In this work, we tackle the problems of efficiency and scalability for predictive coding networks (PCNs) in machine learning. To do so, we propose a library that focuses on performance and simplicity, and use it to implement a large set of standard benchmarks for the community to use for their experiments. As most works in the field propose their own tasks and architectures, do not compare one against each other, and focus on small-scale tasks, a simple and fast open-source library, and a comprehensive set of benchmarks, would address all of these concerns. Then, we perform extensive tests on such benchmarks using both existing algorithms for PCNs, as well as adaptations of other methods popular in the bio-plausible deep learning community. All of this has allowed us to (i) test architectures much larger than commonly used in the literature, on more complex datasets; (ii) reach new state-of-the-art results in all of the tasks and dataset provided; (iii) clearly highlight what the current limitations of PCNs are, allowing us to state important future research directions. With the hope of galvanizing community efforts towards one of the main open problems in the field, scalability, we will release the code, tests, and benchmarks.

Large language models (LLMs), representing a breakthrough advancement in artificial intelligence, have demonstrated substantial application value and development potential in bioinformatics research, particularly showing significant progress in the processing and analysis of complex biological data. This comprehensive review systematically examines the development and applications of LLMs in bioinformatics, with particular emphasis on their advancements in protein and nucleic acid structure prediction, omics analysis, drug design and screening, and biomedical literature mining. This work highlights the distinctive capabilities of LLMs in end-to-end learning and knowledge transfer paradigms. Additionally, this paper thoroughly discusses the major challenges confronting LLMs in current applications, including key issues such as model interpretability and data bias. Furthermore, this review comprehensively explores the potential of LLMs in cross-modal learning and interdisciplinary development. In conclusion, this paper aims to systematically summarize the current research status of LLMs in bioinformatics, objectively evaluate their advantages and limitations, and provide insights and recommendations for future research directions, thereby positioning LLMs as essential tools in bioinformatics research and fostering innovative developments in the biomedical field.

To reduce doctors' workload, deep-learning-based automatic medical report generation has recently attracted more and more research efforts, where deep convolutional neural networks (CNNs) are employed to encode the input images, and recurrent neural networks (RNNs) are used to decode the visual features into medical reports automatically. However, these state-of-the-art methods mainly suffer from three shortcomings: 1) incomprehensive optimization; 2) low-order and unidimensional attention; and 3) repeated generation. In this article, we propose a hybrid reinforced medical report generation method with m-linear attention and repetition penalty mechanism (HReMRG-MR) to overcome these problems. Specifically, a hybrid reward with different weights is employed to remedy the limitations of single-metric-based rewards, and a local optimal weight search algorithm is proposed to significantly reduce the complexity of searching the weights of the rewards from exponential to linear. Furthermore, we use m-linear attention modules to learn multidimensional high-order feature interactions and to achieve multimodal reasoning, while a new repetition penalty is proposed to apply penalties to repeated terms adaptively during the model's training process. Extensive experimental studies on two public benchmark datasets show that HReMRG-MR greatly outperforms the state-of-the-art baselines in terms of all metrics. The effectiveness and necessity of all components in HReMRG-MR are also proved by ablation studies. Additional experiments are further conducted and the results demonstrate that our proposed local optimal weight search algorithm can significantly reduce the search time while maintaining superior medical report generation performances.

The activation levels of biologically significant gene sets are emerging tumor molecular markers and play an irreplaceable role in the tumor research field; however, web-based tools for prognostic analyses using it as a tumor molecular marker remain scarce. We developed a web-based tool PESSA for survival analysis using gene set activation levels. All data analyses were implemented via R. Activation levels of The Molecular Signatures Database (MSigDB) gene sets were assessed using the single sample gene set enrichment analysis (ssGSEA) method based on data from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), The European Genome-phenome Archive (EGA) and supplementary tables of articles. PESSA was used to perform median and optimal cut-off dichotomous grouping of ssGSEA scores for each dataset, relying on the survival and survminer packages for survival analysis and visualisation. PESSA is an open-access web tool for visualizing the results of tumor prognostic analyses using gene set activation levels. A total of 238 datasets from the GEO, TCGA, EGA, and supplementary tables of articles; covering 51 cancer types and 13 survival outcome types; and 13,434 tumor-related gene sets are obtained from MSigDB for pre-grouping. Users can obtain the results, including Kaplan-Meier analyses based on the median and optimal cut-off values and accompanying visualization plots and the Cox regression analyses of dichotomous and continuous variables, by selecting the gene set markers of interest. PESSA (https://smuonco.shinyapps.io/PESSA/ OR http://robinl-lab.com/PESSA) is a large-scale web-based tumor survival analysis tool covering a large amount of data that creatively uses predefined gene set activation levels as molecular markers of tumors.

AI and GPU technologies have been widely applied to solve big data problems. The total data volume worldwide reaches 200 zettabytes in 2022. How to efficiently index the required content among massive data becomes serious. Recently, a promising learned index has been proposed to address this challenge: It has extremely high efficiency while retaining marginal space overhead. However, we notice that previous learned indexes have mainly focused on CPU architecture, while ignoring the advantages of GPU. Because traditional indexes like B-Tree, LSM, and bitmap have greatly benefited from GPU acceleration, a combination of a learned index and GPU has great potentials to reach tremendous speedups. In this paper, we propose a GPU-based learned index, called G-Learned Index, to significantly improve the performance of learned index structures. The primary challenges in developing G-Learned Index lie in the use of thousands of GPU cores including minimization of synchronization and branch divergence, data structure design for parallel operations, and usage of memory bandwidth including limited memory transactions and multi-memory hierarchy. To overcome these challenges, a series of novel technologies are developed, including efficient thread organization, succinct data structures, and heterogeneous memory hierarchy utilization. Compared to the state-of-the-art learned index, the proposed G-Learned Index achieves an average of 174× speedup (and 107× of its parallel version). Meanwhile, we attain 2× less query time over the state-of-the-art GPU B-Tree. Our further exploration of range queries shows that G-Learned Index is 17× faster than CPU multi-dimensional learned index. We have made G-Learned Index available athttps://anonymous.4open.science/r/G-Learned-Index-8D89.

Immune checkpoint inhibitors (ICIs) have completely changed the approach pertaining to tumor diagnostics and treatment. Similarly, immunotherapy has also provided much needed data about mutation, expression and prognosis, affording an unprecedented opportunity for discovering candidate drug targets and screening for immunotherapy-relevant biomarkers. Although existing web tools enable biologists to analyze the expression, mutation and prognostic data of tumors, they are currently unable to facilitate data mining and mechanism analyses specifically related to immunotherapy. Thus, we effectively developed our own web-based tool, called Comprehensive Analysis on Multi-Omics of Immunotherapy in Pan-cancer (CAMOIP), in which we are able to successfully screen various prognostic markers and analyze the mechanisms involved in biomarker expression and function, as well as immunotherapy. The analyses include information relevant to survival analysis, expression analysis, mutational landscape analysis, immune infiltration analysis, immunogenicity analysis and pathway enrichment analysis. This comprehensive analysis of biomarkers for immunotherapy can be carried out by a click of CAMOIP, and the software should greatly encourage the further development of immunotherapy. CAMOIP provides invaluable evidence that bridges the information between the data of cancer genomics based on immunotherapy, providing comprehensive information to users and assisting in making the value of current ICI-treated data available to all users. CAMOIP is available at https://www.camoip.net.

Recently, deep learning methods, in particular, convolutional neural networks (CNNs), have made a massive breakthrough in computer vision. And a big amount of annotated data is the essential cornerstone to reach this success. However, in the medical domain, it is usually difficult (and sometimes even impossible) to get sufficient data for some specific learning tasks. Consequently, in this work, a novel data augmentation solution, called semi-supervised attention-guided CycleGAN (SSA-CycleGAN) is proposed to resolve this problem. Specifically, a cycle-consistency GANs-based model is first proposed to generate synthetic tumor (resp., normal) images from normal (resp., tumor) images. Then, a semi-supervised attention module is further proposed to enhance the model's capability in learning the important details of the training images, which in turns help the generated synthetic images become more realistic. To verify its effectiveness, experimental studies are conducted on three medical image datasets with limited amounts of MRI images, and the proposed SSA-CycleGAN is applied to generate synthetic tumor and normal MRI images for data augmentation. Experimental results show that i) SSA-CycleGAN can add (resp., remove) tumor lesions on (resp., from) the original normal (resp., tumor) images and generate very realistic synthetic tumor (resp. normal) images; and ii) in the ResNet18-based MRI image classification tasks based on these datasets, data augmentation using SSA-CycleGAN achieves much better classification performances than the classic data augmentation methods.

The technology of wireless energy transfer by magnetic resonant coupling has attracted strong interest in recent years. The WET system with multiple loads is more practical and flexible. In this paper, a research on efficiency of WET system by magnetic resonant coupling with two loads is implemented by a full-wave electromagnetic tool. The efficiency and resonant frequency of different angle between the two loads are analyzed. It is shown that the resonant frequencies of two loads are different. The maximum efficiencies of two loads and the WET system can't be obtained at the same time. But the total efficiency of the WET system is about the same. Therefore, for the WET system with multiple loads via magnetic resonant coupling, we can choose the proper resonant frequency and structure to charge two devices as demand. The research will provide design guidelines for the wireless power transfer system with multiple loads.

Vertical-Cavity Surface-Emitting Lasers (VCSELs) are a new generation of semiconductor lasers that have many advantages. In this paper, we present a comprehensive circuit-level VCSEL model that addresses the basic spatial and thermal behavior of VCSELs based on the rate equations without sacrificing the numerical efficiency demanded by the circuit-level simulation of optoelectronic systems. The model is implemented into SPICE-like simulators, and the simulated results exhibit a good agreements with references.