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Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project - an open-source software community focused on omics data analysis. This guide serves as a valuable reference for both learners and educators in the field.

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We first present a simple recursive algorithm that generates cyclic rotation Gray codes for stamp foldings and semi-meanders, where consecutive strings differ by a stamp rotation. These are the first known Gray codes for stamp foldings and semi-meanders, and we thus solve an open problem posted by Sawada and Li in [Electron. J. Comb. 19(2), 2012]. We then introduce an iterative algorithm that generates the same rotation Gray codes for stamp foldings and semi-meanders. Both the recursive and iterative algorithms generate stamp foldings and semi-meanders in constant amortized time and $O(n)$-amortized time per string respectively, using a linear amount of memory.

Sequential neural posterior estimation (SNPE) techniques have been recently proposed for dealing with simulation-based models with intractable likelihoods. Unlike approximate Bayesian computation, SNPE techniques learn the posterior from sequential simulation using neural network-based conditional density estimators by minimizing a specific loss function. The SNPE method proposed by Lueckmann et al. (2017) used a calibration kernel to boost the sample weights around the observed data, resulting in a concentrated loss function. However, the use of calibration kernels may increase the variances of both the empirical loss and its gradient, making the training inefficient. To improve the stability of SNPE, this paper proposes to use an adaptive calibration kernel and several variance reduction techniques. The proposed method greatly speeds up the process of training and provides a better approximation of the posterior than the original SNPE method and some existing competitors as confirmed by numerical experiments. We also manage to demonstrate the superiority of the proposed method for a high-dimensional model with real-world dataset.

Studying the interplay between the geometry of the loss landscape and the optimization trajectories of simple neural networks is a fundamental step for understanding their behavior in more complex settings. This paper reveals the presence of topological obstruction in the loss landscape of shallow ReLU neural networks trained using gradient flow. We discuss how the homogeneous nature of the ReLU activation function constrains the training trajectories to lie on a product of quadric hypersurfaces whose shape depends on the particular initialization of the network's parameters. When the neural network's output is a single scalar, we prove that these quadrics can have multiple connected components, limiting the set of reachable parameters during training. We analytically compute the number of these components and discuss the possibility of mapping one to the other through neuron rescaling and permutation. In this simple setting, we find that the non-connectedness results in a topological obstruction, which, depending on the initialization, can make the global optimum unreachable. We validate this result with numerical experiments.

Determining the difficulty of a text involves assessing various textual features that may impact the reader's text comprehension, yet current research in Vietnamese has only focused on statistical features. This paper introduces a new approach that integrates statistical and semantic approaches to assessing text readability. Our research utilized three distinct datasets: the Vietnamese Text Readability Dataset (ViRead), OneStopEnglish, and RACE, with the latter two translated into Vietnamese. Advanced semantic analysis methods were employed for the semantic aspect using state-of-the-art language models such as PhoBERT, ViDeBERTa, and ViBERT. In addition, statistical methods were incorporated to extract syntactic and lexical features of the text. We conducted experiments using various machine learning models, including Support Vector Machine (SVM), Random Forest, and Extra Trees and evaluated their performance using accuracy and F1 score metrics. Our results indicate that a joint approach that combines semantic and statistical features significantly enhances the accuracy of readability classification compared to using each method in isolation. The current study emphasizes the importance of considering both statistical and semantic aspects for a more accurate assessment of text difficulty in Vietnamese. This contribution to the field provides insights into the adaptability of advanced language models in the context of Vietnamese text readability. It lays the groundwork for future research in this area.

Statistical learning under distribution shift is challenging when neither prior knowledge nor fully accessible data from the target distribution is available. Distributionally robust learning (DRL) aims to control the worst-case statistical performance within an uncertainty set of candidate distributions, but how to properly specify the set remains challenging. To enable distributional robustness without being overly conservative, in this paper, we propose a shape-constrained approach to DRL, which incorporates prior information about the way in which the unknown target distribution differs from its estimate. More specifically, we assume the unknown density ratio between the target distribution and its estimate is isotonic with respect to some partial order. At the population level, we provide a solution to the shape-constrained optimization problem that does not involve the isotonic constraint. At the sample level, we provide consistency results for an empirical estimator of the target in a range of different settings. Empirical studies on both synthetic and real data examples demonstrate the improved accuracy of the proposed shape-constrained approach.

Graph neural networks (GNNs) provide state-of-the-art results in a wide variety of tasks which typically involve predicting features at the vertices of a graph. They are built from layers of graph convolutions which serve as a powerful inductive bias for describing the flow of information among the vertices. Often, more than one data modality is available. This work considers a setting in which several graphs have the same vertex set and a common vertex-level learning task. This generalizes standard GNN models to GNNs with several graph operators that do not commute. We may call this model graph-tuple neural networks (GtNN). In this work, we develop the mathematical theory to address the stability and transferability of GtNNs using properties of non-commuting non-expansive operators. We develop a limit theory of graphon-tuple neural networks and use it to prove a universal transferability theorem that guarantees that all graph-tuple neural networks are transferable on convergent graph-tuple sequences. In particular, there is no non-transferable energy under the convergence we consider here. Our theoretical results extend well-known transferability theorems for GNNs to the case of several simultaneous graphs (GtNNs) and provide a strict improvement on what is currently known even in the GNN case. We illustrate our theoretical results with simple experiments on synthetic and real-world data. To this end, we derive a training procedure that provably enforces the stability of the resulting model.

The success of over-parameterized neural networks trained to near-zero training error has caused great interest in the phenomenon of benign overfitting, where estimators are statistically consistent even though they interpolate noisy training data. While benign overfitting in fixed dimension has been established for some learning methods, current literature suggests that for regression with typical kernel methods and wide neural networks, benign overfitting requires a high-dimensional setting where the dimension grows with the sample size. In this paper, we show that the smoothness of the estimators, and not the dimension, is the key: benign overfitting is possible if and only if the estimator's derivatives are large enough. We generalize existing inconsistency results to non-interpolating models and more kernels to show that benign overfitting with moderate derivatives is impossible in fixed dimension. Conversely, we show that rate-optimal benign overfitting is possible for regression with a sequence of spiky-smooth kernels with large derivatives. Using neural tangent kernels, we translate our results to wide neural networks. We prove that while infinite-width networks do not overfit benignly with the ReLU activation, this can be fixed by adding small high-frequency fluctuations to the activation function. Our experiments verify that such neural networks, while overfitting, can indeed generalize well even on low-dimensional data sets.

In industry, online randomized controlled experiment (a.k.a A/B experiment) is a standard approach to measure the impact of a causal change. These experiments have small treatment effect to reduce the potential blast radius. As a result, these experiments often lack statistical significance due to low signal-to-noise ratio. To improve the precision (or reduce standard error), we introduce the idea of trigger observations where the output of the treatment and the control model are different. We show that the evaluation with full information about trigger observations (full knowledge) improves the precision in comparison to a baseline method. However, detecting all such trigger observations is a costly affair, hence we propose a sampling based evaluation method (partial knowledge) to reduce the cost. The randomness of sampling introduces bias in the estimated outcome. We theoretically analyze this bias and show that the bias is inversely proportional to the number of observations used for sampling. We also compare the proposed evaluation methods using simulation and empirical data. In simulation, evaluation with full knowledge reduces the standard error as much as 85%. In empirical setup, evaluation with partial knowledge reduces the standard error by 36.48%.

Deep learning is usually described as an experiment-driven field under continuous criticizes of lacking theoretical foundations. This problem has been partially fixed by a large volume of literature which has so far not been well organized. This paper reviews and organizes the recent advances in deep learning theory. The literature is categorized in six groups: (1) complexity and capacity-based approaches for analyzing the generalizability of deep learning; (2) stochastic differential equations and their dynamic systems for modelling stochastic gradient descent and its variants, which characterize the optimization and generalization of deep learning, partially inspired by Bayesian inference; (3) the geometrical structures of the loss landscape that drives the trajectories of the dynamic systems; (4) the roles of over-parameterization of deep neural networks from both positive and negative perspectives; (5) theoretical foundations of several special structures in network architectures; and (6) the increasingly intensive concerns in ethics and security and their relationships with generalizability.

Deep learning constitutes a recent, modern technique for image processing and data analysis, with promising results and large potential. As deep learning has been successfully applied in various domains, it has recently entered also the domain of agriculture. In this paper, we perform a survey of 40 research efforts that employ deep learning techniques, applied to various agricultural and food production challenges. We examine the particular agricultural problems under study, the specific models and frameworks employed, the sources, nature and pre-processing of data used, and the overall performance achieved according to the metrics used at each work under study. Moreover, we study comparisons of deep learning with other existing popular techniques, in respect to differences in classification or regression performance. Our findings indicate that deep learning provides high accuracy, outperforming existing commonly used image processing techniques.

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