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The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform (SBWT) has been recently introduced as an algorithmic tool to efficiently represent and query these objects. The longest common prefix (LCP) array for a k-spectrum is an array of length n that stores the length of the longest common prefix of adjacent k-mers as they occur in lexicographical order. The LCP array has at least two important applications, namely to accelerate pseudoalignment algorithms using the SBWT and to allow simulation of variable-order de Bruijn graphs within the SBWT framework. In this paper we explore algorithms to compute the LCP array efficiently from the SBWT representation of the k-spectrum. Starting with a straightforward O(nk) time algorithm, we describe algorithms that are efficient in both theory and practice. We show that the LCP array can be computed in optimal O(n) time, where n is the length of the SBWT of the spectrum. In practical genomics scenarios, we show that this theoretically optimal algorithm is indeed practical, but is often outperformed on smaller values of k by an asymptotically suboptimal algorithm that interacts better with the CPU cache. Our algorithms share some features with both classical Burrows-Wheeler inversion algorithms and LCP array construction algorithms for suffix arrays.

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In this paper, we propose a multidimensional statistical model of intraday electricity prices at the scale of the trading session, which allows all products to be simulated simultaneously. This model, based on Poisson measures and inspired by the Common Shock Poisson Model, reproduces the Samuelson effect (intensity and volatility increases as time to maturity decreases). It also reproduces the price correlation structure, highlighted here in the data, which decreases as two maturities move apart. This model has only three parameters that can be estimated using a moment method that we propose here. We demonstrate the usefulness of the model on a case of storage valuation by dynamic programming over a trading session.

Golden-section search and bisection search are the two main principled algorithms for 1d minimization of quasiconvex (unimodal) functions. The first one only uses function queries, while the second one also uses gradient queries. Other algorithms exist under much stronger assumptions, such as Newton's method. However, to the best of our knowledge, there is no principled exact line search algorithm for general convex functions -- including piecewise-linear and max-compositions of convex functions -- that takes advantage of convexity. We propose two such algorithms: $\Delta$-Bisection is a variant of bisection search that uses (sub)gradient information and convexity to speed up convergence, while $\Delta$-Secant is a variant of golden-section search and uses only function queries. While bisection search reduces the $x$ interval by a factor 2 at every iteration, $\Delta$-Bisection reduces the (sometimes much) smaller $x^*$-gap $\Delta^x$ (the $x$ coordinates of $\Delta$) by at least a factor 2 at every iteration. Similarly, $\Delta$-Secant also reduces the $x^*$-gap by at least a factor 2 every second function query. Moreover, the $y^*$-gap $\Delta^y$ (the $y$ coordinates of $\Delta$) also provides a refined stopping criterion, which can also be used with other algorithms. Experiments on a few convex functions confirm that our algorithms are always faster than their quasiconvex counterparts, often by more than a factor 2. We further design a quasi-exact line search algorithm based on $\Delta$-Secant. It can be used with gradient descent as a replacement for backtracking line search, for which some parameters can be finicky to tune -- and we provide examples to this effect, on strongly-convex and smooth functions. We provide convergence guarantees, and confirm the efficiency of quasi-exact line search on a few single- and multivariate convex functions.

Three-dimensional (3D) reconstruction of head Computed Tomography (CT) images elucidates the intricate spatial relationships of tissue structures, thereby assisting in accurate diagnosis. Nonetheless, securing an optimal head CT scan without deviation is challenging in clinical settings, owing to poor positioning by technicians, patient's physical constraints, or CT scanner tilt angle restrictions. Manual formatting and reconstruction not only introduce subjectivity but also strain time and labor resources. To address these issues, we propose an efficient automatic head CT images 3D reconstruction method, improving accuracy and repeatability, as well as diminishing manual intervention. Our approach employs a deep learning-based object detection algorithm, identifying and evaluating orbitomeatal line landmarks to automatically reformat the images prior to reconstruction. Given the dearth of existing evaluations of object detection algorithms in the context of head CT images, we compared ten methods from both theoretical and experimental perspectives. By exploring their precision, efficiency, and robustness, we singled out the lightweight YOLOv8 as the aptest algorithm for our task, with an mAP of 92.91% and impressive robustness against class imbalance. Our qualitative evaluation of standardized reconstruction results demonstrates the clinical practicability and validity of our method.

We evaluate benchmark deep reinforcement learning (DRL) algorithms on the task of portfolio optimisation under a simulator. The simulator is based on correlated geometric Brownian motion (GBM) with the Bertsimas-Lo (BL) market impact model. Using the Kelly criterion (log utility) as the objective, we can analytically derive the optimal policy without market impact and use it as an upper bound to measure performance when including market impact. We found that the off-policy algorithms DDPG, TD3 and SAC were unable to learn the right Q function due to the noisy rewards and therefore perform poorly. The on-policy algorithms PPO and A2C, with the use of generalised advantage estimation (GAE), were able to deal with the noise and derive a close to optimal policy. The clipping variant of PPO was found to be important in preventing the policy from deviating from the optimal once converged. In a more challenging environment where we have regime changes in the GBM parameters, we found that PPO, combined with a hidden Markov model (HMM) to learn and predict the regime context, is able to learn different policies adapted to each regime. Overall, we find that the sample complexity of these algorithms is too high, requiring more than 2m steps to learn a good policy in the simplest setting, which is equivalent to almost 8,000 years of daily prices.

We consider the problem of learning a set of direct causes of a target variable from an observational joint distribution. Learning directed acyclic graphs (DAGs) that represent the causal structure is a fundamental problem in science. Several results are known when the full DAG is identifiable from the distribution, such as assuming a nonlinear Gaussian data-generating process. Often, we are only interested in identifying the direct causes of one target variable (local causal structure), not the full DAG. In this paper, we discuss different assumptions for the data-generating process of the target variable under which the set of direct causes is identifiable from the distribution. While doing so, we put essentially no assumptions on the variables other than the target variable. In addition to the novel identifiability results, we provide two practical algorithms for estimating the direct causes from a finite random sample and demonstrate their effectiveness on several benchmark datasets. We apply this framework to learn direct causes of the reduction in fertility rates in different countries.

We propose an unconditionally energy-stable, orthonormality-preserving, component-wise splitting iterative scheme for the Kohn-Sham gradient flow based model in the electronic structure calculation. We first study the scheme discretized in time but still continuous in space. The component-wise splitting iterative scheme changes one wave function at a time, similar to the Gauss-Seidel iteration for solving a linear equation system. Rigorous mathematical derivations are presented to show our proposed scheme indeed satisfies the desired properties. We then study the fully-discretized scheme, where the space is further approximated by a conforming finite element subspace. For the fully-discretized scheme, not only the preservation of orthogonality and normalization (together we called orthonormalization) can be quickly shown using the same idea as for the semi-discretized scheme, but also the highlight property of the scheme, i.e., the unconditional energy stability can be rigorously proven. The scheme allows us to use large time step sizes and deal with small systems involving only a single wave function during each iteration step. Several numerical experiments are performed to verify the theoretical analysis, where the number of iterations is indeed greatly reduced as compared to similar examples solved by the Kohn-Sham gradient flow based model in the literature.

State-of-the-art neural networks require extreme computational power to train. It is therefore natural to wonder whether they are optimally trained. Here we apply a recent advancement in stochastic thermodynamics which allows bounding the speed at which one can go from the initial weight distribution to the final distribution of the fully trained network, based on the ratio of their Wasserstein-2 distance and the entropy production rate of the dynamical process connecting them. Considering both gradient-flow and Langevin training dynamics, we provide analytical expressions for these speed limits for linear and linearizable neural networks e.g. Neural Tangent Kernel (NTK). Remarkably, given some plausible scaling assumptions on the NTK spectra and spectral decomposition of the labels -- learning is optimal in a scaling sense. Our results are consistent with small-scale experiments with Convolutional Neural Networks (CNNs) and Fully Connected Neural networks (FCNs) on CIFAR-10, showing a short highly non-optimal regime followed by a longer optimal regime.

Modelling in biology must adapt to increasingly complex and massive data. The efficiency of the inference algorithms used to estimate model parameters is therefore questioned. Many of these are based on stochastic optimization processes which waste a significant part of the computation time due to their rejection sampling approaches. We introduce the Fixed Landscape Inference MethOd (flimo), a new likelihood-free inference method for continuous state-space stochastic models. It applies deterministic gradient-based optimization algorithms to obtain a point estimate of the parameters, minimizing the difference between the data and some simulations according to some prescribed summary statistics. In this sense, it is analogous to Approximate Bayesian Computation (ABC). Like ABC, it can also provide an approximation of the distribution of the parameters. Three applications are proposed: a usual theoretical example, namely the inference of the parameters of g-and-k distributions; a population genetics problem, not so simple as it seems, namely the inference of a selective value from time series in a Wright-Fisher model; and simulations from a Ricker model, representing chaotic population dynamics. In the two first applications, the results show a drastic reduction of the computational time needed for the inference phase compared to the other methods, despite an equivalent accuracy. Even when likelihood-based methods are applicable, the simplicity and efficiency of flimo make it a compelling alternative. Implementations in Julia and in R are available on //metabarcoding.org/flimo. To run flimo, the user must simply be able to simulate data according to the chosen model.

Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.

A core capability of intelligent systems is the ability to quickly learn new tasks by drawing on prior experience. Gradient (or optimization) based meta-learning has recently emerged as an effective approach for few-shot learning. In this formulation, meta-parameters are learned in the outer loop, while task-specific models are learned in the inner-loop, by using only a small amount of data from the current task. A key challenge in scaling these approaches is the need to differentiate through the inner loop learning process, which can impose considerable computational and memory burdens. By drawing upon implicit differentiation, we develop the implicit MAML algorithm, which depends only on the solution to the inner level optimization and not the path taken by the inner loop optimizer. This effectively decouples the meta-gradient computation from the choice of inner loop optimizer. As a result, our approach is agnostic to the choice of inner loop optimizer and can gracefully handle many gradient steps without vanishing gradients or memory constraints. Theoretically, we prove that implicit MAML can compute accurate meta-gradients with a memory footprint that is, up to small constant factors, no more than that which is required to compute a single inner loop gradient and at no overall increase in the total computational cost. Experimentally, we show that these benefits of implicit MAML translate into empirical gains on few-shot image recognition benchmarks.

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