对RAS和RAF蛋白的行为与细胞膜中局部脂质环境之间关系之间的关系的了解对了解癌症形成的基础机制至关重要。在这项工作中，我们采用深度学习（DL）来学习这种关系，通过预测基于脂质膜的RAS和RAS-RAF蛋白复合物的蛋白质定位状态，该状态基于蛋白质结构域周围的脂质密度（CG），相对于脂质膜。分子动力学（MD）模拟。我们的DL模型可以预测六个蛋白质状态，总体准确性超过80％。这项工作的发现为蛋白质如何调节脂质环境提供了新的见解，这反过来又可以帮助设计新型疗法以调节与癌症发展相关的机制中的这种相互作用。

捕获复杂的生物学现象通常需要多尺度建模，在使用有限的昂贵和高保真模型的有限组件开发粗糙和廉价的模型的情况下。在这里，我们在癌症生物学的背景下考虑了这样的多尺度框架，并解决了评估使用分子动力学模型的一维统计数据开发的连续模型的描述能力的挑战。使用深度学习，我们开发了一个高度预测性的分类模型，该模型可以从连续模型中识别复杂和新兴行为。两次模拟证明了超过99.9％的精度，我们的方法证实了蛋白质特异性的“脂质指纹”的存在，即脂质的空间重排以响应感兴趣的蛋白质。通过此演示，我们的模型还提供了对连续模型的外部验证，肯定了这种多尺度建模的价值，并可以通过进一步分析这些指纹来促进新的见解。

While the brain connectivity network can inform the understanding and diagnosis of developmental dyslexia, its cause-effect relationships have not yet enough been examined. Employing electroencephalography signals and band-limited white noise stimulus at 4.8 Hz (prosodic-syllabic frequency), we measure the phase Granger causalities among channels to identify differences between dyslexic learners and controls, thereby proposing a method to calculate directional connectivity. As causal relationships run in both directions, we explore three scenarios, namely channels' activity as sources, as sinks, and in total. Our proposed method can be used for both classification and exploratory analysis. In all scenarios, we find confirmation of the established right-lateralized Theta sampling network anomaly, in line with the temporal sampling framework's assumption of oscillatory differences in the Theta and Gamma bands. Further, we show that this anomaly primarily occurs in the causal relationships of channels acting as sinks, where it is significantly more pronounced than when only total activity is observed. In the sink scenario, our classifier obtains 0.84 and 0.88 accuracy and 0.87 and 0.93 AUC for the Theta and Gamma bands, respectively.

This is paper for the smooth function approximation by neural networks (NN). Mathematical or physical functions can be replaced by NN models through regression. In this study, we get NNs that generate highly accurate and highly smooth function, which only comprised of a few weight parameters, through discussing a few topics about regression. First, we reinterpret inside of NNs for regression; consequently, we propose a new activation function--integrated sigmoid linear unit (ISLU). Then special charateristics of metadata for regression, which is different from other data like image or sound, is discussed for improving the performance of neural networks. Finally, the one of a simple hierarchical NN that generate models substituting mathematical function is presented, and the new batch concept ``meta-batch" which improves the performance of NN several times more is introduced. The new activation function, meta-batch method, features of numerical data, meta-augmentation with metaparameters, and a structure of NN generating a compact multi-layer perceptron(MLP) are essential in this study.

We present a novel dataset named as HPointLoc, specially designed for exploring capabilities of visual place recognition in indoor environment and loop detection in simultaneous localization and mapping. The loop detection sub-task is especially relevant when a robot with an on-board RGB-D camera can drive past the same place (``Point") at different angles. The dataset is based on the popular Habitat simulator, in which it is possible to generate photorealistic indoor scenes using both own sensor data and open datasets, such as Matterport3D. To study the main stages of solving the place recognition problem on the HPointLoc dataset, we proposed a new modular approach named as PNTR. It first performs an image retrieval with the Patch-NetVLAD method, then extracts keypoints and matches them using R2D2, LoFTR or SuperPoint with SuperGlue, and finally performs a camera pose optimization step with TEASER++. Such a solution to the place recognition problem has not been previously studied in existing publications. The PNTR approach has shown the best quality metrics on the HPointLoc dataset and has a high potential for real use in localization systems for unmanned vehicles. The proposed dataset and framework are publicly available: https://github.com/metra4ok/HPointLoc.

In the Earth's magnetosphere, there are fewer than a dozen dedicated probes beyond low-Earth orbit making in-situ observations at any given time. As a result, we poorly understand its global structure and evolution, the mechanisms of its main activity processes, magnetic storms, and substorms. New Artificial Intelligence (AI) methods, including machine learning, data mining, and data assimilation, as well as new AI-enabled missions will need to be developed to meet this Sparse Data challenge.

Recent work leverages the expressive power of generative adversarial networks (GANs) to generate labeled synthetic datasets. These dataset generation methods often require new annotations of synthetic images, which forces practitioners to seek out annotators, curate a set of synthetic images, and ensure the quality of generated labels. We introduce the HandsOff framework, a technique capable of producing an unlimited number of synthetic images and corresponding labels after being trained on less than 50 pre-existing labeled images. Our framework avoids the practical drawbacks of prior work by unifying the field of GAN inversion with dataset generation. We generate datasets with rich pixel-wise labels in multiple challenging domains such as faces, cars, full-body human poses, and urban driving scenes. Our method achieves state-of-the-art performance in semantic segmentation, keypoint detection, and depth estimation compared to prior dataset generation approaches and transfer learning baselines. We additionally showcase its ability to address broad challenges in model development which stem from fixed, hand-annotated datasets, such as the long-tail problem in semantic segmentation.

Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon these advances by designing a novel deep learning architecture consisting of a 3-dimensional convolutional neural network utilizing channel-wise attention and two graph convolutional networks utilizing attention-based aggregation of node features. HAC-Net (Hybrid Attention-Based Convolutional Neural Network) obtains state-of-the-art results on the PDBbind v.2016 core set, the most widely recognized benchmark in the field. We extensively assess the generalizability of our model using multiple train-test splits, each of which maximizes differences between either protein structures, protein sequences, or ligand extended-connectivity fingerprints. Furthermore, we perform 10-fold cross-validation with a similarity cutoff between SMILES strings of ligands in the training and test sets, and also evaluate the performance of HAC-Net on lower-quality data. We envision that this model can be extended to a broad range of supervised learning problems related to structure-based biomolecular property prediction. All of our software is available as open source at https://github.com/gregory-kyro/HAC-Net/.

Machine learning (ML) models are nowadays used in complex applications in various domains, such as medicine, bioinformatics, and other sciences. Due to their black box nature, however, it may sometimes be hard to understand and trust the results they provide. This has increased the demand for reliable visualization tools related to enhancing trust in ML models, which has become a prominent topic of research in the visualization community over the past decades. To provide an overview and present the frontiers of current research on the topic, we present a State-of-the-Art Report (STAR) on enhancing trust in ML models with the use of interactive visualization. We define and describe the background of the topic, introduce a categorization for visualization techniques that aim to accomplish this goal, and discuss insights and opportunities for future research directions. Among our contributions is a categorization of trust against different facets of interactive ML, expanded and improved from previous research. Our results are investigated from different analytical perspectives: (a) providing a statistical overview, (b) summarizing key findings, (c) performing topic analyses, and (d) exploring the data sets used in the individual papers, all with the support of an interactive web-based survey browser. We intend this survey to be beneficial for visualization researchers whose interests involve making ML models more trustworthy, as well as researchers and practitioners from other disciplines in their search for effective visualization techniques suitable for solving their tasks with confidence and conveying meaning to their data.

Magnetic Resonance Fingerprinting (MRF) is an efficient quantitative MRI technique that can extract important tissue and system parameters such as T1, T2, B0, and B1 from a single scan. This property also makes it attractive for retrospectively synthesizing contrast-weighted images. In general, contrast-weighted images like T1-weighted, T2-weighted, etc., can be synthesized directly from parameter maps through spin-dynamics simulation (i.e., Bloch or Extended Phase Graph models). However, these approaches often exhibit artifacts due to imperfections in the mapping, the sequence modeling, and the data acquisition. Here we propose a supervised learning-based method that directly synthesizes contrast-weighted images from the MRF data without going through the quantitative mapping and spin-dynamics simulation. To implement our direct contrast synthesis (DCS) method, we deploy a conditional Generative Adversarial Network (GAN) framework and propose a multi-branch U-Net as the generator. The input MRF data are used to directly synthesize T1-weighted, T2-weighted, and fluid-attenuated inversion recovery (FLAIR) images through supervised training on paired MRF and target spin echo-based contrast-weighted scans. In-vivo experiments demonstrate excellent image quality compared to simulation-based contrast synthesis and previous DCS methods, both visually as well as by quantitative metrics. We also demonstrate cases where our trained model is able to mitigate in-flow and spiral off-resonance artifacts that are typically seen in MRF reconstructions and thus more faithfully represent conventional spin echo-based contrast-weighted images.