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Bernd Meyer

Publications and source records attributed to Bernd Meyer.

18 recordsLinked to original sources

Self-supervised Learning for Acoustic Few-Shot Classification

Labelled data are limited and self-supervised learning is one of the most important approaches for reducing labelling requirements. While it has been extensively explored in the image domain, it has so far not received the same amount of attention in the acoustic domain. Yet, reducing labelling is a key requirement for many acoustic applications. Specifically in bioacoustic, there are rarely sufficient labels for fully supervised learning available. This has led to the widespread use of acoustic recognisers that have been pre-trained on unrelated data for bioacoustic tasks. We posit that training on the actual task data and combining self-supervised pre-training with few-shot classification is a superior approach that has the ability to deliver high accuracy even when only a few labels are available. To this end, we introduce and evaluate a new architecture that combines CNN-based preprocessing with feature extraction based on state space models (SSMs). This combination is motivated by the fact that CNN-based networks alone struggle to capture temporal information effectively, which is crucial for classifying acoustic signals. SSMs, specifically S4 and Mamba, on the other hand, have been shown to have an excellent ability to capture long-range dependencies in sequence data. We pre-train this architecture using contrastive learning on the actual task data and subsequent fine-tuning with an extremely small amount of labelled data. We evaluate the performance of this proposed architecture for ($n$-shot, $n$-class) classification on standard benchmarks as well as real-world data. Our evaluation shows that it outperforms state-of-the-art architectures on the few-shot classification problem.

cs.SD

Deep Active Audio Feature Learning in Resource-Constrained Environments

The scarcity of labelled data makes training Deep Neural Network (DNN) models in bioacoustic applications challenging. In typical bioacoustics applications, manually labelling the required amount of data can be prohibitively expensive. To effectively identify both new and current classes, DNN models must continue to learn new features from a modest amount of fresh data. Active Learning (AL) is an approach that can help with this learning while requiring little labelling effort. Nevertheless, the use of fixed feature extraction approaches limits feature quality, resulting in underutilization of the benefits of AL. We describe an AL framework that addresses this issue by incorporating feature extraction into the AL loop and refining the feature extractor after each round of manual annotation. In addition, we use raw audio processing rather than spectrograms, which is a novel approach. Experiments reveal that the proposed AL framework requires 14.3%, 66.7%, and 47.4% less labelling effort on benchmark audio datasets ESC-50, UrbanSound8k, and InsectWingBeat, respectively, for a large DNN model and similar savings on a microcontroller-based counterpart. Furthermore, we showcase the practical relevance of our study by incorporating data from conservation biology projects. All codes are publicly available on GitHub.

cs.SD

Speeding-up Hybrid Functional based Ab Initio Molecular Dynamics using Multiple Time-stepping and Resonance Free Thermostat

Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at the level of generalized gradient approximation (GGA), which is at the 2nd rung of DFT-functionals in terms of accuracy. Hybrid DFT functionals which form the 4th rung in the accuracy ladder, are not commonly used in AIMD simulations as the computational cost involved is $100$ times or higher. To facilitate AIMD simulations with hybrid functionals, we propose here an approach that could speed up the calculations by ~30 times or more for systems with a few hundred of atoms. We demonstrate that, by achieving this significant speed up and making the compute time of hybrid functional based AIMD simulations at par with that of GGA functionals, we are able to study several complex condensed matter systems and model chemical reactions in solution with hybrid functionals that were earlier unthinkable to be performed.

physics.chem-ph

Water Structures Reveal Local Hydrophobicity on the In2O3(111) Surface

Clean oxide surfaces are generally hydrophilic. Water molecules anchor at undercoordinated surface metal atoms that act as Lewis-acid sites, and they are stabilized by H bonds to undercoordinated surface oxygens. The large unit cell of In2O3(111) provides surface atoms in various configurations, which leads to chemical heterogeneity and a local deviation from this general rule. Experiments (TPD, XPS, ncAFM) agree quantitatively with DFT calculations and show a series of distinct phases. The first three water molecules dissociate at one specific area of the unit cell and desorb above room temperature. The next three adsorb as molecules in the adjacent region. Three more water molecules rearrange this structure and an additional nine pile up above the OH groups. Despite offering undercoordinated In and O sites, the rest of the unit cell is unfavorable for adsorption and remains water-free. The first water layer thus shows ordering into nanoscopic 3D water clusters separated by hydrophobic pockets.

cond-mat.mtrl-sci

Direct assessment of the proton affinity of individual surface hydroxyls with non-contact atomic force microscopy

The state of protonation/deprotonation of surfaces has far-ranging implications in all areas of chemistry: from acid-base catalysis$^1$ and the electro- and photocatalytic splitting of water$^2$, to the behavior of minerals$^3$ and biochemistry$^4$. The acidity of a molecule or a surface site is described by its proton affinity (PA) and pK$_\mathrm{a}$ value (the negative logarithm of the equilibrium constant of the proton transfer reaction in solution). For solids, in contrast to molecules, the acidity of individual sites is difficult to assess. For mineral surfaces such as oxides they are estimated by semi-empirical concepts such as bond-order valence sums$^5$, and also increasingly modeled with first-principles molecular dynamics simulations$^{6,7}$. Currently such predictions cannot be tested - the experimental measures used for comparison are typically average quantities integrated over the whole surface or, in some cases, individual crystal facets$^8$, such as the point of zero charge (pzc)$^9$. Here we assess individual hydroxyls on In$_2$O$_3$(111), a model oxide with four different types of surface oxygen atoms, and probe the strength of their hydrogen bond with the tip of a non-contact atomic force microscope (AFM). The force curves are in quantitative agreement with density-functional theory (DFT) calculations. By relating the results to known proton affinities and pK$_\mathrm{a}$ values of gas-phase molecules, we provide a direct measure of proton affinity distributions at the atomic scale.

cond-mat.mtrl-sci

Tracking Different Ant Species: An Unsupervised Domain Adaptation Framework and a Dataset for Multi-object Tracking

Tracking individuals is a vital part of many experiments conducted to understand collective behaviour. Ants are the paradigmatic model system for such experiments but their lack of individually distinguishing visual features and their high colony densities make it extremely difficult to perform reliable tracking automatically. Additionally, the wide diversity of their species' appearances makes a generalized approach even harder. In this paper, we propose a data-driven multi-object tracker that, for the first time, employs domain adaptation to achieve the required generalisation. This approach is built upon a joint-detection-and-tracking framework that is extended by a set of domain discriminator modules integrating an adversarial training strategy in addition to the tracking loss. In addition to this novel domain-adaptive tracking framework, we present a new dataset and a benchmark for the ant tracking problem. The dataset contains 57 video sequences with full trajectory annotation, including 30k frames captured from two different ant species moving on different background patterns. It comprises 33 and 24 sequences for source and target domains, respectively. We compare our proposed framework against other domain-adaptive and non-domain-adaptive multi-object tracking baselines using this dataset and show that incorporating domain adaptation at multiple levels of the tracking pipeline yields significant improvements. The code and the dataset are available at https://github.com/chamathabeysinghe/da-tracker.

cs.CV

Environmental Sound Classification on the Edge: A Pipeline for Deep Acoustic Networks on Extremely Resource-Constrained Devices

Significant efforts are being invested to bring state-of-the-art classification and recognition to edge devices with extreme resource constraints (memory, speed, and lack of GPU support). Here, we demonstrate the first deep network for acoustic recognition that is small, flexible and compression-friendly yet achieves state-of-the-art performance for raw audio classification. Rather than handcrafting a once-off solution, we present a generic pipeline that automatically converts a large deep convolutional network via compression and quantization into a network for resource-impoverished edge devices. After introducing ACDNet, which produces above state-of-the-art accuracy on ESC-10 (96.65%), ESC-50 (87.10%), UrbanSound8K (84.45%) and AudioEvent (92.57%), we describe the compression pipeline and show that it allows us to achieve 97.22% size reduction and 97.28% FLOP reduction while maintaining close to state-of-the-art accuracy 96.25%, 83.65%, 78.27% and 89.69% on these datasets. We describe a successful implementation on a standard off-the-shelf microcontroller and, beyond laboratory benchmarks, report successful tests on real-world datasets.

cs.SD

Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe$^{2+}$/Fe$^{3+}$ Redox Reaction

Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe$^{2+}$/Fe$^{3+}$ ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE). While hybrid functionals can minimize SIE, AIMD at that level of theory is typically 150 times slower than GGA for systems containing ~100 atoms. Among several approaches reported to speed-up AIMD simulations with hybrid functionals, the noise-stabilized MD (NSMD) procedure, together with the use of localized orbitals to compute the required exchange integrals, is an attractive option. In this work, we demonstrate the application of the NSMD approach for studying the Fe$^{2+}$/Fe$^{3+}$ redox reaction in water. It is shown here that long AIMD trajectories at the level of hybrid density functionals can be obtained using this approach. Redox properties of the aqueous Fe$^{2+}$/Fe$^{3+}$ system computed from these simulations are compared with the available experimental data for validation.

physics.chem-ph

Structural reorientation and compaction of porous MoS2 coatings during wear testing

Industrial upscaling frequently results in a different coating microstructure than the laboratory prototypes presented in the literature. Here, we investigate the wear behavior of physical vapor deposited (PVD) MoS2 coatings: A dense, nanocrystalline MoS2 coating, and a porous, prismatic-textured MoS2 coating. Transmission electron microscopy (TEM) investigations before and after wear testing evidence a crystallographic reorientation towards a basal texture in both samples. A basal texture is usually desirable due to its low-friction properties. This favorable reorientation is associated to a tribological compaction of the porous specimens. Following running-in, sliding under high contact pressure ultimately leads to a wear rate as small as for an ideal grown bulk MoS2 single crystal grown by chemical vapor deposition (CVD). This suggests that the imperfections of industrial grade MoS2 coatings can be remediated by a suitable pretreatment.

cond-mat.mtrl-sci

Resolution of intramolecular dipoles and push-back effect of individual molecules on a metal surface

Molecules consisting of a donor and an acceptor moiety can exhibit large intrinsic dipole moments. Upon deposition on a metal surface, the dipole may be effectively screened and the charge distribution altered due to hybridization with substrate electronic states. Here, we deposit Ethyl-Diaminodicyanoquinone molecules, which exhibit a large dipole moment in gas phase, on a Au(111) surface. Employing a combination of scanning tunneling microscopy and non-contact atomic force microscopy, we find that a significant dipole moment persists in the flat-lying molecules. Density-functional theory calculations reveal that the dipole moment is even increased on the metal substrate as compared to the gas phase. We also show that the local contact potential across the molecular islands is decreased by several tens of meV with respect to the bare metal. We explain this by the induced charge-density redistribution due to the adsorbed molecules, which confine the substrate's wavefunction at the interface. Our local measurements provide direct evidence of this so-called push-back or cushion effect at the scale of individual molecules.

cond-mat.mes-hall

Pruning vs XNOR-Net: A Comprehensive Study of Deep Learning for Audio Classification on Edge-devices

Deep learning has celebrated resounding successes in many application areas of relevance to the Internet of Things (IoT), such as computer vision and machine listening. These technologies must ultimately be brought directly to the edge to fully harness the power of deep learning for the IoT. The obvious challenge is that deep learning techniques can only be implemented on strictly resource-constrained edge devices if the models are radically downsized. This task relies on different model compression techniques, such as network pruning, quantization, and the recent advancement of XNOR-Net. This study examines the suitability of these techniques for audio classification on microcontrollers. We present an application of XNOR-Net for end-to-end raw audio classification and a comprehensive empirical study comparing this approach with pruning-and-quantization methods. We show that raw audio classification with XNOR yields comparable performance to regular full precision networks for small numbers of classes while reducing memory requirements 32-fold and computation requirements 58-fold. However, as the number of classes increases significantly, performance degrades, and pruning-and-quantization based compression techniques take over as the preferred technique being able to satisfy the same space constraints but requiring approximately 8x more computation. We show that these insights are consistent between raw audio classification and image classification using standard benchmark sets. To the best of our knowledge, this is the first study to apply XNOR to end-to-end audio classification and evaluate it in the context of alternative techniques. All codes are publicly available on GitHub.

cs.SD

Improving the Scaling and Performance of Multiple Time Stepping based Molecular Dynamics with Hybrid Density Functionals

Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density functionals from GGA (2nd rung) to hybrid density functionals (4th rung) is much desired pertaining to the accuracy of the latter in describing structure, dynamics, and energetics of molecular and condensed matter systems. On the other hand, hybrid density functional based AIMD simulations are about two orders of magnitude slower than GGA based AIMD for systems containing ~100 atoms using ~100 compute cores. Two methods, namely MTACE and s-MTACE, based on a multiple time step integrator and adaptively compressed exchange operator formalism are able to provide a speed-up of about 7-9 in performing hybrid density functional based AIMD. In this work, we report an implementation of these methods using a task-group based parallelization within the CPMD program package, with the intention to take advantage of the large number of compute cores available on modern high-performance computing platforms. We present here the boost in performance achieved through this algorithm. This work also identifies the computational bottleneck in the s-MTACE method, and proposes a way to overcome that.

physics.comp-ph

Integrating State of the Art Compute, Communication, and Autotuning Strategies to Multiply the Performance of the Application Programm CPMD for Ab Initio Molecular Dynamics Simulations

We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all time critical routines have been revised to maximize the computational throughput and to minimize the communication overhead for optimal performance. Throughout the program missing hybrid MPI+OpenMP parallelization has been added to optimize scaling. For communication intensive routines, as the multiple distributed 3d FFTs of the electronic states and distributed matrix-matrix multiplications related to the $β$-projectors of the pseudopotentials, this MPI+OpenMP parallelization now overlaps computation and communication. The necessary partitioning of the workload is optimized by an auto-tuning algorithm. In addition, the largest global MPI_Allreduce operation has been replaced by highly tuned node-local parallelized operations using MPI shared-memory windows to avoid inter-node communication. A batched algorithm for the multiple 3d FFTs improves the throughput of the MPI_Alltoall communication and, thus, the scalability of the implementation, both for USPP and for the frequently used norm-conserving pseudopotential code path. The enhanced performance and scalability is demonstrated on a mid-sized benchmark system of 256 water molecules and further water systems of from 32 up to 2048 molecules.

physics.comp-ph

Perfect and controllable nesting in the small angle twist bilayer graphene

Parallel ("nested") regions of a Fermi surface (FS) drive instabilities of the electron fluid, for example the spin density wave in elemental chromium. In one-dimensional materials, the FS is trivially fully nested (a single nesting vector connects two "Fermi dots"), while in higher dimensions only a fraction of the FS consists of parallel sheets. We demonstrate that the tiny angle regime of twist bilayer graphene (TBLG) possess a phase, accessible by interlayer bias, in which the FS consists entirely of nestable "Fermi lines": the first example of a completely nested FS in a 2d material. This nested phase is found both in the ideal as well as relaxed structure of the twist bilayer. We demonstrate excellent agreement with recent STM images of topological states in this material and elucidate the connection between these and the underlying Fermiology. We show that the geometry of the "Fermi lines" network is controllable by the strength of the applied interlayer bias, and thus that TBLG offers unprecedented access to the physics of FS nesting in 2d materials.

cond-mat.mtrl-sci

Substrate-Modulated Reductive Graphene Functionalization

Covalently functionalizing mechanical exfoliated monolayer and bilayer graphenides with λ-iodanes led to the discovery that the monolayers supported on a SiO2 substrate are considerably more reactive than bilayers as demonstrated by statistical Raman spectroscopy/microscopy. Supported by DFT calculations we show that ditopic addend binding leads to much more stable products than the corresponding monotopic reactions due to much lower lattice strain of the reactions products. The chemical nature of the substrate (graphene versus SiO2) plays a crucial role.14858-14862.

physics.chem-ph

Well-Ordered In Adatoms at the In$_2$O$_3$(111) Surface Created by Fe Deposition

Metal deposition on oxide surfaces usually results in adatoms, clusters, or islands of the deposited material, where defects in the surface often act as nucleation centers. Here an alternate configuration is reported. After the vapor deposition of Fe on the In$_2$O$_3$(111) surface at room temperature, ordered adatoms are observed with scanning tunneling microscopy. These are identical to the In adatoms that form when the sample is reduced by heating in ultrahigh vacuum. Density functional theory (DFT) calculations confirm that Fe interchanges with In in the topmost layer, pushing the excess In atoms to the surface where they arrange as a well-ordered adatom array.

cond-mat.mtrl-sci

Charge Localization Dynamics induced by Oxygen Vacancies on the Titania TiO$_2$(110) Surface

The dynamics of an F--center created by an oxygen vacancy on the $\mathrm{TiO_{2}(110)}$ rutile surface has been investigated using {\it ab initio} molecular dynamics. These simulations uncover a truly complex, time-dependent behavior of fluctuating electron localization topologies in the vicinity of the oxygen vacancy. Although the two excess electrons are found to populate preferentially the second subsurface layer, they occasionally visit surface sites and also the third subsurface layer. This dynamical behavior of the excess charge explains hitherto conflicting interpretations of both theoretical findings and experimental data.

cond-mat.mtrl-sci

Composition, structure, and stability of the rutile TiO_2(110) surface: oxygen depletion, hydroxylation, hydrogen migration and water adsorption

A comprehensive phase diagram of lowest-energy structures and compositions of the rutile TiO_2(110) surface in equilibrium with a surrounding gas phase at finite temperatures and pressures has been determined using density functional theory in combination with a thermodynamic formalism. The exchange of oxygen, hydrogen, and water molecules with the gas phase is considered. Particular attention is given to the convergence of all calculations with respect to lateral system size and slab thickness. In addition, the reliability of semilocal density functionals to describing the energetics of the reduced surfaces is critically evaluated. For ambient conditions the surface is found to be fully covered by molecularly adsorbed water. At low coverages, in the limit of single, isolated water molecules, molecular and dissociative adsorption become energetically degenerate. Oxygen vacancies form in strongly reducing, oxygen-poor environments. However, already at slightly more moderate conditions it is shown that removing full TiO_2 units from the surface is thermodynamically preferred. In agreement with recent experimental observations it is furthermore confirmed that even under extremely hydrogen-rich environments the surface cannot be fully hydroxylated, but only a maximum coverage with hydrogen of about 0.6-0.7 monolayer can be reached. Finally, calculations of migration paths strongly suggest that hydrogen prefers to diffuse into the bulk over desorbing from the surface into the gas phase.

cond-mat.mtrl-sci