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Calibrating simulation models that take large quantities of multi-dimensional data as input is a hard simulation optimization problem. Existing adaptive sampling strategies offer a methodological solution. However, they may not sufficiently reduce the computational cost for estimation and solution algorithm's progress within a limited budget due to extreme noise levels and heteroskedasticity of system responses. We propose integrating stratification with adaptive sampling for the purpose of efficiency in optimization. Stratification can exploit local dependence in the simulation inputs and outputs. Yet, the state-of-the-art does not provide a full capability to adaptively stratify the data as different solution alternatives are evaluated. We devise two procedures for data-driven calibration problems that involve a large dataset with multiple covariates to calibrate models within a fixed overall simulation budget. The first approach dynamically stratifies the input data using binary trees, while the second approach uses closed-form solutions based on linearity assumptions between the objective function and concomitant variables. We find that dynamical adjustment of stratification structure accelerates optimization and reduces run-to-run variability in generated solutions. Our case study for calibrating a wind power simulation model, widely used in the wind industry, using the proposed stratified adaptive sampling, shows better-calibrated parameters under a limited budget.

Sparse tensor decomposition and completion are common in numerous applications, ranging from machine learning to computational quantum chemistry. Typically, the main bottleneck in optimization of these models are contractions of a single large sparse tensor with a network of several dense matrices or tensors (SpTTN). Prior works on high-performance tensor decomposition and completion have focused on performance and scalability optimizations for specific SpTTN kernels. We present algorithms and a runtime system for identifying and executing the most efficient loop nest for any SpTTN kernel. We consider both enumeration of such loop nests for autotuning and efficient algorithms for finding the lowest cost loop-nest for simpler metrics, such as buffer size or cache miss models. Our runtime system identifies the best choice of loop nest without user guidance, and also provides a distributed-memory parallelization of SpTTN kernels. We evaluate our framework using both real-world and synthetic tensors. Our results demonstrate that our approach outperforms available generalized state-of-the-art libraries and matches the performance of specialized codes.

Generalization of machine learning models can be severely compromised by data poisoning, where adversarial changes are applied to the training data, as well as backdoor attacks that additionally manipulate the test data. These vulnerabilities have led to interest in certifying (i.e., proving) that such changes up to a certain magnitude do not affect test predictions. We, for the first time, certify Graph Neural Networks (GNNs) against poisoning and backdoor attacks targeting the node features of a given graph. Our certificates are white-box and based upon $(i)$ the neural tangent kernel, which characterizes the training dynamics of sufficiently wide networks; and $(ii)$ a novel reformulation of the bilevel optimization problem describing poisoning as a mixed-integer linear program. Consequently, we leverage our framework to provide fundamental insights into the role of graph structure and its connectivity on the worst-case robustness behavior of convolution-based and PageRank-based GNNs. We note that our framework is more general and constitutes the first approach to derive white-box poisoning certificates for NNs, which can be of independent interest beyond graph-related tasks.

Game semantics is a denotational semantics presenting compositionally the computational behaviour of various kinds of effectful programs. One of its celebrated achievement is to have obtained full abstraction results for programming languages with a variety of computational effects, in a single framework. This is known as the semantic cube or Abramsky's cube, which for sequential deterministic programs establishes a correspondence between certain conditions on strategies (''innocence'', ''well-bracketing'', ''visibility'') and the absence of matching computational effects. Outside of the sequential deterministic realm, there are still a wealth of game semantics-based full abstraction results; but they no longer fit in a unified canvas. In particular, Ghica and Murawski's fully abstract model for shared state concurrency (IA) does not have a matching notion of pure parallel program-we say that parallelism and interference (i.e. state plus semaphores) are entangled. In this paper we construct a causal version of Ghica and Murawski's model, also fully abstract for IA. We provide compositional conditions parallel innocence and sequentiality, respectively banning interference and parallelism, and leading to four full abstraction results. To our knowledge, this is the first extension of Abramsky's semantic cube programme beyond the sequential deterministic world.

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

The existence of representative datasets is a prerequisite of many successful artificial intelligence and machine learning models. However, the subsequent application of these models often involves scenarios that are inadequately represented in the data used for training. The reasons for this are manifold and range from time and cost constraints to ethical considerations. As a consequence, the reliable use of these models, especially in safety-critical applications, is a huge challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches, and eventually to increase the generalization capability of these models. Furthermore, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-based models with existing knowledge. The identified approaches are structured according to the categories integration, extraction and conformity. Special attention is given to applications in the field of autonomous driving.

Data augmentation, the artificial creation of training data for machine learning by transformations, is a widely studied research field across machine learning disciplines. While it is useful for increasing the generalization capabilities of a model, it can also address many other challenges and problems, from overcoming a limited amount of training data over regularizing the objective to limiting the amount data used to protect privacy. Based on a precise description of the goals and applications of data augmentation (C1) and a taxonomy for existing works (C2), this survey is concerned with data augmentation methods for textual classification and aims to achieve a concise and comprehensive overview for researchers and practitioners (C3). Derived from the taxonomy, we divided more than 100 methods into 12 different groupings and provide state-of-the-art references expounding which methods are highly promising (C4). Finally, research perspectives that may constitute a building block for future work are given (C5).

Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.

The notion of uncertainty is of major importance in machine learning and constitutes a key element of machine learning methodology. In line with the statistical tradition, uncertainty has long been perceived as almost synonymous with standard probability and probabilistic predictions. Yet, due to the steadily increasing relevance of machine learning for practical applications and related issues such as safety requirements, new problems and challenges have recently been identified by machine learning scholars, and these problems may call for new methodological developments. In particular, this includes the importance of distinguishing between (at least) two different types of uncertainty, often refereed to as aleatoric and epistemic. In this paper, we provide an introduction to the topic of uncertainty in machine learning as well as an overview of hitherto attempts at handling uncertainty in general and formalizing this distinction in particular.

Spectral clustering is a leading and popular technique in unsupervised data analysis. Two of its major limitations are scalability and generalization of the spectral embedding (i.e., out-of-sample-extension). In this paper we introduce a deep learning approach to spectral clustering that overcomes the above shortcomings. Our network, which we call SpectralNet, learns a map that embeds input data points into the eigenspace of their associated graph Laplacian matrix and subsequently clusters them. We train SpectralNet using a procedure that involves constrained stochastic optimization. Stochastic optimization allows it to scale to large datasets, while the constraints, which are implemented using a special-purpose output layer, allow us to keep the network output orthogonal. Moreover, the map learned by SpectralNet naturally generalizes the spectral embedding to unseen data points. To further improve the quality of the clustering, we replace the standard pairwise Gaussian affinities with affinities leaned from unlabeled data using a Siamese network. Additional improvement can be achieved by applying the network to code representations produced, e.g., by standard autoencoders. Our end-to-end learning procedure is fully unsupervised. In addition, we apply VC dimension theory to derive a lower bound on the size of SpectralNet. State-of-the-art clustering results are reported on the Reuters dataset. Our implementation is publicly available at //github.com/kstant0725/SpectralNet .