This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for identifying similarities and discovering mutual patterns and important motifs among DNA, RNA, and protein sequences. Building on recent advancements in solving this problem through a general search framework, this paper introduces two novel heuristic approaches designed to enhance the search process by steering it towards promising regions in the search space. The first heuristic employs a probabilistic model to evaluate partial solutions during the search process. The second heuristic is based on a neural network model trained offline using a genetic algorithm. A key aspect of this approach is extracting problem-specific features of partial solutions and the complete problem instance. An effective hybrid method, referred to as the learning beam search, is developed by combining the trained neural network model with a beam search framework. An important contribution of this paper is found in the generation of real-world instances where scientific abstracts serve as input strings, and a set of frequently occurring academic words from the literature are used as restricted patterns. Comprehensive experimental evaluations demonstrate the effectiveness of the proposed approaches in solving the RLCS problem. Finally, an empirical explainability analysis is applied to the obtained results. In this way, key feature combinations and their respective contributions to the success or failure of the algorithms across different problem types are identified.

The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and designing degenerated primers, among others. There are efficient exact algorithms that have reached high-quality solutions for binary sequences. However, there is still room for improvement concerning the quality of solutions over DNA and protein sequences. In this paper, we introduce a three-stage algorithm that comprises the following process: first, we apply a novel alphabet pruning method to reduce the search space for effectively finding promising search regions. Second, a variant of beam search to find a heuristic solution is employed. This method utilizes a newly developed guiding function based on an expected distance heuristic score of partial solutions. Last, we introduce a local search to improve the quality of the solution obtained from the beam search. Furthermore, due to the lack of real-world benchmarks, two real-world datasets are introduced to verify the robustness of the method. The extensive experimental results show that the proposed method outperforms the previous approaches from the literature.

Despite its popularity in sentence-level relation extraction, distantly supervised data is rarely utilized by existing work in document-level relation extraction due to its noisy nature and low information density. Among its current applications, distantly supervised data is mostly used as a whole for pertaining, which is of low time efficiency. To fill in the gap of efficient and robust utilization of distantly supervised training data, we propose Efficient Multi-Supervision for document-level relation extraction, in which we first select a subset of informative documents from the massive dataset by combining distant supervision with expert supervision, then train the model with Multi-Supervision Ranking Loss that integrates the knowledge from multiple sources of supervision to alleviate the effects of noise. The experiments demonstrate the effectiveness of our method in improving the model performance with higher time efficiency than existing baselines.

Automated Driving (AD) systems have the potential to increase safety, comfort and energy efficiency. Recently, major automotive companies have started testing and validating AD systems (ADS) on public roads. Nevertheless, the commercial deployment and wide adoption of ADS have been moderate, partially due to system functional insufficiencies (FI) that undermine passenger safety and lead to hazardous situations on the road. FIs are defined in ISO 21448 Safety Of The Intended Functionality (SOTIF). FIs are insufficiencies in sensors, actuators and algorithm implementations, including neural networks and probabilistic calculations. Examples of FIs in ADS include inaccurate ego-vehicle localization on the road, incorrect prediction of a cyclist maneuver, unreliable detection of a pedestrian, etc. The main goal of our study is to formulate a generic architectural design pattern, which is compatible with existing methods and ADS, to improve FI mitigation and enable faster commercial deployment of ADS. First, we studied the 2021 autonomous vehicles disengagement reports published by the California Department of Motor Vehicles (DMV). The data clearly show that disengagements are five times more often caused by FIs rather than by system faults. We then made a comprehensive list of insufficiencies and their characteristics by analyzing over 10 hours of publicly available road test videos. In particular, we identified insufficiency types in four major categories: world model, motion plan, traffic rule, and operational design domain. The insufficiency characterization helps making the SOTIF analyses of triggering conditions more systematic and comprehensive. Based on our FI characterization, simulation experiments and literature survey, we define a novel generic architectural design pattern Daruma to dynamically select the channel that is least likely to have a FI at the moment.

This work focuses on developing an effective meta-heuristic approach to protect against simultaneous attacks on nodes of a network modeled using a graph. Specifically, we focus on the $k$-strong Roman domination problem, a generalization of the well-known Roman domination problem on graphs. This general problem is about assigning integer weights to nodes that represent the number of field armies stationed at each node in order to satisfy the protection constraints while minimizing the total weights. These constraints concern the protection of a graph against any simultaneous attack consisting of $k \in \mathbb{N}$ nodes. An attack is considered repelled if each node labeled 0 can be defended by borrowing an army from one of its neighboring nodes, ensuring that the neighbor retains at least one army for self-defense. The $k$-SRD problem has practical applications in various areas, such as developing counter-terrorism strategies or managing supply chain disruptions. The solution to this problem is notoriously difficult to find, as even checking the feasibility of the proposed solution requires an exponential number of steps. We propose a variable neighborhood search algorithm in which the feasibility of the solution is checked by introducing the concept of quasi-feasibility, which is realized by careful sampling within the set of all possible attacks. Extensive experimental evaluations show the scalability and robustness of the proposed approach compared to the two exact approaches from the literature. Experiments are conducted with random networks from the literature and newly introduced random wireless networks as well as with real-world networks. A practical application scenario, using real-world networks, involves applying our approach to graphs extracted from GeoJSON files containing geographic features of hundreds of cities or larger regions.

Local causal discovery is of great practical significance, as there are often situations where the discovery of the global causal structure is unnecessary, and the interest lies solely on a single target variable. Most existing local methods utilize conditional independence relations, providing only a partially directed graph, and assume acyclicity for the ground-truth structure, even though real-world scenarios often involve cycles like feedback mechanisms. In this work, we present a general, unified local causal discovery method with linear non-Gaussian models, whether they are cyclic or acyclic. We extend the application of independent component analysis from the global context to independent subspace analysis, enabling the exact identification of the equivalent local directed structures and causal strengths from the Markov blanket of the target variable. We also propose an alternative regression-based method in the particular acyclic scenarios. Our identifiability results are empirically validated using both synthetic and real-world datasets.

A recent study on the interpretability of real-valued convolutional neural networks (CNNs) {Stankovic_Mandic_2023CNN} has revealed a direct and physically meaningful link with the task of finding features in data through matched filters. However, applying this paradigm to illuminate the interpretability of complex-valued CNNs meets a formidable obstacle: the extension of matched filtering to a general class of noncircular complex-valued data, referred to here as the widely linear matched filter (WLMF), has been only implicit in the literature. To this end, to establish the interpretability of the operation of complex-valued CNNs, we introduce a general WLMF paradigm, provide its solution and undertake analysis of its performance. For rigor, our WLMF solution is derived without imposing any assumption on the probability density of noise. The theoretical advantages of the WLMF over its standard strictly linear counterpart (SLMF) are provided in terms of their output signal-to-noise-ratios (SNRs), with WLMF consistently exhibiting enhanced SNR. Moreover, the lower bound on the SNR gain of WLMF is derived, together with condition to attain this bound. This serves to revisit the convolution-activation-pooling chain in complex-valued CNNs through the lens of matched filtering, which reveals the potential of WLMFs to provide physical interpretability and enhance explainability of general complex-valued CNNs. Simulations demonstrate the agreement between the theoretical and numerical results.

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This work is the first to propose the concept of a semantic numeration system (SNS) as a certain class of context-based numeration methods. The development of the SNS concept required the introduction of fundamentally new concepts such as a cardinal abstract entity, a cardinal semantic operator, a cardinal abstract object, a numeration space and a multicardinal number. The main attention is paid to the key elements of semantic numeration systems - cardinal semantic operators. A classification of semantic numeration systems is given.

Deep learning usually requires big data, with respect to both volume and variety. However, most remote sensing applications only have limited training data, of which a small subset is labeled. Herein, we review three state-of-the-art approaches in deep learning to combat this challenge. The first topic is transfer learning, in which some aspects of one domain, e.g., features, are transferred to another domain. The next is unsupervised learning, e.g., autoencoders, which operate on unlabeled data. The last is generative adversarial networks, which can generate realistic looking data that can fool the likes of both a deep learning network and human. The aim of this article is to raise awareness of this dilemma, to direct the reader to existing work and to highlight current gaps that need solving.