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Biclustering algorithms play a central role in the biotechnological and biomedical domains. The knowledge extracted supports the extraction of putative regulatory modules, essential to understanding diseases, aiding therapy research, and advancing biological knowledge. However, given the NP-hard nature of the biclustering task, algorithms with optimality guarantees tend to scale poorly in the presence of high-dimensionality data. To this end, we propose a pipeline for clustering-based vertical partitioning that takes into consideration both parallelization and cross-partition pattern merging needs. Given a specific type of pattern coherence, these clusters are built based on the likelihood that variables form those patterns. Subsequently, the extracted patterns per cluster are then merged together into a final set of closed patterns. This approach is evaluated using five published datasets. Results show that in some of the tested data, execution times yield statistically significant improvements when variables are clustered together based on the likelihood to form specific types of patterns, as opposed to partitions based on dissimilarity or randomness. This work offers a departuring step on the efficiency impact of vertical partitioning criteria along the different stages of pattern mining and biclustering algorithms. Availability: All the code is freely available at //github.com/JupitersMight/pattern_merge under the MIT license.

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In building practical applications of evolutionary computation (EC), two optimizations are essential. First, the parameters of the search method need to be tuned to the domain in order to balance exploration and exploitation effectively. Second, the search method needs to be distributed to take advantage of parallel computing resources. This paper presents BLADE (BLAnket Distributed Evolution) as an approach to achieving both goals simultaneously. BLADE uses blankets (i.e., masks on the genetic representation) to tune the evolutionary operators during the search, and implements the search through hub-and-spoke distribution. In the paper, (1) the blanket method is formalized for the (1 + 1)EA case as a Markov chain process. Its effectiveness is then demonstrated by analyzing dominant and subdominant eigenvalues of stochastic matrices, suggesting a generalizable theory; (2) the fitness-level theory is used to analyze the distribution method; and (3) these insights are verified experimentally on three benchmark problems, showing that both blankets and distribution lead to accelerated evolution. Moreover, a surprising synergy emerges between them: When combined with distribution, the blanket approach achieves more than $n$-fold speedup with $n$ clients in some cases. The work thus highlights the importance and potential of optimizing evolutionary computation in practical applications.

Detecting the dimensionality of graphs is a central topic in machine learning. While the problem has been tackled empirically as well as theoretically, existing methods have several drawbacks. On the one hand, empirical tools are computationally heavy and lack theoretical foundation. On the other hand, theoretical approaches do not apply to graphs with heterogeneous degree distributions, which is often the case for complex real-world networks. To address these drawbacks, we consider geometric inhomogeneous random graphs (GIRGs) as a random graph model, which captures a variety of properties observed in practice. These include a heterogeneous degree distribution and non-vanishing clustering coefficient, which is the probability that two random neighbours of a vertex are adjacent. In GIRGs, $n$ vertices are distributed on a $d$-dimensional torus and weights are assigned to the vertices according to a power-law distribution. Two vertices are then connected with a probability that depends on their distance and their weights. Our first result shows that the clustering coefficient of GIRGs scales inverse exponentially with respect to the number of dimensions, when the latter is at most logarithmic in $n$. This gives a first theoretical explanation for the low dimensionality of real-world networks observed by Almagro et. al. [Nature '22]. Our second result is a linear-time algorithm for determining the dimensionality of a given GIRG. We prove that our algorithm returns the correct number of dimensions with high probability when the input is a GIRG. As a result, our algorithm bridges the gap between theory and practice, as it not only comes with a rigorous proof of correctness but also yields results comparable to that of prior empirical approaches, as indicated by our experiments on real-world instances.

There is no convincing evidence that backpropagation is a biologically plausible mechanism, and further studies of alternative learning methods are needed. A novel online clustering algorithm is presented that can produce arbitrary shaped clusters from inputs in an unsupervised manner, and requires no prior knowledge of the number of clusters in the input data. This is achieved by finding correlated outputs from functions that capture commonly occurring input patterns. The algorithm can be deemed more biologically plausible than model optimization through backpropagation, although practical applicability may require additional research. However, the method yields satisfactory results on several toy datasets on a noteworthy range of hyperparameters.

Partitioning the vertices of a (hyper)graph into k roughly balanced blocks such that few (hyper)edges run between blocks is a key problem for large-scale distributed processing. A current trend for partitioning huge (hyper)graphs using low computational resources are streaming algorithms. In this work, we propose FREIGHT: a Fast stREamInG Hypergraph parTitioning algorithm which is an adaptation of the widely-known graph-based algorithm Fennel. By using an efficient data structure, we make the overall running of FREIGHT linearly dependent on the pin-count of the hypergraph and the memory consumption linearly dependent on the numbers of nets and blocks. The results of our extensive experimentation showcase the promising performance of FREIGHT as a highly efficient and effective solution for streaming hypergraph partitioning. Our algorithm demonstrates competitive running time with the Hashing algorithm, with a difference of a maximum factor of four observed on three fourths of the instances. Significantly, our findings highlight the superiority of FREIGHT over all existing (buffered) streaming algorithms and even the in-memory algorithm HYPE, with respect to both cut-net and connectivity measures. This indicates that our proposed algorithm is a promising hypergraph partitioning tool to tackle the challenge posed by large-scale and dynamic data processing.

State-of-the-art parametric and non-parametric style transfer approaches are prone to either distorted local style patterns due to global statistics alignment, or unpleasing artifacts resulting from patch mismatching. In this paper, we study a novel semi-parametric neural style transfer framework that alleviates the deficiency of both parametric and non-parametric stylization. The core idea of our approach is to establish accurate and fine-grained content-style correspondences using graph neural networks (GNNs). To this end, we develop an elaborated GNN model with content and style local patches as the graph vertices. The style transfer procedure is then modeled as the attention-based heterogeneous message passing between the style and content nodes in a learnable manner, leading to adaptive many-to-one style-content correlations at the local patch level. In addition, an elaborated deformable graph convolutional operation is introduced for cross-scale style-content matching. Experimental results demonstrate that the proposed semi-parametric image stylization approach yields encouraging results on the challenging style patterns, preserving both global appearance and exquisite details. Furthermore, by controlling the number of edges at the inference stage, the proposed method also triggers novel functionalities like diversified patch-based stylization with a single model.

We examine the use of the Euler-Maclaurin formula and new derived uniform asymptotic expansions for the numerical evaluation of the Lerch transcendent $\Phi(z, s, a)$ for $z, s, a \in \mathbb{C}$ to arbitrary precision. A detailed analysis of these expansions is accompanied by rigorous error bounds. A complete scheme of computation for large and small values of the parameters and argument is described along with algorithmic details to achieve high performance. The described algorithm has been extensively tested in different regimes of the parameters and compared with current state-of-the-art codes. An open-source implementation of $\Phi(z, s, a)$ based on the algorithms described in this paper is available.

Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.

The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.

Residual networks (ResNets) have displayed impressive results in pattern recognition and, recently, have garnered considerable theoretical interest due to a perceived link with neural ordinary differential equations (neural ODEs). This link relies on the convergence of network weights to a smooth function as the number of layers increases. We investigate the properties of weights trained by stochastic gradient descent and their scaling with network depth through detailed numerical experiments. We observe the existence of scaling regimes markedly different from those assumed in neural ODE literature. Depending on certain features of the network architecture, such as the smoothness of the activation function, one may obtain an alternative ODE limit, a stochastic differential equation or neither of these. These findings cast doubts on the validity of the neural ODE model as an adequate asymptotic description of deep ResNets and point to an alternative class of differential equations as a better description of the deep network limit.

The accurate and interpretable prediction of future events in time-series data often requires the capturing of representative patterns (or referred to as states) underpinning the observed data. To this end, most existing studies focus on the representation and recognition of states, but ignore the changing transitional relations among them. In this paper, we present evolutionary state graph, a dynamic graph structure designed to systematically represent the evolving relations (edges) among states (nodes) along time. We conduct analysis on the dynamic graphs constructed from the time-series data and show that changes on the graph structures (e.g., edges connecting certain state nodes) can inform the occurrences of events (i.e., time-series fluctuation). Inspired by this, we propose a novel graph neural network model, Evolutionary State Graph Network (EvoNet), to encode the evolutionary state graph for accurate and interpretable time-series event prediction. Specifically, Evolutionary State Graph Network models both the node-level (state-to-state) and graph-level (segment-to-segment) propagation, and captures the node-graph (state-to-segment) interactions over time. Experimental results based on five real-world datasets show that our approach not only achieves clear improvements compared with 11 baselines, but also provides more insights towards explaining the results of event predictions.

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