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In this paper, we present a new procedure to automatically generate interpretable hyperelastic material models. This approach is based on symbolic regression which represents an evolutionary algorithm searching for a mathematical model in the form of an algebraic expression. This results in a relatively simple model with good agreement to experimental data. By expressing the strain energy function in terms of its invariants or other parameters, it is possible to interpret the resulting algebraic formulation in a physical context. In addition, a direct implementation of the obtained algebraic equation is possible. For the validation of the proposed approach, benchmark tests on the basis of the generalized Mooney-Rivlin model are presented. In all these tests, the chosen ansatz can find the predefined models. Additionally, this method is applied for the multi-axial loading data set of vulcanized rubber. Finally, a data set for a temperature-dependent thermoplastic polyester elastomer is evaluated. In latter cases, good agreement with the experimental data is obtained.

We introduce a novel, practically relevant variation of the anomaly detection problem in multi-variate time series: intrinsic anomaly detection. It appears in diverse practical scenarios ranging from DevOps to IoT, where we want to recognize failures of a system that operates under the influence of a surrounding environment. Intrinsic anomalies are changes in the functional dependency structure between time series that represent an environment and time series that represent the internal state of a system that is placed in said environment. We formalize this problem, provide under-studied public and new purpose-built data sets for it, and present methods that handle intrinsic anomaly detection. These address the short-coming of existing anomaly detection methods that cannot differentiate between expected changes in the system's state and unexpected ones, i.e., changes in the system that deviate from the environment's influence. Our most promising approach is fully unsupervised and combines adversarial learning and time series representation learning, thereby addressing problems such as label sparsity and subjectivity, while allowing to navigate and improve notoriously problematic anomaly detection data sets.

Under a mild technical assumption, we prove a necessary and sufficient condition for a totally real compacdt set in $\mathbb{C}^n$ to be rationally convex. This generalizes a classical result of Duval-Sibony

Time series models aim for accurate predictions of the future given the past, where the forecasts are used for important downstream tasks like business decision making. In practice, deep learning based time series models come in many forms, but at a high level learn some continuous representation of the past and use it to output point or probabilistic forecasts. In this paper, we introduce a novel autoregressive architecture, VQ-AR, which instead learns a \emph{discrete} set of representations that are used to predict the future. Extensive empirical comparison with other competitive deep learning models shows that surprisingly such a discrete set of representations gives state-of-the-art or equivalent results on a wide variety of time series datasets. We also highlight the shortcomings of this approach, explore its zero-shot generalization capabilities, and present an ablation study on the number of representations. The full source code of the method will be available at the time of publication with the hope that researchers can further investigate this important but overlooked inductive bias for the time series domain.

Faced with problems of increasing complexity, recent research in Bayesian Optimisation (BO) has focused on adapting deep probabilistic models as flexible alternatives to Gaussian Processes (GPs). In a similar vein, this paper investigates the feasibility of employing state-of-the-art probabilistic transformers in BO. Upon further investigation, we observe two drawbacks stemming from their training procedure and loss definition, hindering their direct deployment as proxies in black-box optimisation. First, we notice that these models are trained on uniformly distributed inputs, which impairs predictive accuracy on non-uniform data - a setting arising from any typical BO loop due to exploration-exploitation trade-offs. Second, we realise that training losses (e.g., cross-entropy) only asymptotically guarantee accurate posterior approximations, i.e., after arriving at the global optimum, which generally cannot be ensured. At the stationary points of the loss function, however, we observe a degradation in predictive performance especially in exploratory regions of the input space. To tackle these shortcomings we introduce two components: 1) a BO-tailored training prior supporting non-uniformly distributed points, and 2) a novel approximate posterior regulariser trading-off accuracy and input sensitivity to filter favourable stationary points for improved predictive performance. In a large panel of experiments, we demonstrate, for the first time, that one transformer pre-trained on data sampled from random GP priors produces competitive results on 16 benchmark black-boxes compared to GP-based BO. Since our model is only pre-trained once and used in all tasks without any retraining and/or fine-tuning, we report an order of magnitude time-reduction, while matching and sometimes outperforming GPs.

The Schr\"odinger equation is at the heart of modern quantum mechanics. Since exact solutions of the ground state are typically intractable, standard approaches approximate Schr\"odinger equation as forms of nonlinear generalized eigenvalue problems $F(V)V = SV\Lambda$ in which $F(V)$, the matrix to be decomposed, is a function of its own top-$k$ smallest eigenvectors $V$, leading to a "self-consistency problem". Traditional iterative methods heavily rely on high-quality initial guesses of $V$ generated via domain-specific heuristics methods based on quantum mechanics. In this work, we eliminate such a need for domain-specific heuristics by presenting a novel framework, Self-consistent Gradient-like Eigen Decomposition (SCGLED) that regards $F(V)$ as a special "online data generator", thus allows gradient-like eigendecomposition methods in streaming $k$-PCA to approach the self-consistency of the equation from scratch in an iterative way similar to online learning. With several critical numerical improvements, SCGLED is robust to initial guesses, free of quantum-mechanism-based heuristics designs, and neat in implementation. Our experiments show that it not only can simply replace traditional heuristics-based initial guess methods with large performance advantage (achieved averagely 25x more precise than the best baseline in similar wall time), but also is capable of finding highly precise solutions independently without any traditional iterative methods.

Antibodies are canonically Y-shaped multimeric proteins capable of highly specific molecular recognition. The CDRH3 region located at the tip of variable chains of an antibody dominates antigen-binding specificity. Therefore, it is a priority to design optimal antigen-specific CDRH3 regions to develop therapeutic antibodies. However, the combinatorial nature of CDRH3 sequence space makes it impossible to search for an optimal binding sequence exhaustively and efficiently using computational approaches. Here, we present \texttt{AntBO}: a combinatorial Bayesian optimisation framework enabling efficient \textit{in silico} design of the CDRH3 region. Ideally, antibodies are expected to have high target specificity and developability. We introduce a CDRH3 trust region that restricts the search to sequences with favourable developability scores to achieve this goal. For benchmarking, \texttt{AntBO} uses the \texttt{Absolut!} software suite as a black-box oracle to score the target specificity and affinity of designed antibodies \textit{in silico} in an unconstrained fashion~\citep{robert2021one}. The experiments performed for $159$ discretised antigens used in \texttt{Absolut!} demonstrate the benefit of \texttt{AntBO} in designing CDRH3 regions with diverse biophysical properties. In under $200$ calls to black-box oracle, \texttt{AntBO} can suggest antibody sequences that outperform the best binding sequence drawn from 6.9 million experimentally obtained CDRH3s and a commonly used genetic algorithm baseline. Additionally, \texttt{AntBO} finds very-high affinity CDRH3 sequences in only 38 protein designs whilst requiring no domain knowledge. We conclude \texttt{AntBO} brings automated antibody design methods closer to what is practically viable for in vitro experimentation.