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Traditional clustering algorithms often struggle to capture the complex relationships within graphs and generalise to arbitrary clustering criteria. The emergence of graph neural networks (GNNs) as a powerful framework for learning representations of graph data provides new approaches to solving the problem. Previous work has shown GNNs to be capable of proposing partitionings using a variety of criteria, however, these approaches have not yet been extended to work on Markov chains or kinetic networks. These arise frequently in the study of molecular systems and are of particular interest to the biochemical modelling community. In this work, we propose several GNN-based architectures to tackle the graph partitioning problem for Markov Chains described as kinetic networks. This approach aims to minimize how much a proposed partitioning changes the Kemeny constant. We propose using an encoder-decoder architecture and show how simple GraphSAGE-based GNNs with linear layers can outperform much larger and more expressive attention-based models in this context. As a proof of concept, we first demonstrate the method's ability to cluster randomly connected graphs. We also use a linear chain architecture corresponding to a 1D free energy profile as our kinetic network. Subsequently, we demonstrate the effectiveness of our method through experiments on a data set derived from molecular dynamics. We compare the performance of our method to other partitioning techniques such as PCCA+. We explore the importance of feature and hyperparameter selection and propose a general strategy for large-scale parallel training of GNNs for discovering optimal graph partitionings.

Traditional clustering algorithms often struggle to capture the complex relationships within graphs and generalise to arbitrary clustering criteria. The emergence of graph neural networks (GNNs) as a powerful framework for learning representations of graph data provides new approaches to solving the problem. Previous work has shown GNNs to be capable of proposing partitionings using a variety of criteria, however, these approaches have not yet been extended to work on Markov chains or kinetic networks. These arise frequently in the study of molecular systems and are of particular interest to the biochemical modelling community. In this work, we propose several GNN-based architectures to tackle the graph partitioning problem for Markov Chains described as kinetic networks. This approach aims to minimize how much a proposed partitioning changes the Kemeny constant. We propose using an encoder-decoder architecture and show how simple GraphSAGE-based GNNs with linear layers can outperform much larger and more expressive attention-based models in this context. As a proof of concept, we first demonstrate the method's ability to cluster randomly connected graphs. We also use a linear chain architecture corresponding to a 1D free energy profile as our kinetic network. Subsequently, we demonstrate the effectiveness of our method through experiments on a data set derived from molecular dynamics. We compare the performance of our method to other partitioning techniques such as PCCA+. We explore the importance of feature and hyperparameter selection and propose a general strategy for large-scale parallel training of GNNs for discovering optimal graph partitionings.

We embark on a systematic study of the $(k+1)$-th derivative of $x^{k-r}H(x^r)$, where $H(x):=-x\log x-(1-x)\log(1-x)$ is the binary entropy and $k>r\geq 1$ are integers. Our motivation is the conjectural entropy inequality $\alpha_k H(x^k)\geq x^{k-1}H(x)$, where $0<\alpha_k<1$ is given by a functional equation. The $k=2$ case was the key technical tool driving recent breakthroughs on the union-closed sets conjecture. We express $ \frac{d^{k+1}}{dx^{k+1}}x^{k-r}H(x^r)$ as a rational function, an infinite series, and a sum over generalized Stirling numbers. This allows us to reduce the proof of the entropy inequality for real $k$ to showing that an associated polynomial has only two real roots in the interval $(0,1)$, which also allows us to prove the inequality for fractional exponents such as $k=3/2$. The proof suggests a new framework for proving tight inequalities for the sum of polynomials times the logarithms of polynomials, which converts the inequality into a statement about the real roots of a simpler associated polynomial.

A new $H(\textrm{divdiv})$-conforming finite element is presented, which avoids the need for super-smoothness by redistributing the degrees of freedom to edges and faces. This leads to a hybridizable mixed method with superconvergence for the biharmonic equation. Moreover, new finite element divdiv complexes are established. Finally, new weak Galerkin and $C^0$ discontinuous Galerkin methods for the biharmonic equation are derived.

A Gr\"obner basis computation for the Weyl algebra with respect to a tropical term order and by using a homogenization-dehomogenization technique is sufficiently sluggish. A significant number of reductions to zero occur. To improve the computation, a tropical F5 algorithm is developed for this context. As a member of the family of signature-based algorithms, this algorithm keeps track of where Weyl algebra elements come from to anticipate reductions to zero. The total order for ordering module monomials or signatures in this paper is designed as close as possible to the definition of the tropical term order. As in Vaccon et al. (2021), this total order is not compatible with the tropical term order.

Gate-defined quantum dots are a promising candidate system to realize scalable, coupled qubit systems and serve as a fundamental building block for quantum computers. However, present-day quantum dot devices suffer from imperfections that must be accounted for, which hinders the characterization, tuning, and operation process. Moreover, with an increasing number of quantum dot qubits, the relevant parameter space grows sufficiently to make heuristic control infeasible. Thus, it is imperative that reliable and scalable autonomous tuning approaches are developed. In this report, we outline current challenges in automating quantum dot device tuning and operation with a particular focus on datasets, benchmarking, and standardization. We also present ideas put forward by the quantum dot community on how to overcome them.

We study the problem of contextual feature selection, where the goal is to learn a predictive function while identifying subsets of informative features conditioned on specific contexts. Towards this goal, we generalize the recently proposed stochastic gates (STG) Yamada et al. [2020] by modeling the probabilistic gates as conditional Bernoulli variables whose parameters are predicted based on the contextual variables. Our new scheme, termed conditional-STG (c-STG), comprises two networks: a hypernetwork that establishes the mapping between contextual variables and probabilistic feature selection parameters and a prediction network that maps the selected feature to the response variable. Training the two networks simultaneously ensures the comprehensive incorporation of context and feature selection within a unified model. We provide a theoretical analysis to examine several properties of the proposed framework. Importantly, our model leads to improved flexibility and adaptability of feature selection and, therefore, can better capture the nuances and variations in the data. We apply c-STG to simulated and real-world datasets, including healthcare, housing, and neuroscience, and demonstrate that it effectively selects contextually meaningful features, thereby enhancing predictive performance and interpretability.

Natural data observed in $\mathbb{R}^n$ is often constrained to an $m$-dimensional manifold $\mathcal{M}$, where $m < n$. This work focuses on the task of building theoretically principled generative models for such data. Current generative models learn $\mathcal{M}$ by mapping an $m$-dimensional latent variable through a neural network $f_\theta: \mathbb{R}^m \to \mathbb{R}^n$. These procedures, which we call pushforward models, incur a straightforward limitation: manifolds cannot in general be represented with a single parameterization, meaning that attempts to do so will incur either computational instability or the inability to learn probability densities within the manifold. To remedy this problem, we propose to model $\mathcal{M}$ as a neural implicit manifold: the set of zeros of a neural network. We then learn the probability density within $\mathcal{M}$ with a constrained energy-based model, which employs a constrained variant of Langevin dynamics to train and sample from the learned manifold. In experiments on synthetic and natural data, we show that our model can learn manifold-supported distributions with complex topologies more accurately than pushforward models.

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.

In multi-turn dialog, utterances do not always take the full form of sentences \cite{Carbonell1983DiscoursePA}, which naturally makes understanding the dialog context more difficult. However, it is essential to fully grasp the dialog context to generate a reasonable response. Hence, in this paper, we propose to improve the response generation performance by examining the model's ability to answer a reading comprehension question, where the question is focused on the omitted information in the dialog. Enlightened by the multi-task learning scheme, we propose a joint framework that unifies these two tasks, sharing the same encoder to extract the common and task-invariant features with different decoders to learn task-specific features. To better fusing information from the question and the dialog history in the encoding part, we propose to augment the Transformer architecture with a memory updater, which is designed to selectively store and update the history dialog information so as to support downstream tasks. For the experiment, we employ human annotators to write and examine a large-scale dialog reading comprehension dataset. Extensive experiments are conducted on this dataset, and the results show that the proposed model brings substantial improvements over several strong baselines on both tasks. In this way, we demonstrate that reasoning can indeed help better response generation and vice versa. We release our large-scale dataset for further research.