The paper presents an improved upper bound (achievability result) on the optimal tradeoff between Normalized Delivery Time (NDT) and computation load for distributed computing MapReduce systems in certain ranges of the parameters. The upper bound is based on interference alignment combined with zero-forcing. The paper further provides a lower bound (converse) on the optimal NDT-computation tradeoff that can be achieved when IVAs are partitioned into sub-IVAs, and these sub-IVAs are then transmitted (in an arbitrary form) by a single node, without cooperation among nodes. For appropriate linear functions (e.g., XORs), such non-cooperative schemes can achieve some of the best NDT-computation tradeoff points so far obtained in the literature. However, as our lower bound shows, any non-cooperative scheme achieves a worse NDT-computation tradeoff than our new proposed scheme for certain parameters, thus proving the necessity of cooperative schemes like zero-forcing to attain the optimal NDT-computation tradeoff.

RNA subcellular localization is a key determinant of RNA function and regulation, yet existing computational approaches rely primarily on sequence or simplified structural descriptors, limiting their scalability to long transcripts, their ability to model inter-label dependencies, and their applicability across RNA types. Here, we present Graph-based RNA Substructure-Aware Subcellular localization Prediction (GRASP), a unified graph neural network framework for predicting RNA subcellular localization using a heterogeneous graph representation that is RNA substructure-aware. GRASP presents each RNA as a multi-scale graph comprising nucleotide nodes and secondary-structure-derived substructure nodes, connected by relational edges, enabling joint modeling of base-level interactions and regional structural context. The model further incorporates multi-label dependency learning to capture co-localization patterns across cellular compartments within a unified framework. Across multiple benchmark datasets and RNA types, GRASP consistently outperforms state-of-the-art sequence-based and structure-informed methods, achieving substantial improvements in accuracy, F1-score, and area under the curve (AUC) while maintaining strong scalability to long transcripts. In addition, the graph-based representation provides biologically interpretable insights into structural determinants of RNA localization. The source code and data are available at https://github.com/ABILiLab/GRASP, and the web server is accessible at https://grasp.biotools.bio.

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, including chromatin modification, cell cycle regulation, transcription, and translation. Recent studies have revealed that the biological functions of lncRNAs are closely associated with their subcellular localizations, making accurate localization prediction critical for understanding their biological roles in cellular regulation and disease mechanisms. However, most existing methods mainly rely on sequence features while neglecting structural information, and they are often limited to single-label predictions covering only a small number of subcellular compartments. In this study, we proposed an efficient deep learning framework, LncTracker, for multi-label prediction of lncRNA subcellular localizations across seven distinct compartments. LncTracker adopts a multi-channel architecture that integrates diverse input features into model training, including both primary sequence and secondary structure information. Secondary structures are converted into attributed graphs to capture spatial relationships among nucleotides, including adjacency and base-pairing connections. These structural features are then combined with sequence-based features to predict subcellular localization probabilities. Such a design enables LncTracker to learn joint representations of sequences and structures, thereby enhancing predictive performance and robustness. Benchmarking experiments demonstrated the superiority of LncTracker over state-of-the-art approaches, particularly in handling imbalanced localization scenarios. Furthermore, we leveraged LncTracker to identify sequence motifs critical for each subcellular localization and analysed key sub-structures contributing to predictions.

Surgical phase recognition (SPR) is essential for surgical workflow analysis and provides immediate guidance during procedures. Existing methods aggregate frame-level information into a global representation and treat the task as frame-wise classification. However, this pipeline lacks a feedback mechanism for integrating historical information into local temporal modeling. To address this limitation, we propose the Bidirectional Branch Query Network (B2Q-Net), which reformulates the SPR task as the bidirectional query between phase-level features and frame-level features. B2Q-Net incorporates historical information during the initialization of phase queries. This enables bidirectional information flow during iterative refinement of two-level feature maps between phases and frames. Furthermore, we introduce a dual-scale selector (DSS) to generate high-quality phase queries for the current video clip. These phase queries retrieve historical information from the proposed state space query (SSQ) module, which uses learnable tokens as the historical state space to preserve historical information. Extensive evaluations on three datasets demonstrate that B2Q-Net consistently outperforms state-of-the-art methods in recognition accuracy while achieving an inference speed of 106 fps. The B2Q-Net code is available at https://github.com/vsislab/B2Q-Net.

We consider a$\mathrm{K}$user interference network with general connectivity, described by a matrix N, and general message flows, described by a matrix M. Previous studies have demonstrated that the standard interference alignment (IA) scheme might not be optimal for networks with sparse connectivity. In this paper, we formalize a general IA coding scheme and an intuitive number-filling puzzle for given M and N in a way that the score of the solution to the puzzle determines the optimum sum degrees that can be achieved by the IA scheme. A solution to the puzzle is proposed for a general class of symmetric channels, and it is shown that this solution leads to enhanced Sum-DoF compared to the standard IA scheme.

Single-cell ribonucleic acid sequencing (scRNA-seq) technology can be used to perform high-resolution analysis of the transcriptomes of individual cells. Therefore, its application has gained popularity for accurately analyzing the ever-increasing content of heterogeneous single-cell datasets. Central to interpreting scRNA-seq data is the clustering of cells to decipher transcriptomic diversity and infer cell behavior patterns. However, its complexity necessitates the application of advanced methodologies capable of resolving the inherent heterogeneity and limited gene expression characteristics of single-cell data. Herein, we introduce a novel deep learning-based algorithm for single-cell clustering, designated scDFN, which can significantly enhance the clustering of scRNA-seq data through a fusion network strategy. The scDFN algorithm applies a dual mechanism involving an autoencoder to extract attribute information and an improved graph autoencoder to capture topological nuances, integrated via a cross-network information fusion mechanism complemented by a triple self-supervision strategy. This fusion is optimized through a holistic consideration of four distinct loss functions. A comparative analysis with five leading scRNA-seq clustering methodologies across multiple datasets revealed the superiority of scDFN, as determined by better the Normalized Mutual Information (NMI) and the Adjusted Rand Index (ARI) metrics. Additionally, scDFN demonstrated robust multi-cluster dataset performance and exceptional resilience to batch effects. Ablation studies highlighted the key roles of the autoencoder and the improved graph autoencoder components, along with the critical contribution of the four joint loss functions to the overall efficacy of the algorithm. Through these advancements, scDFN set a new benchmark in single-cell clustering and can be used as an effective tool for the nuanced analysis of single-cell transcriptomics.

Liquid-liquid phase separation (LLPS) is one of the mechanisms mediating the compartmentalization of macromolecules (proteins and nucleic acids) in cells, forming biomolecular condensates or membraneless organelles. Consequently, the systematic identification of potential LLPS proteins is crucial for understanding the phase separation process and its biological mechanisms. A two-task predictor, Opt_PredLLPS, was developed to discover potential phase separation proteins and further evaluate their mechanism. The first task model of Opt_PredLLPS combines a convolutional neural network (CNN) and bidirectional long short-term memory (BiLSTM) through a fully connected layer, where the CNN utilizes evolutionary information features as input, and BiLSTM utilizes multimodal features as input. If a protein is predicted to be an LLPS protein, it is input into the second task model to predict whether this protein needs to interact with its partners to undergo LLPS. The second task model employs the XGBoost classification algorithm and 37 physicochemical properties following a three-step feature selection. The effectiveness of the model was validated on multiple benchmark datasets, and in silico saturation mutagenesis was used to identify regions that play a key role in phase separation. These findings may assist future research on the LLPS mechanism and the discovery of potential phase separation proteins.

Subcellular localization of messenger ribonucleic acid (mRNA) is a universal mechanism for precise and efficient control of the translation process. Although many computational methods have been constructed by researchers for predicting mRNA subcellular localization, very few of these computational methods have been designed to predict subcellular localization with multiple localization annotations, and their generalization performance could be improved. In this study, the prediction model MSlocPRED was constructed to identify multi-label mRNA subcellular localization. First, the preprocessed Dataset 1 and Dataset 2 are transformed into the form of images. The proposed MDNDO-SMDU resampling technique is then used to balance the number of samples in each category in the training dataset. Finally, deep transfer learning was used to construct the predictive model MSlocPRED to identify subcellular localization for 16 classes (Dataset 1) and 18 classes (Dataset 2). The results of comparative tests of different resampling techniques show that the resampling technique proposed in this study is more effective in preprocessing for subcellular localization. The prediction results of the datasets constructed by intercepting different NC end (Both the 5' and 3' untranslated regions that flank the protein-coding sequence and influence mRNA function without encoding proteins themselves.) lengths show that for Dataset 1 and Dataset 2, the prediction performance is best when the NC end is intercepted by 35 nucleotides, respectively. The results of both independent testing and five-fold cross-validation comparisons with established prediction tools show that MSlocPRED is significantly better than established tools for identifying multi-label mRNA subcellular localization. Additionally, to understand how the MSlocPRED model works during the prediction process, SHapley Additive exPlanations was used to explain it. The predictive model and associated datasets are available on the following github: https://github.com/ZBYnb1/MSlocPRED/tree/main.

MOTIVATION: The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular processes. To advance our comprehension of gene regulatory networks, it is essential to develop computational tools for accurately identifying the subcellular localizations of mRNAs. However, considering multi-localization phenomena remains limited in existing approaches, with none considering the influence of RNA's secondary structure. RESULTS: In this study, we propose Allocator, a multi-view parallel deep learning framework that seamlessly integrates the RNA sequence-level and structure-level information, enhancing the prediction of mRNA multi-localization. The Allocator models equip four efficient feature extractors, each designed to handle different inputs. Two are tailored for sequence-based inputs, incorporating multilayer perceptron and multi-head self-attention mechanisms. The other two are specialized in processing structure-based inputs, employing graph neural networks. Benchmarking results underscore Allocator's superiority over state-of-the-art methods, showcasing its strength in revealing intricate localization associations. AVAILABILITY AND IMPLEMENTATION: The webserver of Allocator is available at http://Allocator.unimelb-biotools.cloud.edu.au; the source code and datasets are available on GitHub (https://github.com/lifuyi774/Allocator) and Zenodo (https://doi.org/10.5281/zenodo.13235798).

We consider a full-duplex wireless Distributed Computing (DC) system under the MapReduce framework. New upper and lower bounds on the optimal tradeoff between Normalized Delivery Time (NDT) and computation load are presented. The upper bound strictly improves over the previous reported upper bounds and is based on two novel interference alignment (IA) schemes tailored to the interference cancellation capabilities of the nodes. Our second IA scheme additionally applies a zero-forcing strategy that allows to accumulate all interference at any of the nodes on the same (small) subspace, leaving the remaining space for useful signals. The lower bound is proved through information-theoretic converse arguments based on carefully chosen multi-access channel (MAC) type arguments and by finding solutions to the optimization problems resulting from these arguments. The lower bound matches an existing upper bound based on zero-forcing and interference cancellation (but no IA) in the regime where each node can store at least half of the files. While optimal in this regime, zero-forcing and interference cancellation are not sufficient to obtain the optimal NDT in scenarios where each node cannot store half of the files. This follows from the previously established optimal NDT under zero-forcing and interference cancellation and our new IA-schemes.

Distributed computing frameworks such as MapReduce and Spark are often used to process large-scale data computing jobs. In wireless scenarios, exchanging data among distributed nodes would seriously suffer from the communication bottleneck due to limited communication resources such as bandwidth and power. To address this problem, we propose a coded parallel computing (CPC) scheme for distributed computing systems where distributed nodes exchange information over a half-duplex wireless interference network. The CPC scheme achieves the multicast gain by utilizing coded computing to multicast coded symbols intended to multiple receiver nodes and the cooperative transmission gain by allowing multiple transmitter nodes to jointly deliver messages via interference alignment. To measure communication performance, we apply the widely used latency-oriented metric: normalized delivery time (NDT). It is shown that CPC can significantly reduce the NDT by jointly exploiting the parallel transmission and coded multicasting opportunities. Surprisingly, when the number of computation nodes K tends to infinity and the computation load is fixed, CPC approaches zero NDT while all state-of-the-art schemes achieve positive values of NDT. Finally, we establish an information-theoretic lower bound for the NDT-computation load trade-off over the half-duplex network, and prove our scheme achieves the minimum NDT within a multiplicative gap of 3, i.e., our scheme is order optimal.

We consider a full-duplex wireless Distributed Computing (DC) system under the MapReduce framework. New upper and lower bounds on the optimal tradeoff between Normalized Delivery Time (NDT) and computation load are presented. The upper bound strictly improves over the previous reported upper bounds and is based on a novel interference alignment (IA) scheme tailored to the interference cancellation capabilities of MapReduce nodes. The lower bound is proved through information-theoretic converse arguments.

A-to-I editing is the most prevalent RNA editing event, which refers to the change of adenosine (A) bases to inosine (I) bases in double-stranded RNAs. Several studies have revealed that A-to-I editing can regulate cellular processes and is associated with various human diseases. Therefore, accurate identification of A-to-I editing sites is crucial for understanding RNA-level (i.e. transcriptional) modifications and their potential roles in molecular functions. To date, various computational approaches for A-to-I editing site identification have been developed; however, their performance is still unsatisfactory and needs further improvement. In this study, we developed a novel stacked-ensemble learning model, ATTIC (A-To-I ediTing predICtor), to accurately identify A-to-I editing sites across three species, including Homo sapiens, Mus musculus and Drosophila melanogaster. We first comprehensively evaluated 37 RNA sequence-derived features combined with 14 popular machine learning algorithms. Then, we selected the optimal base models to build a series of stacked ensemble models. The final ATTIC framework was developed based on the optimal models improved by the feature selection strategy for specific species. Extensive cross-validation and independent tests illustrate that ATTIC outperforms state-of-the-art tools for predicting A-to-I editing sites. We also developed a web server for ATTIC, which is publicly available at http://web.unimelb-bioinfortools.cloud.edu.au/ATTIC/. We anticipate that ATTIC can be utilized as a useful tool to accelerate the identification of A-to-I RNA editing events and help characterize their roles in post-transcriptional regulation.

MOTIVATION: The rapid accumulation of high-throughput sequence data demands the development of effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotation simply focus on the use of protein-level information but ignore inter-relationships among annotations. RESULTS: Here, we established PFresGO, an attention-based deep-learning approach that incorporates hierarchical structures in Gene Ontology (GO) graphs and advances in natural language processing algorithms for the functional annotation of proteins. PFresGO employs a self-attention operation to capture the inter-relationships of GO terms, updates its embedding accordingly and uses a cross-attention operation to project protein representations and GO embedding into a common latent space to identify global protein sequence patterns and local functional residues. We demonstrate that PFresGO consistently achieves superior performance across GO categories when compared with 'state-of-the-art' methods. Importantly, we show that PFresGO can identify functionally important residues in protein sequences by assessing the distribution of attention weightings. PFresGO should serve as an effective tool for the accurate functional annotation of proteins and functional domains within proteins. AVAILABILITY AND IMPLEMENTATION: PFresGO is available for academic purposes at https://github.com/BioColLab/PFresGO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Multiple instance learning (MIL) is a powerful technique to classify whole slide images (WSIs) for diagnostic pathology. The key challenge of MIL on WSI classification is to discover the critical instances that trigger the bag label. However, tumor heterogeneity significantly hinders the algorithm's performance. RESULTS: Here, we propose a novel multiplex-detection-based multiple instance learning (MDMIL) which targets tumor heterogeneity by multiplex detection strategy and feature constraints among samples. Specifically, the internal query generated after the probability distribution analysis and the variational query optimized throughout the training process are utilized to detect potential instances in the form of internal and external assistance, respectively. The multiplex detection strategy significantly improves the instance-mining capacity of the deep neural network. Meanwhile, a memory-based contrastive loss is proposed to reach consistency on various phenotypes in the feature space. The novel network and loss function jointly achieve high robustness towards tumor heterogeneity. We conduct experiments on three computational pathology datasets, e.g. CAMELYON16, TCGA-NSCLC, and TCGA-RCC. Benchmarking experiments on the three datasets illustrate that our proposed MDMIL approach achieves superior performance over several existing state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: MDMIL is available for academic purposes at https://github.com/ZacharyWang-007/MDMIL.

We consider a cooperative X-channel with K transmitters (TXs) and K receivers (Rxs) where Txs and Rxs are gathered into groups of size r respectively. Txs belonging to the same group cooperate to jointly transmit a message to each of the K − r Rxs in all other groups, and each Rx individually decodes all its intended messages. By introducing a new interference alignment (IA) scheme, we prove that when K/r is an integer the Sum Degrees of Freedom (Sum-DoF) of this channel is lower bounded by 2r if K/r ∈ {2, 3} and by $\frac{{K(K - r) - {r^2}}}{{2K - 3r}}$ if K/r ≥ 4. We also prove that the Sum-DoF is upper bounded by $\frac{{{\text{K}}({\text{K}} - {\text{r}})}}{{2{\text{K}} - 3{\text{r}}}}$. The proposed IA scheme finds application in a wireless distributed MapReduce framework, where it improves the normalized data delivery time (NDT) compared to the state of the art.

Subcellular localization of messenger RNAs (mRNAs) plays a key role in the spatial regulation of gene activity. The functions of mRNAs have been shown to be closely linked with their localizations. As such, understanding of the subcellular localizations of mRNAs can help elucidate gene regulatory networks. Despite several computational methods that have been developed to predict mRNA localizations within cells, there is still much room for improvement in predictive performance, especially for the multiple-location prediction. In this study, we proposed a novel multi-label multi-class predictor, termed Clarion, for mRNA subcellular localization prediction. Clarion was developed based on a manually curated benchmark dataset and leveraged the weighted series method for multi-label transformation. Extensive benchmarking tests demonstrated Clarion achieved competitive predictive performance and the weighted series method plays a crucial role in securing superior performance of Clarion. In addition, the independent test results indicate that Clarion outperformed the state-of-the-art methods and can secure accuracy of 81.47, 91.29, 79.77, 92.10, 89.15, 83.74, 80.74, 79.23 and 84.74% for chromatin, cytoplasm, cytosol, exosome, membrane, nucleolus, nucleoplasm, nucleus and ribosome, respectively. The webserver and local stand-alone tool of Clarion is freely available at http://monash.bioweb.cloud.edu.au/Clarion/.

MOTIVATION: Different from traditional linear RNAs (containing 5' and 3' ends), circular RNAs (circRNAs) are a special type of RNAs that have a closed ring structure. Accumulating evidence has indicated that circRNAs can directly bind proteins and participate in a myriad of different biological processes. RESULTS: For identifying the interaction of circRNAs with 37 different types of circRNA-binding proteins (RBPs), we develop an ensemble neural network, termed PASSION, which is based on the concatenated artificial neural network (ANN) and hybrid deep neural network frameworks. Specifically, the input of the ANN is the optimal feature subset for each RBP, which has been selected from six types of feature encoding schemes through incremental feature selection and application of the XGBoost algorithm. In turn, the input of the hybrid deep neural network is a stacked codon-based scheme. Benchmarking experiments indicate that the ensemble neural network reaches the average best area under the curve (AUC) of 0.883 across the 37 circRNA datasets when compared with XGBoost, k-nearest neighbor, support vector machine, random forest, logistic regression and Naive Bayes. Moreover, each of the 37 RBP models is extensively tested by performing independent tests, with the varying sequence similarity thresholds of 0.8, 0.7, 0.6 and 0.5, respectively. The corresponding average AUC obtained are 0.883, 0.876, 0.868 and 0.883, respectively, highlighting the effectiveness and robustness of PASSION. Extensive benchmarking experiments demonstrate that PASSION achieves a competitive performance for identifying binding sites between circRNA and RBPs, when compared with several state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: A user-friendly web server of PASSION is publicly accessible at http://flagship.erc.monash.edu/PASSION/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

As a candidate radio access technique for 5G, Non- Orthogonal Multiple Access (NOMA) has become an important research topic. Radio Frequency (RF) jamming attack can reduce the communication efficiency in NOMA system. Moreover, the jammer equipped Reinforcement Learning (RL) algorithm will be more destructive. On the other hand, the base station (BS) can implement RL to counter the jamming attack. Thus, the whole system evolves to a multi-agent RL system. The interaction between agents results in a highly dynamic environment and the equilibrium state of the system cannot be intuitively predicted. In the past few years, based on Evolutionary Game Theory (EGT), numbers of researchers have developed useful tools to study the multi-agent RL system in detail. The EGT tools give us insight into the equilibrium of the system and make it possible to compare the performance of different RL algorithms. In this paper, we investigate the anti-jamming problem in the NOMA system where both the base station and the jammer equip RL algorithm. We establish the two-player game and demonstrate the existence and uniqueness of equilibrium. Three RL algorithms and their learning dynamics are introduced, which are Q-learning, Lenient Frequency adjusted Q-learning and Regret Minimization. In experiments, the simulation result shows consistency to the theoretical result given by EGT. Regret Minimization outperforms the other two algorithms in term of average reward and converging rate.

The threat of radio frequency jamming attack to cognitive radio network is an issue that has been discussed for a long time. Q-learning is a widely used anti-jamming algorithm due to its model-free characteristic. However, the traditional Q-learning based anti-jamming algorithms suffer from some limitations when dealing with high-dimensional or continuous inputs. The recently proposed double Deep Q-learning Network (DQN) overcomes this weakness by approximating the table based Q function with a deep neural network. In this paper, we apply the double DQN algorithm with frequency hopping strategy against RF jamming attack in a multi-user environment. We test the performances of three types of neural networks which are the fully connected network (FCN), the convolutional neural network (CNN) and the long short term memory (LSTM). The simulation shows the effectiveness of the double DQN algorithm. Meanwhile, the FCN agent gives the best result concerning stability.

The agencies responsible for transportation corridors tend to hold large volumes of data that can be relevant for both operations and planning. Meanwhile, it is a challenge for these agencies to prioritize their investments addressing risk, benefits, and costs. The agencies recognize an opportunity to improve project selection and programming with a centralized database of performance measures that will aid a consistent application of evaluation metrics. To support the identification, planning, and selection of highway transportation projects, this research has used a data structure known as dynamic segmentation for cross-referencing heterogeneous data sources including projects, traffic, safety, bridge and pavement conditions, etc. The result is a multiscale method for agencies to utilize big-data analytics and multicriteria decision analysis to assemble evidence for project selection and prioritization. The paper describes an approach to (1) visualize multiple attributes along linearized road corridors to identify future projects, minimize conflicts with current projects, and identify potential project synergies and (2) prioritize projects to the Top-20 with multiple performance factors. The methods are demonstrated at several geographic scales. The effort supports a fast, repeatable, and evidence-driven prioritization of projects and provides a complement to the use of electronic map data that has been overwhelming the available computing resources.