10.2174/1570163043334965openalex-snapshot
Strategies for Compound Selection

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Molecular Similarity: Methods and Performance
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Efficient computation of positional population counts using SIMD instructions
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Optimized succinct data structures for massive data
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Index Structures for Fast Similarity Search for Binary Vectors
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GSA: a GPU-accelerated structure similarity algorithm and its application in progressive virtual screening
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Chemoinformatics: A view of the field and current trends in method development
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Identification of potential inhibitors against nuclear Dam1 complex subunit Ask1 of Candida albicans using virtual screening and MD simulations
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Parallel accelerated vector similarity calculations for genomics applications
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Parallel accelerated Custom Correlation Coefficient calculations for genomics applications
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On Bidirectional Transitions between Localist and Distributed Representations: The Case of Common Substrings Search Using Vector Symbolic Architecture
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RISC: Rapid Inverted-Index Based Search of Chemical Fingerprints
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Automated Recycling of Chemistry for Virtual Screening and Library Design
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Construction and Use of Fragment-Augmented Molecular Hasse Diagrams
inferred← citeshttps://doi.org/10.1021/ci500150topenalex-snapshot
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces
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Methods for accuracy‐preserving acceleration of large‐scale comparisons in CPU‐based iris recognition systems
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Clustering the Planet: An Exascale Approach to Determining Global Climatype Zones
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Hyperdimensional Computing in Industrial Systems: The Use-Case of Distributed Fault Isolation in a Power Plant
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Generating FPGA accelerators for chemical similarity assessment
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KNN in the Jaccard space
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OrthCredential: A New Network Capability Design for High-Performance Access Control
inferred← citeshttps://doi.org/10.1109/ijcnn54540.2023.10191473openalex-snapshot
Subgraph-Oriented Heterogeneous Drug-Target Interaction Identification
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Efficient Computation of Linkage Disequilibria as Dense Linear Algebra Operations
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A hybrid implementation of Hamming weight
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Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for Chronic Pain and Opioid Addiction
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Evolutionary algorithms for overlapping correlation clustering
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USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints
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Blazing Signature Filter: a library for fast pairwise similarity comparisons
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The chemfp project
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Second-generation PLINK: rising to the challenge of larger and richer datasets
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Attacking the opioid epidemic: determining the epistatic and pleiotropic genetic architectures for chronic pain and opioid addiction
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Enhance similarity searching algorithm with optimized fast population count method based on parallel design
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