Gigapixel Medical图像提供了大量的数据，包括形态学纹理和空间信息。由于组织学的数据量表较大，​​深度学习方法作为特征提取器起着越来越重要的作用。现有的解决方案在很大程度上依赖卷积神经网络（CNN）进行全局像素级分析，从而使潜在的局部几何结构（例如肿瘤微环境中的细胞之间的相互作用均未探索。事实证明，医学图像中的拓扑结构与肿瘤进化密切相关，可以很好地表征图。为了获得下游肿瘤学任务的更全面的表示，我们提出了一个融合框架，以增强CNN捕获的全局图像级表示，并使用图形神经网络（GNN）学习的细胞级空间信息的几何形状。融合层优化了全局图像和单元图的协作特征之间的集成。已经开发了两种融合策略：一种具有MLP的融合策略，这很简单，但通过微调而有效，而Transformer获得了融合多个网络的冠军。我们评估了从大型患者群体和胃癌策划的组织学数据集中的融合策略，以完成三个生物标志物预测任务。两种型号的表现都优于普通CNN或GNN，在各种网络骨架上达到了超过5％的AUC提高。实验结果在医学图像分析中将图像水平的形态特征与细胞空间关系相结合的必要性。代码可在https://github.com/yiqings/hegnnenhancecnn上找到。

Given the increasingly intricate forms of partial differential equations (PDEs) in physics and related fields, computationally solving PDEs without analytic solutions inevitably suffers from the trade-off between accuracy and efficiency. Recent advances in neural operators, a kind of mesh-independent neural-network-based PDE solvers, have suggested the dawn of overcoming this challenge. In this emerging direction, Koopman neural operator (KNO) is a representative demonstration and outperforms other state-of-the-art alternatives in terms of accuracy and efficiency. Here we present KoopmanLab, a self-contained and user-friendly PyTorch module of the Koopman neural operator family for solving partial differential equations. Beyond the original version of KNO, we develop multiple new variants of KNO based on different neural network architectures to improve the general applicability of our module. These variants are validated by mesh-independent and long-term prediction experiments implemented on representative PDEs (e.g., the Navier-Stokes equation and the Bateman-Burgers equation) and ERA5 (i.e., one of the largest high-resolution data sets of global-scale climate fields). These demonstrations suggest the potential of KoopmanLab to be considered in diverse applications of partial differential equations.

Temporal sentence grounding (TSG) aims to identify the temporal boundary of a specific segment from an untrimmed video by a sentence query. All existing works first utilize a sparse sampling strategy to extract a fixed number of video frames and then conduct multi-modal interactions with query sentence for reasoning. However, we argue that these methods have overlooked two indispensable issues: 1) Boundary-bias: The annotated target segment generally refers to two specific frames as corresponding start and end timestamps. The video downsampling process may lose these two frames and take the adjacent irrelevant frames as new boundaries. 2) Reasoning-bias: Such incorrect new boundary frames also lead to the reasoning bias during frame-query interaction, reducing the generalization ability of model. To alleviate above limitations, in this paper, we propose a novel Siamese Sampling and Reasoning Network (SSRN) for TSG, which introduces a siamese sampling mechanism to generate additional contextual frames to enrich and refine the new boundaries. Specifically, a reasoning strategy is developed to learn the inter-relationship among these frames and generate soft labels on boundaries for more accurate frame-query reasoning. Such mechanism is also able to supplement the absent consecutive visual semantics to the sampled sparse frames for fine-grained activity understanding. Extensive experiments demonstrate the effectiveness of SSRN on three challenging datasets.

Time-series anomaly detection is an important task and has been widely applied in the industry. Since manual data annotation is expensive and inefficient, most applications adopt unsupervised anomaly detection methods, but the results are usually sub-optimal and unsatisfactory to end customers. Weak supervision is a promising paradigm for obtaining considerable labels in a low-cost way, which enables the customers to label data by writing heuristic rules rather than annotating each instance individually. However, in the time-series domain, it is hard for people to write reasonable labeling functions as the time-series data is numerically continuous and difficult to be understood. In this paper, we propose a Label-Efficient Interactive Time-Series Anomaly Detection (LEIAD) system, which enables a user to improve the results of unsupervised anomaly detection by performing only a small amount of interactions with the system. To achieve this goal, the system integrates weak supervision and active learning collaboratively while generating labeling functions automatically using only a few labeled data. All of these techniques are complementary and can promote each other in a reinforced manner. We conduct experiments on three time-series anomaly detection datasets, demonstrating that the proposed system is superior to existing solutions in both weak supervision and active learning areas. Also, the system has been tested in a real scenario in industry to show its practicality.

This paper investigates the use of artificial neural networks (ANNs) to solve differential equations (DEs) and the construction of the loss function which meets both differential equation and its initial/boundary condition of a certain DE. In section 2, the loss function is generalized to $n^\text{th}$ order ordinary differential equation(ODE). Other methods of construction are examined in Section 3 and applied to three different models to assess their effectiveness.

Kernels are efficient in representing nonlocal dependence and they are widely used to design operators between function spaces. Thus, learning kernels in operators from data is an inverse problem of general interest. Due to the nonlocal dependence, the inverse problem can be severely ill-posed with a data-dependent singular inversion operator. The Bayesian approach overcomes the ill-posedness through a non-degenerate prior. However, a fixed non-degenerate prior leads to a divergent posterior mean when the observation noise becomes small, if the data induces a perturbation in the eigenspace of zero eigenvalues of the inversion operator. We introduce a data-adaptive prior to achieve a stable posterior whose mean always has a small noise limit. The data-adaptive prior's covariance is the inversion operator with a hyper-parameter selected adaptive to data by the L-curve method. Furthermore, we provide a detailed analysis on the computational practice of the data-adaptive prior, and demonstrate it on Toeplitz matrices and integral operators. Numerical tests show that a fixed prior can lead to a divergent posterior mean in the presence of any of the four types of errors: discretization error, model error, partial observation and wrong noise assumption. In contrast, the data-adaptive prior always attains posterior means with small noise limits.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

Inferring knowledge from clinical trials using knowledge graph embedding is an emerging area. However, customizing graph embeddings for different use cases remains a significant challenge. We propose custom2vec, an algorithmic framework to customize graph embeddings by incorporating user preferences in training the embeddings. It captures user preferences by adding custom nodes and links derived from manually vetted results of a separate information retrieval method. We propose a joint learning objective to preserve the original network structure while incorporating the user's custom annotations. We hypothesize that the custom training improves user-expected predictions, for example, in link prediction tasks. We demonstrate the effectiveness of custom2vec for clinical trials related to non-small cell lung cancer (NSCLC) with two customization scenarios: recommending immuno-oncology trials evaluating PD-1 inhibitors and exploring similar trials that compare new therapies with a standard of care. The results show that custom2vec training achieves better performance than the conventional training methods. Our approach is a novel way to customize knowledge graph embeddings and enable more accurate recommendations and predictions.

Because of the widespread existence of noise and data corruption, recovering the true regression parameters with a certain proportion of corrupted response variables is an essential task. Methods to overcome this problem often involve robust least-squares regression, but few methods perform well when confronted with severe adaptive adversarial attacks. In many applications, prior knowledge is often available from historical data or engineering experience, and by incorporating prior information into a robust regression method, we develop an effective robust regression method that can resist adaptive adversarial attacks. First, we propose the novel TRIP (hard Thresholding approach to Robust regression with sImple Prior) algorithm, which improves the breakdown point when facing adaptive adversarial attacks. Then, to improve the robustness and reduce the estimation error caused by the inclusion of priors, we use the idea of Bayesian reweighting to construct the more robust BRHT (robust Bayesian Reweighting regression via Hard Thresholding) algorithm. We prove the theoretical convergence of the proposed algorithms under mild conditions, and extensive experiments show that under different types of dataset attacks, our algorithms outperform other benchmark ones. Finally, we apply our methods to a data-recovery problem in a real-world application involving a space solar array, demonstrating their good applicability.

One of the key challenges in deploying RL to real-world applications is to adapt to variations of unknown environment contexts, such as changing terrains in robotic tasks and fluctuated bandwidth in congestion control. Existing works on adaptation to unknown environment contexts either assume the contexts are the same for the whole episode or assume the context variables are Markovian. However, in many real-world applications, the environment context usually stays stable for a stochastic period and then changes in an abrupt and unpredictable manner within an episode, resulting in a segment structure, which existing works fail to address. To leverage the segment structure of piecewise stable context in real-world applications, in this paper, we propose a \textit{\textbf{Se}gmented \textbf{C}ontext \textbf{B}elief \textbf{A}ugmented \textbf{D}eep~(SeCBAD)} RL method. Our method can jointly infer the belief distribution over latent context with the posterior over segment length and perform more accurate belief context inference with observed data within the current context segment. The inferred belief context can be leveraged to augment the state, leading to a policy that can adapt to abrupt variations in context. We demonstrate empirically that SeCBAD can infer context segment length accurately and outperform existing methods on a toy grid world environment and Mujuco tasks with piecewise-stable context.