TY - JOUR A1 - Russo, Francesco F. A1 - Nowatzky, Yannek A1 - Jaeger, Carsten A1 - Parr, Maria K. A1 - Benner, Philipp A1 - Muth, Thilo A1 - Lisec, Jan T1 - Machine learning methods for compound annotation in non‐targeted mass spectrometry—A brief overview of fingerprinting, in silico fragmentation and de novo methods N2 - Non‐targeted screenings (NTS) are essential tools in different fields, such as forensics, health and environmental sciences. NTSs often employ mass spectrometry (MS) methods due to their high throughput and sensitivity in comparison to, for example, nuclear magnetic resonance–based methods. As the identification of mass spectral signals, called annotation, is labour intensive, it has been used for developing supporting tools based on machine learning (ML). However, both the diversity of mass spectral signals and the sheer quantity of different ML tools developed for compound annotation present a challenge for researchers in maintaining a comprehensive overview of the field.In this work, we illustrate which ML‐based methods are available for compound annotation in non‐targeted MS experiments and provide a nuanced comparison of the ML models used in MS data analysis, unravelling their unique features and performance metrics. Through this overview we support researchers to judiciously apply these tools in their daily research. This review also offers a detailed exploration of methods and datasets to show gaps in current methods, and promising target areas, offering a starting point for developers intending to improve existing methodologies. KW - Mass Spectrometry KW - Spectra annotation KW - Machine learning PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-608732 DO - https://doi.org/10.1002/rcm.9876 VL - 38 IS - 20 SP - 1 EP - 15 PB - Wiley AN - OPUS4-60873 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Riebesell, Janosh A1 - Goodall, Rhys E. A. A1 - Benner, Philipp A1 - Chiang, Yuan A1 - Deng, Bowen A1 - Ceder, Gerbrand A1 - Asta, Mark A1 - Lee, Alpha A. A1 - Jain, Anubhav A1 - Persson, Kristin A. T1 - A framework to evaluate machine learning crystal stability predictions N2 - The rapid adoption of machine learning in various scientific domains calls for the development of best practices and community agreed-upon benchmarking tasks and metrics. We present Matbench Discovery as an example evaluation framework for machine learning energy models, here applied as pre-filters to first-principles computed data in a high-throughput search for stable inorganic crystals. We address the disconnect between (1) thermodynamic stability and formation energy and (2) retrospective and prospective benchmarking for materials discovery. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with adaptive user-defined weighting of various performance metrics allowing researchers to prioritize the metrics they value most. To answer the question of which machine learning methodology performs best at materials discovery, our initial release includes random forests, graph neural networks, one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials. We highlight a misalignment between commonly used regression metrics and more task-relevant classification metrics for materials discovery. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV per atom above the convex hull. The benchmark results demonstrate that universal interatomic potentials have advanced sufficiently to effectively and cheaply pre-screen thermodynamic stable hypothetical materials in future expansions of high-throughput materials databases. KW - Machine Learning KW - Interatomic Potentials PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-637139 DO - https://doi.org/10.1038/s42256-025-01055-1 SN - 2522-5839 VL - 7 IS - 6 SP - 836 EP - 847 PB - Springer Science and Business Media LLC AN - OPUS4-63713 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Nowatzky, Yannek A1 - Russo, Francesco Friedrich A1 - Lisec, Jan A1 - Kister, Alexander A1 - Reinert, Knut A1 - Muth, Thilo A1 - Benner, Philipp T1 - FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events N2 - Non-targeted metabolomics holds great promise for advancing precision medicine and biomarker discovery. However, identifying compounds from tandem mass spectra remains a challenging task due to the incomplete nature of spectral reference libraries. Augmenting these libraries with simulated mass spectra can provide the necessary references to resolve unmatched spectra, but generating high-quality data is difficult. In this study, we present FIORA, an open-source graph neural network designed to simulate tandem mass spectra. Our main contribution lies in utilizing the molecular neighborhood of bonds to learn breaking patterns and derive fragment ion probabilities. FIORA not only surpasses state-of-the-art fragmentation algorithms, ICEBERG and CFM-ID, in prediction quality, but also facilitates the prediction of additional features, such as retention time and collision cross section. Utilizing GPU acceleration, FIORA enables rapid validation of putative compound annotations and large-scale expansion of spectral reference libraries with high-quality predictions. KW - Metabolomics KW - Machine Learning KW - Mass spectrometry KW - Bioinformatics PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-627585 DO - https://doi.org/10.1038/s41467-025-57422-4 SN - 2041-1723 VL - 16 IS - 1 SP - 1 EP - 17 PB - Springer Science and Business Media LLC AN - OPUS4-62758 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Nowatzky, Yannek A1 - Benner, Philipp A1 - Reinert, K. A1 - Muth, Thilo T1 - Mistle: bringing spectral library predictions to metaproteomics with an efficient search index N2 - Motivation: Deep learning has moved to the forefront of tandem mass spectrometry-driven proteomics and authentic prediction for peptide fragmentation is more feasible than ever. Still, at this point spectral prediction is mainly used to validate database search results or for confined search spaces. Fully predicted spectral libraries have not yet been efficiently adapted to large search space problems that often occur in metaproteomics or proteogenomics. Results: In this study, we showcase a workflow that uses Prosit for spectral library predictions on two common metaproteomes and implement an indexing and search algorithm, Mistle, to efficiently identify experimental mass spectra within the library. Hence, the workflow emulates a classic protein sequence database search with protein digestion but builds a searchable index from spectral predictions as an in-between step. We compare Mistle to popular search engines, both on a spectral and database search level, and provide evidence that this approach is more accurate than a database search using MSFragger. Mistle outperforms other spectral library search engines in terms of run time and proves to be extremely memory efficient with a 4- to 22-fold decrease in RAM usage. This makes Mistle universally applicable to large search spaces, e.g. covering comprehensive sequence databases of diverse microbiomes. Availability and implementation: Mistle is freely available on GitHub at https://github.com/BAMeScience/Mistle. KW - Mass spectrometry KW - Proteomics KW - Algorithms KW - Metaproteomics PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-579373 DO - https://doi.org/10.1093/bioinformatics/btad376 SN - 1367-4811 VL - 39 IS - 6 SP - 1 EP - 12 PB - Oxford University Press CY - Oxford, Great Britain AN - OPUS4-57937 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Naik, Aakash A1 - Ertural, Christina A1 - Dhamrait, Nidal A1 - Benner, Philipp A1 - George, Janine T1 - A Quantum-Chemical Bonding Database for Solid-State Materials N2 - An in-depth insight into the chemistry and nature of the individual chemical bonds is essential for understanding materials. Bonding analysis is thus expected to provide important features for large-scale data analysis and machine learning of material properties. Such chemical bonding information can be computed using the LOBSTER software package, which post-processes modern density functional theory data by projecting the plane wave-based wave functions onto an atomic orbital basis. With the help of a fully automatic workflow, the VASP and LOBSTER software packages are used to generate the data. We then perform bonding analyses on 1520 compounds (insulators and semiconductors) and provide the results as a database. The projected densities of states and bonding indicators are benchmarked on standard density-functional theory computations and available heuristics, respectively. Lastly, we illustrate the predictive power of bonding descriptors by constructing a machine learning model for phononic properties, which shows an increase in prediction accuracies by 27% (mean absolute errors) compared to a benchmark model differing only by not relying on any quantum-chemical bonding features. KW - Bonding Analysis KW - DFT KW - High-throughput KW - Database KW - Phonons KW - Machine Learning PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-582892 DO - https://doi.org/10.1038/s41597-023-02477-5 VL - 10 IS - 1 SP - 1 EP - 18 AN - OPUS4-58289 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Batatia, Ilyes A1 - Benner, Philipp A1 - Chiang, Yuan A1 - Elena, Alin M. A1 - Kovács, Dávid P. A1 - Riebesell, Janosh A1 - Advincula, Xavier R. A1 - Asta, Mark A1 - Avaylon, Matthew A1 - Baldwin, William J. A1 - Berger, Fabian A1 - Bernstein, Noam A1 - Bhowmik, Arghya A1 - Bigi, Filippo A1 - Blau, Samuel M. A1 - Cărare, Vlad A1 - Ceriotti, Michele A1 - Chong, Sanggyu A1 - Darby, James P. A1 - De, Sandip A1 - Della Pia, Flaviano A1 - Deringer, Volker L. A1 - Elijošius, Rokas A1 - El-Machachi, Zakariya A1 - Fako, Edvin A1 - Falcioni, Fabio A1 - Ferrari, Andrea C. A1 - Gardner, John L. A. A1 - Gawkowski, Mikołaj J. A1 - Genreith-Schriever, Annalena A1 - George, Janine A1 - Goodall, Rhys E. A. A1 - Grandel, Jonas A1 - Grey, Clare P. A1 - Grigorev, Petr A1 - Han, Shuang A1 - Handley, Will A1 - Heenen, Hendrik H. A1 - Hermansson, Kersti A1 - Ho, Cheuk Hin A1 - Hofmann, Stephan A1 - Holm, Christian A1 - Jaafar, Jad A1 - Jakob, Konstantin S. A1 - Jung, Hyunwook A1 - Kapil, Venkat A1 - Kaplan, Aaron D. A1 - Karimitari, Nima A1 - Naik, Aakash A. A1 - Csányi, Gábor T1 - A foundation model for atomistic materials chemistry N2 - Atomistic simulations of matter, especially those that leverage first-principles (ab initio) electronic structure theory, provide a microscopic view of the world, underpinning much of our understanding of chemistry and materials science. Over the last decade or so, machine-learned force fields have transformed atomistic modeling by enabling simulations of ab initio quality over unprecedented time and length scales. However, early machine-learning (ML) force fields have largely been limited by (i) the substantial computational and human effort required to develop and validate potentials for each particular system of interest and (ii) a general lack of transferability from one chemical system to the next. Here, we show that it is possible to create a general-purpose atomistic ML model, trained on a public dataset of moderate size, that is capable of running stable molecular dynamics for a wide range of molecules and materials. We demonstrate the power of the MACE-MP-0 model—and its qualitative and at times quantitative accuracy—on a diverse set of problems in the physical sciences, including properties of solids, liquids, gases, chemical reactions, interfaces, and even the dynamics of a small protein. The model can be applied out of the box as a starting or “foundation” model for any atomistic system of interest and, when desired, can be fine-tuned on just a handful of application-specific data points to reach ab initio accuracy. Establishing that a stable force-field model can cover almost all materials changes atomistic modeling in a fundamental way: experienced users obtain reliable results much faster, and beginners face a lower barrier to entry. Foundation models thus represent a step toward democratizing the revolution in atomic-scale modeling that has been brought about by ML force fields. KW - Materials Design KW - Thermal Conducitivity KW - Nanoparticles KW - Batteries PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-647829 DO - https://doi.org/10.1063/5.0297006 SN - 0021-9606 VL - 163 IS - 18 SP - 1 EP - 89 PB - AIP Publishing AN - OPUS4-64782 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Amariamir, Sasan A1 - George, Janine A1 - Benner, Philipp T1 - SynCoTrain: a dual classifier PU-learning framework for synthesizability prediction N2 - Material discovery is a cornerstone of modern science, driving advancements in diverse disciplines from biomedical technology to climate solutions. Predicting synthesizability, a critical factor in realizing novel materials, remains a complex challenge due to the limitations of traditional heuristics and thermodynamic proxies. While stability metrics such as formation energy offer partial insights, they fail to account for kinetic factors and technological constraints that influence synthesis outcomes. These challenges are further compounded by the scarcity of negative data, as failed synthesis attempts are often unpublished or context-specific. We present SynCoTrain, a semi-supervised machine learning model designed to predict the synthesizability of materials. SynCoTrain employs a co-training framework leveraging two complementary graph convolutional neural networks: SchNet and ALIGNN. By iteratively exchanging predictions between classifiers, SynCoTrain mitigates model bias and enhances generalizability. Our approach uses Positive and Unlabeled (PU) learning to address the absence of explicit negative data, iteratively refining predictions through collaborative learning. The model demonstrates robust performance, achieving high recall on internal and leave-out test sets. By focusing on oxide crystals, a well-characterized material family with extensive experimental data, we establish SynCoTrain as a reliable tool for predicting synthesizability while balancing dataset variability and computational efficiency. This work highlights the potential of co-training to advance high-throughput materials discovery and generative research, offering a scalable solution to the challenge of synthesizability prediction. KW - Synthesizability KW - Accelerated Materials Design KW - Materials Acceleration Platforms KW - Materials Design KW - Materials Discovery KW - Co-training PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-637907 DO - https://doi.org/10.1039/D4DD00394B SN - 2635-098X VL - 4 IS - 6 SP - 1437 EP - 1448 PB - Royal Society of Chemistry (RSC) AN - OPUS4-63790 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Albakri, Bashar A1 - Turski Silva Diniz, Analice A1 - Benner, Philipp A1 - Muth, Thilo A1 - Nakajima, Shinichi A1 - Favaro, Marco A1 - Kister, Alexander ED - Hillman, Robert T1 - Machine learning-assisted equivalent circuit identification for dielectric spectroscopy of polymers N2 - Polymers have become indispensable across fields of application, and understanding their structure–property relationships and dynamic behaviour is essential for performance optimization. Polymer membranes, particularly ion exchange membranes, play a crucial role in renewable energy conversion technologies, fuel cells, solar energy conversion, and energy storage. In this context, broadband dielectric spectroscopy (BDS) offers a powerful, non-destructive approach to investigate the electrical response and relaxation dynamics of polymers. These properties are investigated by parametrizing the system’s impedance response in terms of a network of circuit elements, i.e. the electrical equivalent circuit (EEC), whose impedance resembles the one of the system under investigation. However, the determination of the EEC from BDS data is challenging due to system complexity, interdependencies of circuit elements, and researcher biases. In this work, we propose a novel approach that incorporates a convolutional neural network (CNN) model to predict the EEC topology. By reducing user bias and enhancing data analysis, this approach aims to make BDS accessible to both experienced users and those with limited expertise. We show that the combination of machine learning and BDS provides valuable insights into the dynamic behaviour of polymer membranes, thus facilitating the design and characterization of tailored polymers for various applications. We also show that our model outperforms state-of-the-art machine learning methods with a top-5 accuracy of around 80% for predicting the circuit topology and a parameter fitting error as low as 0.05%. KW - Polymer membranes KW - Electrochemical impedance spectroscopy KW - Broadband dielectric spectroscopy KW - Deep learning KW - Machine learning KW - Equivalent circuit PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-602138 DO - https://doi.org/10.1016/j.electacta.2024.144474 SN - 0013-4686 VL - 496 SP - 1 EP - 13 PB - Elsevier Ltd. AN - OPUS4-60213 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -