We implement AntClust, a clustering algorithm based on the chemical recognition system of ants and use it to cluster images of cars. We will give a short recap summary of the main working principles of the algorithm as devised by the original paper [1]. Further, we will describe how to define a similarity function for images and how the implementation is used to cluster images of cars from the vehicle re-identification data set. We then test the clustering performance of AntClust against DBSCAN, HDBSCAN and OPTICS. Finally one of the core parts in AntClust, the rule set can be easily redefined with our implementation, enabling a way for other bio-inspired algorithms to find rules in an automated process. The implementation can be found on GitLab [9].
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Chemical reactivity models are developed to predict chemical reaction outcomes in the form of classification (success/failure) or regression (product yield) tasks. The vast majority of the reported models are trained solely on chemical information such as reactants, products, reagents, and solvents, but not on the details of a synthetic protocol. Herein incorporation of procedural text with the aim to augment the Graphormer reactivity model and improve its accuracy is presented. Two major approaches are used: training an adapter Graphormer model that is provided with a GPT-2-derived latent representation of the text procedure (ReacLLaMA-Adapter) and labeling an unlabeled part of a dataset with the LLaMA 2 model followed by training the Graphormer on an extended dataset (Zero-Shot Labeling ReacLLaMA). Both methodologies enhance the discernment of unpromising reactions, thereby providing more accurate models with improved specificity.
We consider the Boussinesq-Peregrine (BP) system as described by Lannes [Lannes, D. (2013). The water waves problem: mathematical analysis and asymptotics (Vol. 188). American Mathematical Soc.], within the shallow water regime, and study the inverse problem of determining the time and space variations of the channel bottom profile, from measurements of the wave profile and its velocity on the free surface. A well-posedness result within a Sobolev framework for (BP), considering a time dependent bottom, is presented. Then, the inverse problem is reformulated as a nonlinear PDEconstrained optimization one. An existence result of the minimum, under constraints on the admissible set of bottoms, is presented. Moreover, an implementation of the gradient descent approach, via the adjoint method, is considered. For solving numerically both, the forward (BP) and its adjoint system, we derive a universal and low-dissipation scheme, which contains non-conservative products. The scheme is based on the FORCE-{\alpha} method proposed in [Toro, E. F., Saggiorato, B., Tokareva, S., and Hidalgo, A. (2020). Low-dissipation centred schemes for hyperbolic equations in conservative and non-conservative form. Journal of Computational Physics, 416, 109545]. Finally, we implement this methodology to recover three different bottom profiles; a smooth bottom, a discontinuous one, and a continuous profile with a large gradient. We compare with two classical discretizations for (BP) and the adjoint system. These results corroborate the effectiveness of the proposed methodology to recover bottom profiles.
The analysis of survey data is a frequently arising issue in clinical trials, particularly when capturing quantities which are difficult to measure. Typical examples are questionnaires about patient's well-being, pain, or consent to an intervention. In these, data is captured on a discrete scale containing only a limited number of possible answers, from which the respondent has to pick the answer which fits best his/her personal opinion. This data is generally located on an ordinal scale as answers can usually be arranged in an ascending order, e.g., "bad", "neutral", "good" for well-being. Since responses are usually stored numerically for data processing purposes, analysis of survey data using ordinary linear regression models are commonly applied. However, assumptions of these models are often not met as linear regression requires a constant variability of the response variable and can yield predictions out of the range of response categories. By using linear models, one only gains insights about the mean response which may affect representativeness. In contrast, ordinal regression models can provide probability estimates for all response categories and yield information about the full response scale beyond the mean. In this work, we provide a concise overview of the fundamentals of latent variable based ordinal models, applications to a real data set, and outline the use of state-of-the-art-software for this purpose. Moreover, we discuss strengths, limitations and typical pitfalls. This is a companion work to a current vignette-based structured interview study in paediatric anaesthesia.
We present an overview of recent developments on the convergence analysis of numerical methods for inviscid multidimensional compressible flows that preserve underlying physical structures. We introduce the concept of generalized solutions, the so-called dissipative solutions, and explain their relationship to other commonly used solution concepts. In numerical experiments we apply K-convergence of numerical solutions and approximate turbulent solutions together with the Reynolds stress defect and the energy defect.
Extracting consistent statistics between relevant free-energy minima of a molecular system is essential for physics, chemistry and biology. Molecular dynamics (MD) simulations can aid in this task but are computationally expensive, especially for systems that require quantum accuracy. To overcome this challenge, we develop an approach combining enhanced sampling with deep generative models and active learning of a machine learning potential (MLP). We introduce an adaptive Markov chain Monte Carlo framework that enables the training of one Normalizing Flow (NF) and one MLP per state. We simulate several Markov chains in parallel until they reach convergence, sampling the Boltzmann distribution with an efficient use of energy evaluations. At each iteration, we compute the energy of a subset of the NF-generated configurations using Density Functional Theory (DFT), we predict the remaining configuration's energy with the MLP and actively train the MLP using the DFT-computed energies. Leveraging the trained NF and MLP models, we can compute thermodynamic observables such as free-energy differences or optical spectra. We apply this method to study the isomerization of an ultrasmall silver nanocluster, belonging to a set of systems with diverse applications in the fields of medicine and catalysis.
A popular method for variance reduction in observational causal inference is propensity-based trimming, the practice of removing units with extreme propensities from the sample. This practice has theoretical grounding when the data are homoscedastic and the propensity model is parametric (Yang and Ding, 2018; Crump et al. 2009), but in modern settings where heteroscedastic data are analyzed with non-parametric models, existing theory fails to support current practice. In this work, we address this challenge by developing new methods and theory for sample trimming. Our contributions are three-fold: first, we describe novel procedures for selecting which units to trim. Our procedures differ from previous work in that we trim not only units with small propensities, but also units with extreme conditional variances. Second, we give new theoretical guarantees for inference after trimming. In particular, we show how to perform inference on the trimmed subpopulation without requiring that our regressions converge at parametric rates. Instead, we make only fourth-root rate assumptions like those in the double machine learning literature. This result applies to conventional propensity-based trimming as well and thus may be of independent interest. Finally, we propose a bootstrap-based method for constructing simultaneously valid confidence intervals for multiple trimmed sub-populations, which are valuable for navigating the trade-off between sample size and variance reduction inherent in trimming. We validate our methods in simulation, on the 2007-2008 National Health and Nutrition Examination Survey, and on a semi-synthetic Medicare dataset and find promising results in all settings.
We consider time-harmonic scalar transmission problems between dielectric and dispersive materials with generalized Lorentz frequency laws. For certain frequency ranges such equations involve a sign-change in their principle part. Due to the resulting loss of coercivity properties, the numerical simulation of such problems is demanding. Furthermore, the related eigenvalue problems are nonlinear and give rise to additional challenges. We present a new finite element method for both of these types of problems, which is based on a weakly coercive reformulation of the PDE. The new scheme can handle $C^{1,1}$-interfaces consisting piecewise of elementary geometries. Neglecting quadrature errors, the method allows for a straightforward convergence analysis. In our implementation we apply a simple, but nonstandard quadrature rule to achieve negligible quadrature errors. We present computational experiments in 2D and 3D for both source and eigenvalue problems which confirm the stability and convergence of the new scheme.
The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.
This paper focuses on the need for a rigorous theory of layered control architectures (LCAs) for complex engineered and natural systems, such as power systems, communication networks, autonomous robotics, bacteria, and human sensorimotor control. All deliver extraordinary capabilities, but they lack a coherent theory of analysis and design, partly due to the diverse domains across which LCAs can be found. In contrast, there is a core universal set of control concepts and theory that applies very broadly and accommodates necessary domain-specific specializations. However, control methods are typically used only to design algorithms in components within a larger system designed by others, typically with minimal or no theory. This points towards a need for natural but large extensions of robust performance from control to the full decision and control stack. It is encouraging that the successes of extant architectures from bacteria to the Internet are due to strikingly universal mechanisms and design patterns. This is largely due to convergent evolution by natural selection and not intelligent design, particularly when compared with the sophisticated design of components. Our aim here is to describe the universals of architecture and sketch tentative paths towards a useful design theory.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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