TY - JOUR A1 - Altenburg, T. A1 - Giese, S. A1 - Wang, S. A1 - Muth, Thilo A1 - Renard, B.Y. T1 - Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides JF - Nature Machine Intelligence N2 - Mass spectrometry-based proteomics provides a holistic snapshot of the entire protein set of living cells on a molecular level. Currently, only a few deep learning approaches exist that involve peptide fragmentation spectra, which represent partial sequence information of proteins. Commonly, these approaches lack the ability to characterize less studied or even unknown patterns in spectra because of their use of explicit domain knowledge. Here, to elevate unrestricted learning from spectra, we introduce ‘ad hoc learning of fragmentation’ (AHLF), a deep learning model that is end-to-end trained on 19.2 million spectra from several phosphoproteomic datasets. AHLF is interpretable, and we show that peak-level feature importance values and pairwise interactions between peaks are in line with corresponding peptide fragments. We demonstrate our approach by detecting post-translational modifications, specifically protein phosphorylation based on only the fragmentation spectrum without a database search. AHLF increases the area under the receiver operating characteristic curve (AUC) by an average of 9.4% on recent phosphoproteomic data compared with the current state of the art on this task. Furthermore, use of AHLF in rescoring search results increases the number of phosphopeptide identifications by a margin of up to 15.1% at a constant false discovery rate. To show the broad applicability of AHLF, we use transfer learning to also detect cross-linked peptides, as used in protein structure analysis, with an AUC of up to 94%. KW - Mass spectrometry KW - Machine learning KW - Deep learning KW - Peptide identification PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-547580 DO - https://doi.org/10.1038/s42256-022-00467-7 SN - 2522-5839 VL - 4 SP - 378 EP - 388 PB - Springer Nature CY - London AN - OPUS4-54758 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hauffen, J. C. A1 - Kästner, L. A1 - Ahmadi, Samim A1 - Jung, P. A1 - Caire, G. A1 - Ziegler, Mathias T1 - Learned block iterative shrinkage thresholding algorithm for photothermal super resolution imaging JF - Sensors N2 - Block-sparse regularization is already well known in active thermal imaging and is used for multiple-measurement-based inverse problems. The main bottleneck of this method is the choice of regularization parameters which differs for each experiment. We show the benefits of using a learned block iterative shrinkage thresholding algorithm (LBISTA) that is able to learn the choice of regularization parameters, without the need to manually select them. In addition, LBISTA enables the determination of a suitable weight matrix to solve the underlying inverse problem. Therefore, in this paper we present LBISTA and compare it with state-of-the-art block iterative shrinkage thresholding using synthetically generated and experimental test data from active thermography for defect reconstruction. Our results show that the use of the learned block-sparse optimization approach provides smaller normalized mean square errors for a small fixed number of iterations. Thus, this allows us to improve the convergence speed and only needs a few iterations to generate accurate defect reconstruction in photothermal super-resolution imaging. KW - Thermography KW - Laser KW - Machine learning KW - Optimization KW - Non-destructive testing KW - NDT KW - Neural network KW - Defect reconstruction KW - Block-sparsity KW - Active thermal imaging KW - Regularization KW - Laser thermography PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-554598 DO - https://doi.org/10.3390/s22155533 SN - 1424-8220 VL - 22 IS - 15 SP - 1 EP - 15 PB - MDPI CY - Basel AN - OPUS4-55459 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Abad Andrade, Carlos Enrique A1 - You, Zengchao A1 - Richter, Silke A1 - Benner, Philipp A1 - Recknagel, Sebastian T1 - The use of reference materials to improve the calibration strategy in glow discharge optical emission spectroscopy with machine learning N2 - Glow discharge optical emission spectroscopy (GD-OES) is a technique for the analysis of solids such as metals, semiconductors, and ceramics. A low-pressure glow discharge plasma is applied in this system, which ‘sputters’ and promotes the sample atoms to a higher energy state. When the atoms return to their ground state, they emit light with characteristic wavelengths, which a spectrometer can detect. Thus, GD-OES combines the advantages of ICP-OES with solid sampling techniques, which enables it to determine the bulk elemental composition and depth profiles. However, direct solid sampling methods such as glow-discharge spectroscopy require reference materials for calibration due to the strong matrix effect. Reference materials are essential when the accuracy and reliability of measurement results need to be guaranteed to generate confidence in the analysis. These materials are frequently used to determine measurement uncertainty, validate methods, suitability testing, and quality assurance. In addition, they guarantee that measurement results can be compared to recognized reference values. Unfortunately, the availability of certified reference materials suited to calibrate all elements in different matrix materials is limited. Therefore various calibration strategies and the preparation of traceable matrix-matched calibration standards will be discussed. Machine learning is an essential component of the growing field of data science. Through statistical methods, algorithms are trained to make classifications or predictions, uncovering key insights within data mining projects. Therefore, it was tried in our work to combine GD-OES with machine learning strategies to establish a new and robust calibration model, which can be used to identify the elemental composition and concentration of metals from a single spectrum. For this purpose, copper reference materials from different manufacturers, which contain various impurity elements, were investigated using GD-OES. The obtained spectra information are evaluated with different algorithms (e.g., gradient boosting and artificial neural networks), and the results are compared and discussed in detail. T2 - Winter Conference on Plasma Chemistry 2022 CY - Tucson, AZ, USA DA - 17.01.2022 KW - GDOES KW - Machine learning KW - Reference materials KW - Calibration KW - Cooper PY - 2022 AN - OPUS4-56497 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Friedrich, Alexander A1 - Heckel, Thomas A1 - Casperson, Ralf A1 - Zhang, Tianyun A1 - Olm, G. A1 - Islam, A. A1 - Simroth, A. T1 - AI-based analysis of eddy current and ultrasonic rail testing data N2 - Non-destructive testing of rail tracks is carried out by using rail inspection cars equipped with ultrasonic and eddy current measurement. The evaluation of test data is mainly done manually, supported by a software tool which pre-selects relevant indications shown to the evaluators. The resulting indications have to be checked on-site using hand-held testing equipment. Maintenance interventions are then derived on the basis of these on-site findings. Overall aim of the AIFRI (Artificial Intelligence For Rail Inspection) project - funded by the German Federal Ministry of Digital and Transport (BMDV) as part of the mFUND programme under funding code 19FS2014 – is to increase the degree of automation of the inspection process from the evaluation of the data to the planning of maintenance interventions. The accuracy of defect detection shall be increased by applying AI methods in order to enable an automated classification of detected indications into risk classes. For this purpose, data from both eddy current inspections and ultrasonic inspections will be used in combination. Within the framework of this data-driven project, relevant defect patterns and artefacts present in the rail are analysed and implemented into a configurable digital twin. With the help of this digital twin virtual defects can be generated and used to train AI algorithms for detection and classification. With the help of reliability assessment trained AI algorithms will be evaluated with regard to the resulting quality in defect detection and characterisation. A particular aspect of the development of AI methods is the data fusion of different NDT data sources: Thereby, synergies are used that arise from linking eddy current and ultrasonic inspection data in a combined model. In the course of the project a demonstrator consisting of the developed IT-tool and an asset management system will be implemented and tested in the field using real-world data. T2 - NDT in Railway CY - Berlin, Germany DA - 26.09.2022 KW - NDT KW - Eddy current KW - Ultra sound KW - Simulation KW - Machine learning PY - 2022 UR - https://www.dgzfp.de/seminar/railway/#5 AN - OPUS4-57236 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Morcillo, Dalia A1 - Winckelmann, Alexander A1 - Richter, Silke A1 - Recknagel, Sebastian A1 - Jacobsen, Lars A1 - Frick, Daniel A1 - Schmidt, Anita A1 - Leonhardt, Robert A1 - Panne, Ulrich A1 - Abad Andrade, Carlos Enrique T1 - High-resolution absorption isotopic spectrometry as a tool for aging studies of Li-ion batteries N2 - Lithium (Li) is the key element in the manufacturing of batteries. Isotopic study of Li may help to identify the causes of battery aging due to isotopic fractionation during charge/discharge cycles. Isotopic ratio determination is based on monitoring the isotopic components of lithium by their spin-orbit coupling and its isotopic shift of about 15 pm for the 22P←22S electronic transition around 670.788 nm. In this work, we propose improvements to our previous work [1] by using a higher-resolution double echelle modular spectrometer (HR-DEMON II) coupled to a continuum source graphite furnace atomic absorption spectrometer (HR-CS-GF-AAS) for the isotopic analysis of Li. The data analysis was carried out by using a decision-tree-based ensemble machine learning (ML) algorithm (XGBoost). A set of samples with 6Li isotope amount fractions ranging from 0.0004 to 0.99 mol mol-1 was used for the algorithm's training. Subsequently, the procedure was validated by a set of stock chemicals (Li2CO3, LiNO3, LiCl, and LiOH) and a BAM candidate reference material, a cathode material (NMC111). Finally, the ML model was applied to determine the isotope ratio of geological samples, including anorthosite, granite, soil, rhyolite, nepheline syenite, and basalt and battery samples. These samples were measured as digested without any further purification step. Improvements in the optical resolution resolve the lithium isotopic components of the atomic spectra. In the studied geological samples, were found δ7Li values between -0.5 and 4.5 ‰ with a precision range of 1 to 2 ‰. In addition, the proposed method was validated with multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS), and these results are comparable and compatible. T2 - Caltech-BAM Meeting CY - Online meeting DA - 10.08.2022 KW - Lithium isotope KW - Machine learning KW - Battery KW - High-resolution absorption isotopic spectrometry PY - 2022 AN - OPUS4-56380 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -