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Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery
Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.
Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)
Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active—while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.
Explore Information Content Efficiently from Current and Future Hyperspectral Satellite Missions using a Spectral Fingerprinting Method
Hyperspectral remote sensors from current and future missions provide measurements of the Top of Atmosphere (TOA) radiance or reflectance spectra with high information content. For example, the Atmospheric Infrared Sounder (AIRS), together with the Cross-track Infrared Sounder (CrIS), and the Infrared Atmospheric Sounding Interferometer (IASI) have provided more than 20 years radiance measurements with thousands of spectral channels. These measurements will be continued for the next two decades with the same or more advanced hyperspectral sensors. The upcoming missions such as NASA’s CLARREO Pathfinder (CPF) and ESA’s TRUTHS will provide unprecedented accurate TOA hyperspectral radiance measurements in solar spectral region. Traditional ways to derive Climate Data Records (CDRs) from these measurements are performing spatial and temporal averages of the retrieved Level-2 products. However, it is a time-consuming process to generate decades of Level-2 data from Level-1 data. Furthermore, the differences in Level-2 algorithms used for different satellite sensors will introduce errors in derived CDRs. In this presentation, we will describe a spectral fingerprinting method to generate high-quality CDRs directly from spatiotemporally averaged Level-1 data. By using consistent radiative kernels which contain the spectral information of various atmospheric and surface CDRs, we can reduce the errors due to algorithm inconsistency. Additionally, the spectral fingerprinting method reduces the time needed to generate CDRs by more than three orders of magnitude. This makes it easy to reprocess CDRs once the Level-1 data from different satellites have been improved via either re-calibrations or inter-satellite calibrations. We will present results of applying spectral fingerprinting method to 20-years of AIRS and CrIS data. The resulting CDRs include: 1) vertical profiles of atmospheric temperature and water vapor, 2) cloud properties such as optical depth, effective size, and height, 3) vertical profiles or column amounts for atmospheric trace gases such as O3 and CO, and 4) surface emissivity spectra and skin temperatures. These CDRs will be publicly available at NASA GES DISC in late 2024. The same fingerprinting method is planned to be applied to future CPF and TRUTHS data for solar spectral region.
Transformer Masked Autoencoders for RF Device Fingerprinting
Machine learning methods for RF device fingerprinting typically rely on CNN-based models. Transformer-based models have outperformed CNNs for modulation classification tasks, but there are few implementations for device fingerprinting. We train a transformer for device fingerprinting with the largest device count to date and explore several variations of the architecture. Additionally, we demonstrate that pre-training an RF transformer as a Masked Autoencoder improves classification accuracy, as has been observed for CNN fingerprinting models and vision transformers.
Fingerprinting of Materials: Technical Supplement
This supplement to the Guidelines for Maintaining a Chemical Fingerprinting Program has been developed to assist NASA personnel, contractors, and sub-contractors in defining the technical aspects and basic concepts which can be used in chemical fingerprinting programs. This material is not meant to be totally inclusive to all chemical fingerprinting programs, but merely to present current concepts. Each program will be tailored to meet the needs of the individual organizations using chemical fingerprinting to improve their quality and reliability in the production of aerospace systems.
Chemical Fingerprinting of Materials Developed Due to Environmental Issues
Instrumental chemical analysis methods are developed and used to chemically fingerprint new and modified External Tank materials made necessary by changing environmental requirements. Chemical fingerprinting can detect and diagnose variations in material composition. To chemically characterize each material, fingerprint methods are selected from an extensive toolbox based on the material's chemistry and the ability of the specific methods to detect the material's critical ingredients. Fingerprint methods have been developed for a variety of materials including Thermal Protection System foams, adhesives, primers, and composites.
A Radiometric Consistent Spectral Fingerprinting Algorithm for Continuity Products of Hyperspectral Sounders
A radiometric consistent climate fingerprinting methodology has been developed to derive long-term temperature, water vapor, cloud, trace gases, and surface skin temperature anomaly time series from the hyper-spectral sounder measurements of multiple platforms. The spectral fingerprinting methodology requires the use of radiative kernels that are radiometrically consistent with observations. Radiative kernels are built using space-time averaged Jacobians that are physically retrieved from observations under all sky conditions. The physical retrieval algorithm uses the Principal Component based Radiative Transfer Model (PCRTM) for the forward simulation. The incorporation of multiple scattering simulation in PCRTM allows the direct radiative relationship between single field-of-view (FOV) radiance observations and corresponding thermal dynamic variables including cloud properties to be established. Therefore, radiance ?closure? can be achieved under all-sky conditions by the fingerprinting scheme. This methodology has been used to derive climate anomalies from the space-time averaged spectra of AIRS/AMSU and CrIS/ATMS. The use of a consistent fingerprinting scheme provides an effective mean of generating continuity product by merging observations from different platforms and therefore facilitating the long-term climate trend study.
Position-Specific Carbon Isotope Fingerprinting of Fluorinated Organics and Degradation Products
Fluorinated organic compounds are of growing environmental and forensic relevance due to their widespread use in pharmaceuticals, agrochemicals, and consumer products, their environmental persistence, and potential ecological and human health impacts. Elucidating their sources and transformation pathways is therefore a major focus of current research. Stable carbon isotope analysis provides a powerful approach for tracing molecular origins and linking parent compounds to degradation products. Recent isotope measurements have largely relied on mass-spectrometry techniques, which provide only an average isotope ratio across a compound. In this work, we employ a novel nuclear magnetic resonance (NMR) spectroscopy tool to determine position-specific carbon isotope ratios ( 13 C/ 12 C) in organofluorine compounds and their degradation products. This approach enables isotope measurements without combustion or extensive purification and, crucially, resolves ratios at individual carbon positions rather than bulk averages. The resulting intramolecular isotope fingerprints are unique to a molecule’s source. Applied to selected pharmaceuticals and pesticides, these fingerprints allow discrimination of chemically identical compounds. Moreover, we show that the 13 C/ 12 C signature at the fluorinated carbon persists through degradation, demonstrated for lansoprazole and fipronil. The 19 F NMR data produced for the 13 C/ 12 C analyses are also well suited for impurity profiling, providing an additional dimension for fingerprinting fluorinated organics. These findings suggest that position-specific isotope analysis can serve as part of a broader suite of tools for source characterization of organofluorine compounds and their breakdown derivatives, with potential applications in product validation, forensics, and linking these compounds to their breakdown products.
Genomic fingerprints of the world’s soil ecosystems
Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.
Frequency Emitter Geolocation Using Signal Strength Fingerprinting Informed By 3D Propagation Modeling
This work focuses on the problem of RF geolocation in complex multipath environments. Using 3D electromagnetic propagation modeling to characterize environments of interest will enable more accurate RF geolocation. Specifically, a path-loss radio map can be generated in simulation for use in received signal strength indicators (RSSI) fingerprinting, or pattern matching. RSSI fingerprinting is an example of data-based method that takes site specific information into account which should allow for better performance than other model-based methods that use a generalized model of electromagnetic propagation. This modeling capability will also be used to evaluate the relative performance of RSSI fingerprinting, pathloss model based RSSI methods such as differential received signal strength circles (DRSS), RSSI joint gaussian estimation, and time-difference of arrival (TDOA). New methods using this simulation derived electromagnetic characterization could improve the efficacy of currently deployed and future RF spectral monitoring solutions. Wireless InSite developed by Remcom is used as the simulation tool of choice in this work. An indoor location is simulated with a grid of fixed receivers and a grid of transmit locations. Using the output of the Wireless InSite simulation the response from a given transmit location to a given receive location can be generated. During the first year of the project various geolocation methods evaluated on purely synthetic, but realistic, data. The second year focused on testing and validating the efficacy of simulation informed RF geolocation using two physical testbeds. This work has shown that data-based approaches are more accurate than model-based ones at the expensive of requiring measured or simulated site-specific training data.
Chemical Fingerprinting of Materials Developed Due To Environmental Issues
This paper presents viewgraphs on chemical fingerprinting of materials developed due to environmental issues. Some of the topics include: 1) Aerospace Materials; 2) Building Blocks of Capabilities; 3) Spectroscopic Techniques; 4) Chromatographic Techniques; 5) Factors that Determine Fingerprinting Approach; and 6) Fingerprinting: Combination of instrumental analysis methods that diagnostically characterize a material.
Fusion of Hyperspectral Sounder Products Via Spectral Fingerprinting Methodology
Satellite based measurements of top-of-atmosphere (TOA) spectral radiances in the infrared (IR) region have been in existence for almost two decades and are expected to be continued in the following decades. The data from multiple hyper-spectral IR sounders can therefore be combined to build a long-term data record to further global scale climate trend research. Challenges associated with the fusion of data from different sensors come from the stability and consistency requirement on the climate record. The direct radiance observations from different sounders need to be homogenized by reconciling the differences in calibration, spectral response function (SRF), and spatial-temporal sampling. When geophysical variables derived from radiances measured by different sounders are combined to form long-term climate records, the impacts of any inconsistencies between overlapping measurements on the retrieval must be carefully assessed in order to estimate the uncertainty of the corresponding climate anomalies/trends derived. This paper presents a novel climate fingerprinting methodology and establishes a rigorously-defined inverse relationship that allows us to efficiently evaluate the change in essential climate variables from the change in spectral radiances measured in prescribed spatial and temporal averaging scales. The inverse spectral fingerprinting relationship is constructed based on a unified spectral kernel scheme, providing a direct means for quantifying the potential discontinuity in the derived climate anomalies due to inconsistencies between overlapping measurements. We show in this paper a sample application of using the spectral fingerprinting scheme to derive long-term, global-scale surface temperatures from the Climate Hyperspectral Infrared Radiance Product (CHIRP) and quantify the inter-satellite biases.
Dual-Polarization Radar Fingerprints of Precipitation Physics: A Review
This article reviews how precipitation microphysics processes are observed in dual-polarization radar observations. These so-called “fingerprints” of precipitation processes are observed as vertical gradients in radar observables. Fingerprints of rain processes are first reviewed, followed by processes involving snow and ice. Then, emerging research is introduced, which includes more quantitative analysis of these dual-polarization radar fingerprints to obtain microphysics model parameters and microphysical process rates. New results based on a detailed rain shaft bin microphysical model are presented, and we conclude with an outlook of potentially fruitful future research directions.
A locally-connected neural network for fingerprint recognition
Fingerprint recognition is typically done by matching graphs or templates of extracted minutia from whole fingerprint images.
Deriving Climate Change Signal from Hyperspectral Sounders Using Spectral Fingerprinting Method
Hyperspectral observations from satellite-based sensors provide high information content for the Earth’s atmospheric temperature, water vapor and trace gas vertical profiles. We have developed a radiometrically consistent spectral fingerprinting method to derive climate change signals from Aqua AIRS/AMSU and S-NPP CrIS/ATMS data. The climate variables include temperature and water vapor profiles, cloud, trace gases, and surface skin temperature. The radiative kernels obtained via a single field of view physical retrieval algorithm under all-sky conditions. A key component to this work is a Principal Component-based Radiative Transfer Model (PCRTM). It is 4 orders of magnitude faster than a line-by-line radiative transfer model while keeping a similar accuracy (0.03 K RMS errors with close to zero bias). The PCRTM includes multiple scattering of clouds and non-thermodynamics equilibrium of CO2 in the RT calculations. Instead of quantifying the radiometric differences between AIRS/AMSU and CrIS/ATMS measurements directly using Simultaneous Nadir Overpass (SNO) or Double Difference Technique (DDT), we use the radiometric consistent fingerprinting scheme to derive two sets of space-time averaged anomalies from the Level 1 data of AIRS/AMSU and CrIS/ATMS. The derived anomalies in geophysical space will form a long-term, stable, and continuous climate data record. We can further infer the causes of any offset or drift by studying the differences between two overlapping data sets. For example, the offset in surface skin temperature anomaly time series will most likely caused by the Blackbody temperature calibration errors of the sounder instruments.
Decoding THz‐Driven Dynamic Fingerprints of Ferroelectric Nanotwin Networks
Ultrafast polarization dynamics in ferroelectrics are of considerable interest for high-speed tunable dielectrics and electro-optics. Extended domain wall networks formed in ferroelectric twin nanodomains can support collective dynamics in the terahertz regime but require techniques that track polarization and strain evolution driven by ultrafast stimulus. Here, we use multi-modal probing of THz-pulse-driven excitations in PbTiO 3 /SrTiO 3 superlattices by combining X-ray free electron laser measurements that directly tracks lattice changes, with optical second harmonic generation that tracks the electronic potential coupled with the lattice potential. Dynamical phase-field modeling enables fingerprinting of these collective modes as superpositions of domain “breathing” through wall oscillations and polarization “rotations” with still walls. Ultrafast domain wall motion at 0.1–0.5 THz is observed at practical fields of 100 kV/cm with wall velocities of >4000 m/s, approaching typical speed of sound in PbTiO 3 . A unique “charging” mode is discovered that can electrically charge and discharge domain walls on ∼4 ps time scale thus dynamically tuning wall conductivity. Integrated experimental and theoretical fingerprinting of the dynamical landscape presented here enables ultrafast control of ferroics for high-speed microelectronics and optical applications.
Cluster-Graph Fingerprinting: A Framework for Quantitative Analysis of Machine-Learned Interatomic Model Training and Simulation Data
Machine-learned interatomic models represent a significant advancement in simulation methods, extending the predictive ability of first-principles methods to previously inaccessible length and time scales. However, the data-driven nature of these models can lead to difficult-to-detect errors that can compromise prediction accuracy. To address this challenge, we introduce a novel fingerprinting approach based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES) ML-IAM graph-based descriptor. Our strategy enables efficient and statistically rigorous analysis of system configurations used in ML-IAM training and those generated by their application, e.g., in molecular dynamics simulations. We demonstrate that these fingerprints can effectively assess novelty of a configuration relative to an existing data set and determine dissimilarity among individual configurations, which are two key tasks in workflows for active learning-based ML-IAM training, data set curation, and on-the-fly uncertainty quantification.