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Reactive transport in porous media plays a pivotal role in subsurface reservoir processes, influencing fluid properties and geochemical characteristics. However, coupling fluid flow and transport with geochemical reactions is computationally intensive, requiring geochemical calculations at each grid cell and each time step within a discretized simulation domain. Although recent advancements have integrated machine learning techniques as surrogates for geochemical simulations, ensuring computational efficiency and accuracy remains a challenge. This chapter investigates machine learning models as replacements for a geochemical module in a reactive transport in porous media simulation. We test this approach on a well-documented cation exchange problem. While the surrogate models excel in isolated predictions, they fall short in rollout predictions over successive time steps. By introducing modifications, including physics-based constraints and tailored dataset generation strategies, we show that machine learning surrogates can achieve accurate rollout predictions. Our findings emphasize that, when judiciously designed, machine learning surrogates can substantially expedite the cation exchange problem without compromising accuracy, offering significant potential for a range of reactive transport applications.

Latent variable models serve as powerful tools to infer underlying dynamics from observed neural activity. However, due to the absence of ground truth data, prediction benchmarks are often employed as proxies. In this study, we reveal the limitations of the widely-used 'co-smoothing' prediction framework and propose an improved few-shot prediction approach that encourages more accurate latent dynamics. Utilizing a student-teacher setup with Hidden Markov Models, we demonstrate that the high co-smoothing model space can encompass models with arbitrary extraneous dynamics within their latent representations. To address this, we introduce a secondary metric -- a few-shot version of co-smoothing. This involves performing regression from the latent variables to held-out channels in the data using fewer trials. Our results indicate that among models with near-optimal co-smoothing, those with extraneous dynamics underperform in the few-shot co-smoothing compared to 'minimal' models devoid of such dynamics. We also provide analytical insights into the origin of this phenomenon. We further validate our findings on real neural data using two state-of-the-art methods: LFADS and STNDT. In the absence of ground truth, we suggest a proxy measure to quantify extraneous dynamics. By cross-decoding the latent variables of all model pairs with high co-smoothing, we identify models with minimal extraneous dynamics. We find a correlation between few-shot co-smoothing performance and this new measure. In summary, we present a novel prediction metric designed to yield latent variables that more accurately reflect the ground truth, offering a significant improvement for latent dynamics inference.

Existing approaches for device placement ignore the topological features of computation graphs and rely mostly on heuristic methods for graph partitioning. At the same time, they either follow a grouper-placer or an encoder-placer architecture, which requires understanding the interaction structure between code operations. To bridge the gap between encoder-placer and grouper-placer techniques, we propose a novel framework for the task of device placement, relying on smaller computation graphs extracted from the OpenVINO toolkit using reinforcement learning. The framework consists of five steps, including graph coarsening, node representation learning and policy optimization. It facilitates end-to-end training and takes into consideration the directed and acyclic nature of the computation graphs. We also propose a model variant, inspired by graph parsing networks and complex network analysis, enabling graph representation learning and personalized graph partitioning jointly, using an unspecified number of groups. To train the entire framework, we utilize reinforcement learning techniques by employing the execution time of the suggested device placements to formulate the reward. We demonstrate the flexibility and effectiveness of our approach through multiple experiments with three benchmark models, namely Inception-V3, ResNet, and BERT. The robustness of the proposed framework is also highlighted through an ablation study. The suggested placements improve the inference speed for the benchmark models by up to $58.2\%$ over CPU execution and by up to $60.24\%$ compared to other commonly used baselines.

Characteristic formulae give a complete logical description of the behaviour of processes modulo some chosen notion of behavioural semantics. They allow one to reduce equivalence or preorder checking to model checking, and are exactly the formulae in the modal logics characterizing classic behavioural equivalences and preorders for which model checking can be reduced to equivalence or preorder checking. This paper studies the complexity of determining whether a formula is characteristic for some finite, loop-free process in each of the logics providing modal characterizations of the simulation-based semantics in van Glabbeek's branching-time spectrum. Since characteristic formulae in each of those logics are exactly the consistent and prime ones, it presents complexity results for the satisfiability and primality problems, and investigates the boundary between modal logics for which those problems can be solved in polynomial time and those for which they become computationally hard. Amongst other contributions, this article also studies the complexity of constructing characteristic formulae in the modal logics characterizing simulation-based semantics, both when such formulae are presented in explicit form and via systems of equations.

The simulation of nanophotonic structures relies on electromagnetic solvers, which play a crucial role in understanding their behavior. However, these solvers often come with a significant computational cost, making their application in design tasks, such as optimization, impractical. To address this challenge, machine learning techniques have been explored for accurate and efficient modeling and design of photonic devices. Deep neural networks, in particular, have gained considerable attention in this field. They can be used to create both forward and inverse models. An inverse modeling approach avoids the need for coupling a forward model with an optimizer and directly performs the prediction of the optimal design parameters values. In this paper, we propose an inverse modeling method for nanophotonic structures, based on a mixture density network model enhanced by transfer learning. Mixture density networks can predict multiple possible solutions at a time including their respective importance as Gaussian distributions. However, multiple challenges exist for mixture density network models. An important challenge is that an upper bound on the number of possible simultaneous solutions needs to be specified in advance. Also, another challenge is that the model parameters must be jointly optimized, which can result computationally expensive. Moreover, optimizing all parameters simultaneously can be numerically unstable and can lead to degenerate predictions. The proposed approach allows overcoming these limitations using transfer learning-based techniques, while preserving a high accuracy in the prediction capability of the design solutions given an optical response as an input. A dimensionality reduction step is also explored. Numerical results validate the proposed method.

Quantum computing has recently emerged as a transformative technology. Yet, its promised advantages rely on efficiently translating quantum operations into viable physical realizations. In this work, we use generative machine learning models, specifically denoising diffusion models (DMs), to facilitate this transformation. Leveraging text-conditioning, we steer the model to produce desired quantum operations within gate-based quantum circuits. Notably, DMs allow to sidestep during training the exponential overhead inherent in the classical simulation of quantum dynamics -- a consistent bottleneck in preceding ML techniques. We demonstrate the model's capabilities across two tasks: entanglement generation and unitary compilation. The model excels at generating new circuits and supports typical DM extensions such as masking and editing to, for instance, align the circuit generation to the constraints of the targeted quantum device. Given their flexibility and generalization abilities, we envision DMs as pivotal in quantum circuit synthesis, enhancing both practical applications but also insights into theoretical quantum computation.

Rough surface lubrication simulation is crucial for designing and optimizing tribological performance. Despite the growing application of Physical Information Neural Networks (PINNs) in hydrodynamic lubrication analysis, their use has been primarily limited to smooth surfaces. This is due to traditional PINN methods suffer from spectral bias, favoring to learn low-frequency features and thus failing to analyze rough surfaces with high-frequency signals. To date, no PINN methods have been reported for rough surface lubrication. To overcome these limitations, this work introduces a novel multi-scale lubrication neural network architecture that utilizes a trainable Fourier feature network. By incorporating learnable feature embedding frequencies, this architecture automatically adapts to various frequency components, thereby enhancing the analysis of rough surface characteristics. This method has been tested across multiple surface morphologies, and the results have been compared with those obtained using the finite element method (FEM). The comparative analysis demonstrates that this approach achieves a high consistency with FEM results. Furthermore, this novel architecture surpasses traditional Fourier feature networks with fixed feature embedding frequencies in both accuracy and computational efficiency. Consequently, the multi-scale lubrication neural network model offers a more efficient tool for rough surface lubrication analysis.

Integrative analysis of multiple heterogeneous datasets has become standard practice in many research fields, especially in single-cell genomics and medical informatics. Existing approaches oftentimes suffer from limited power in capturing nonlinear structures, insufficient account of noisiness and effects of high-dimensionality, lack of adaptivity to signals and sample sizes imbalance, and their results are sometimes difficult to interpret. To address these limitations, we propose a novel kernel spectral method that achieves joint embeddings of two independently observed high-dimensional noisy datasets. The proposed method automatically captures and leverages possibly shared low-dimensional structures across datasets to enhance embedding quality. The obtained low-dimensional embeddings can be utilized for many downstream tasks such as simultaneous clustering, data visualization, and denoising. The proposed method is justified by rigorous theoretical analysis. Specifically, we show the consistency of our method in recovering the low-dimensional noiseless signals, and characterize the effects of the signal-to-noise ratios on the rates of convergence. Under a joint manifolds model framework, we establish the convergence of ultimate embeddings to the eigenfunctions of some newly introduced integral operators. These operators, referred to as duo-landmark integral operators, are defined by the convolutional kernel maps of some reproducing kernel Hilbert spaces (RKHSs). These RKHSs capture the either partially or entirely shared underlying low-dimensional nonlinear signal structures of the two datasets. Our numerical experiments and analyses of two single-cell omics datasets demonstrate the empirical advantages of the proposed method over existing methods in both embeddings and several downstream tasks.

It has long been believed that the brain is highly modular both in terms of structure and function, although recent evidence has led some to question the extent of both types of modularity. We used artificial neural networks to test the hypothesis that structural modularity is sufficient to guarantee functional specialization, and find that in general, this doesn't necessarily hold. We then systematically tested which features of the environment and network do lead to the emergence of specialization. We used a simple toy environment, task and network, allowing us precise control, and show that in this setup, several distinct measures of specialization give qualitatively similar results. We further find that in this setup (1) specialization can only emerge in environments where features of that environment are meaningfully separable, (2) specialization preferentially emerges when the network is strongly resource-constrained, and (3) these findings are qualitatively similar across the different variations of network architectures that we tested, but that the quantitative relationships depend on the precise architecture. Finally, we show that functional specialization varies dynamically across time, and demonstrate that these dynamics depend on both the timing and bandwidth of information flow in the network. We conclude that a static notion of specialization, based on structural modularity, is likely too simple a framework for understanding intelligence in situations of real-world complexity, from biology to brain-inspired neuromorphic systems. We propose that thoroughly stress testing candidate definitions of functional modularity in simplified scenarios before extending to more complex data, network models and electrophysiological recordings is likely to be a fruitful approach.