包括机器学习在内的计算分析方法对基因组学和医学领域具有重大影响。高通量基因表达分析方法，例如微阵列技术和RNA测序产生大量数据。传统上，统计方法用于基因表达数据的比较分析。但是，针对样品观察分类或发现特征基因的分类的更复杂的分析需要复杂的计算方法。在这篇综述中，我们编译了用于分析表达微阵列数据的各种统计和计算工具。即使在表达微阵列的背景下讨论了这些方法，也可以将它们应用于RNA测序和定量蛋白质组学数据集的分析。我们讨论缺失价值的类型以及其插补中通常采用的方法和方法。我们还讨论了数据归一化，特征选择和特征提取的方法。最后，详细描述了分类和类发现方法及其评估参数。我们认为，这项详细的审查将帮助用户根据预期结果选择适当的方法来预处理和分析其数据。

Determining and predicting reservoir formation properties for newly drilled wells represents a significant challenge. One of the variations of these properties evaluation is well-interval similarity. Many methodologies for similarity learning exist: from rule-based approaches to deep neural networks. Recently, articles adopted, e.g. recurrent neural networks to build a similarity model as we deal with sequential data. Such an approach suffers from short-term memory, as it pays more attention to the end of a sequence. Neural network with Transformer architecture instead cast their attention over all sequences to make a decision. To make them more efficient in terms of computational time, we introduce a limited attention mechanism similar to Informer and Performer architectures. We conduct experiments on open datasets with more than 20 wells making our experiments reliable and suitable for industrial usage. The best results were obtained with our adaptation of the Informer variant of Transformer with ROC AUC 0.982. It outperforms classical approaches with ROC AUC 0.824, Recurrent neural networks with ROC AUC 0.934 and straightforward usage of Transformers with ROC AUC 0.961.

Markowitz mean-variance portfolios with sample mean and covariance as input parameters feature numerous issues in practice. They perform poorly out of sample due to estimation error, they experience extreme weights together with high sensitivity to change in input parameters. The heavy-tail characteristics of financial time series are in fact the cause for these erratic fluctuations of weights that consequently create substantial transaction costs. In robustifying the weights we present a toolbox for stabilizing costs and weights for global minimum Markowitz portfolios. Utilizing a projected gradient descent (PGD) technique, we avoid the estimation and inversion of the covariance operator as a whole and concentrate on robust estimation of the gradient descent increment. Using modern tools of robust statistics we construct a computationally efficient estimator with almost Gaussian properties based on median-of-means uniformly over weights. This robustified Markowitz approach is confirmed by empirical studies on equity markets. We demonstrate that robustified portfolios reach the lowest turnover compared to shrinkage-based and constrained portfolios while preserving or slightly improving out-of-sample performance.

Network Intrusion and Detection Systems (NIDS) are essential for malicious traffic and cyberattack detection in modern networks. Artificial intelligence-based NIDS are powerful tools that can learn complex data correlations for accurate attack prediction. Graph Neural Networks (GNNs) provide an opportunity to analyze network topology along with flow features which makes them particularly suitable for NIDS applications. However, successful application of such tool requires large amounts of carefully collected and labeled data for training and testing. In this paper we inspect different versions of ToN-IoT dataset and point out inconsistencies in some versions. We filter the full version of ToN-IoT and present a new version labeled ToN-IoT-R. To ensure generalization we propose a new standardized and compact set of flow features which are derived solely from NetFlowv5-compatible data. We separate numeric data and flags into different categories and propose a new dataset-agnostic normalization approach for numeric features. This allows us to preserve meaning of flow flags and we propose to conduct targeted analysis based on, for instance, network protocols. For flow classification we use E-GraphSage algorithm with modified node initialization technique that allows us to add node degree to node features. We achieve high classification accuracy on ToN-IoT-R and compare it with previously published results for ToN-IoT, NF-ToN-IoT, and NF-ToN-IoT-v2. We highlight the importance of careful data collection and labeling and appropriate data preprocessing choice and conclude that the proposed set of features is more applicable for real NIDS due to being less demanding to traffic monitoring equipment while preserving high flow classification accuracy.

Migraine is a high-prevalence and disabling neurological disorder. However, information migraine management in real-world settings could be limited to traditional health information sources. In this paper, we (i) verify that there is substantial migraine-related chatter available on social media (Twitter and Reddit), self-reported by migraine sufferers; (ii) develop a platform-independent text classification system for automatically detecting self-reported migraine-related posts, and (iii) conduct analyses of the self-reported posts to assess the utility of social media for studying this problem. We manually annotated 5750 Twitter posts and 302 Reddit posts. Our system achieved an F1 score of 0.90 on Twitter and 0.93 on Reddit. Analysis of information posted by our 'migraine cohort' revealed the presence of a plethora of relevant information about migraine therapies and patient sentiments associated with them. Our study forms the foundation for conducting an in-depth analysis of migraine-related information using social media data.

Triplet extraction aims to extract entities and their corresponding relations in unstructured text. Most existing methods train an extraction model on high-quality training data, and hence are incapable of extracting relations that were not observed during training. Generalizing the model to unseen relations typically requires fine-tuning on synthetic training data which is often noisy and unreliable. In this paper, we argue that reducing triplet extraction to a template filling task over a pre-trained language model can equip the model with zero-shot learning capabilities and enable it to leverage the implicit knowledge in the language model. Embodying these ideas, we propose a novel framework, ZETT (ZEro-shot Triplet extraction by Template infilling), that is based on end-to-end generative transformers. Our experiments show that without any data augmentation or pipeline systems, ZETT can outperform previous state-of-the-art models with 25% less parameters. We further show that ZETT is more robust in detecting entities and can be incorporated with automatically generated templates for relations.

Task-oriented dialogue (TOD) systems have been applied in a range of domains to support human users to achieve specific goals. Systems are typically constructed for a single domain or language and do not generalise well beyond this. Their extension to other languages in particular is restricted by the lack of available training data for many of the world's languages. To support work on Natural Language Understanding (NLU) in TOD across multiple languages and domains simultaneously, we constructed MULTI3NLU++, a multilingual, multi-intent, multi-domain dataset. MULTI3NLU++ extends the English-only NLU++ dataset to include manual translations into a range of high, medium and low resource languages (Spanish, Marathi, Turkish and Amharic), in two domains (banking and hotels). MULTI3NLU++ inherits the multi-intent property of NLU++, where an utterance may be labelled with multiple intents, providing a more realistic representation of a user's goals and aligning with the more complex tasks that commercial systems aim to model. We use MULTI3NLU++ to benchmark state-of-the-art multilingual language models as well as Machine Translation and Question Answering systems for the NLU task of intent detection for TOD systems in the multilingual setting. The results demonstrate the challenging nature of the dataset, particularly in the low-resource language setting.

Automatic machine translation (MT) metrics are widely used to distinguish the translation qualities of machine translation systems across relatively large test sets (system-level evaluation). However, it is unclear if automatic metrics are reliable at distinguishing good translations from bad translations at the sentence level (segment-level evaluation). In this paper, we investigate how useful MT metrics are at detecting the success of a machine translation component when placed in a larger platform with a downstream task. We evaluate the segment-level performance of the most widely used MT metrics (chrF, COMET, BERTScore, etc.) on three downstream cross-lingual tasks (dialogue state tracking, question answering, and semantic parsing). For each task, we only have access to a monolingual task-specific model. We calculate the correlation between the metric's ability to predict a good/bad translation with the success/failure on the final task for the Translate-Test setup. Our experiments demonstrate that all metrics exhibit negligible correlation with the extrinsic evaluation of the downstream outcomes. We also find that the scores provided by neural metrics are not interpretable mostly because of undefined ranges. Our analysis suggests that future MT metrics be designed to produce error labels rather than scores to facilitate extrinsic evaluation.

The one-inclusion graph algorithm of Haussler, Littlestone, and Warmuth achieves an optimal in-expectation risk bound in the standard PAC classification setup. In one of the first COLT open problems, Warmuth conjectured that this prediction strategy always implies an optimal high probability bound on the risk, and hence is also an optimal PAC algorithm. We refute this conjecture in the strongest sense: for any practically interesting Vapnik-Chervonenkis class, we provide an in-expectation optimal one-inclusion graph algorithm whose high probability risk bound cannot go beyond that implied by Markov's inequality. Our construction of these poorly performing one-inclusion graph algorithms uses Varshamov-Tenengolts error correcting codes. Our negative result has several implications. First, it shows that the same poor high-probability performance is inherited by several recent prediction strategies based on generalizations of the one-inclusion graph algorithm. Second, our analysis shows yet another statistical problem that enjoys an estimator that is provably optimal in expectation via a leave-one-out argument, but fails in the high-probability regime. This discrepancy occurs despite the boundedness of the binary loss for which arguments based on concentration inequalities often provide sharp high probability risk bounds.

We analyze Newton's method with lazy Hessian updates for solving general possibly non-convex optimization problems. We propose to reuse a previously seen Hessian for several iterations while computing new gradients at each step of the method. This significantly reduces the overall arithmetical complexity of second-order optimization schemes. By using the cubic regularization technique, we establish fast global convergence of our method to a second-order stationary point, while the Hessian does not need to be updated each iteration. For convex problems, we justify global and local superlinear rates for lazy Newton steps with quadratic regularization, which is easier to compute. The optimal frequency for updating the Hessian is once every $d$ iterations, where $d$ is the dimension of the problem. This provably improves the total arithmetical complexity of second-order algorithms by a factor $\sqrt{d}$.