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Scalable addressing of high dimensional constrained combinatorial optimization problems is a challenge that arises in several science and engineering disciplines. Recent work introduced novel application of graph neural networks for solving quadratic-cost combinatorial optimization problems. However, effective utilization of models such as graph neural networks to address general problems with higher order constraints is an unresolved challenge. This paper presents a framework, HypOp, which advances the state of the art for solving combinatorial optimization problems in several aspects: (i) it generalizes the prior results to higher order constrained problems with arbitrary cost functions by leveraging hypergraph neural networks; (ii) enables scalability to larger problems by introducing a new distributed and parallel training architecture; (iii) demonstrates generalizability across different problem formulations by transferring knowledge within the same hypergraph; (iv) substantially boosts the solution accuracy compared with the prior art by suggesting a fine-tuning step using simulated annealing; (v) shows a remarkable progress on numerous benchmark examples, including hypergraph MaxCut, satisfiability, and resource allocation problems, with notable run time improvements using a combination of fine-tuning and distributed training techniques. We showcase the application of HypOp in scientific discovery by solving a hypergraph MaxCut problem on NDC drug-substance hypergraph. Through extensive experimentation on various optimization problems, HypOp demonstrates superiority over existing unsupervised learning-based solvers and generic optimization methods.

High-quality, high-resolution medical imaging is essential for clinical care. Raman-based biomedical optical imaging uses non-ionizing infrared radiation to evaluate human tissues in real time and is used for early cancer detection, brain tumor diagnosis, and intraoperative tissue analysis. Unfortunately, optical imaging is vulnerable to image degradation due to laser scattering and absorption, which can result in diagnostic errors and misguided treatment. Restoration of optical images is a challenging computer vision task because the sources of image degradation are multi-factorial, stochastic, and tissue-dependent, preventing a straightforward method to obtain paired low-quality/high-quality data. Here, we present Restorative Step-Calibrated Diffusion (RSCD), an unpaired image restoration method that views the image restoration problem as completing the finishing steps of a diffusion-based image generation task. RSCD uses a step calibrator model to dynamically determine the severity of image degradation and the number of steps required to complete the reverse diffusion process for image restoration. RSCD outperforms other widely used unpaired image restoration methods on both image quality and perceptual evaluation metrics for restoring optical images. Medical imaging experts consistently prefer images restored using RSCD in blinded comparison experiments and report minimal to no hallucinations. Finally, we show that RSCD improves performance on downstream clinical imaging tasks, including automated brain tumor diagnosis and deep tissue imaging. Our code is available at //github.com/MLNeurosurg/restorative_step-calibrated_diffusion.

Lung and colon cancer are serious worldwide health challenges that require early and precise identification to reduce mortality risks. However, diagnosis, which is mostly dependent on histopathologists' competence, presents difficulties and hazards when expertise is insufficient. While diagnostic methods like imaging and blood markers contribute to early detection, histopathology remains the gold standard, although time-consuming and vulnerable to inter-observer mistakes. Limited access to high-end technology further limits patients' ability to receive immediate medical care and diagnosis. Recent advances in deep learning have generated interest in its application to medical imaging analysis, specifically the use of histopathological images to diagnose lung and colon cancer. The goal of this investigation is to use and adapt existing pre-trained CNN-based models, such as Xception, DenseNet201, ResNet101, InceptionV3, DenseNet121, DenseNet169, ResNet152, and InceptionResNetV2, to enhance classification through better augmentation strategies. The results show tremendous progress, with all eight models reaching impressive accuracy ranging from 97% to 99%. Furthermore, attention visualization techniques such as GradCAM, GradCAM++, ScoreCAM, Faster Score-CAM, and LayerCAM, as well as Vanilla Saliency and SmoothGrad, are used to provide insights into the models' classification decisions, thereby improving interpretability and understanding of malignant and benign image classification.

In the field of lung cancer research, particularly in the analysis of overall survival (OS), artificial intelligence (AI) serves crucial roles with specific aims. Given the prevalent issue of missing data in the medical domain, our primary objective is to develop an AI model capable of dynamically handling this missing data. Additionally, we aim to leverage all accessible data, effectively analyzing both uncensored patients who have experienced the event of interest and censored patients who have not, by embedding a specialized technique within our AI model, not commonly utilized in other AI tasks. Through the realization of these objectives, our model aims to provide precise OS predictions for non-small cell lung cancer (NSCLC) patients, thus overcoming these significant challenges. We present a novel approach to survival analysis with missing values in the context of NSCLC, which exploits the strengths of the transformer architecture to account only for available features without requiring any imputation strategy. More specifically, this model tailors the transformer architecture to tabular data by adapting its feature embedding and masked self-attention to mask missing data and fully exploit the available ones. By making use of ad-hoc designed losses for OS, it is able to account for both censored and uncensored patients, as well as changes in risks over time. We compared our method with state-of-the-art models for survival analysis coupled with different imputation strategies. We evaluated the results obtained over a period of 6 years using different time granularities obtaining a Ct-index, a time-dependent variant of the C-index, of 71.97, 77.58 and 80.72 for time units of 1 month, 1 year and 2 years, respectively, outperforming all state-of-the-art methods regardless of the imputation method used.

Place recognition is the foundation for enabling autonomous systems to achieve independent decision-making and safe operations. It is also crucial in tasks such as loop closure detection and global localization within SLAM. Previous methods utilize mundane point cloud representations as input and deep learning-based LiDAR-based Place Recognition (LPR) approaches employing different point cloud image inputs with convolutional neural networks (CNNs) or transformer architectures. However, the recently proposed Mamba deep learning model, combined with state space models (SSMs), holds great potential for long sequence modeling. Therefore, we developed OverlapMamba, a novel network for place recognition, which represents input range views (RVs) as sequences. In a novel way, we employ a stochastic reconstruction approach to build shift state space models, compressing the visual representation. Evaluated on three different public datasets, our method effectively detects loop closures, showing robustness even when traversing previously visited locations from different directions. Relying on raw range view inputs, it outperforms typical LiDAR and multi-view combination methods in time complexity and speed, indicating strong place recognition capabilities and real-time efficiency.

Integrating the different data modalities of cancer patients can significantly improve the predictive performance of patient survival. However, most existing methods ignore the simultaneous utilization of rich semantic features at different scales in pathology images. When collecting multimodal data and extracting features, there is a likelihood of encountering intra-modality missing data, introducing noise into the multimodal data. To address these challenges, this paper proposes a new end-to-end framework, FORESEE, for robustly predicting patient survival by mining multimodal information. Specifically, the cross-fusion transformer effectively utilizes features at the cellular level, tissue level, and tumor heterogeneity level to correlate prognosis through a cross-scale feature cross-fusion method. This enhances the ability of pathological image feature representation. Secondly, the hybrid attention encoder (HAE) uses the denoising contextual attention module to obtain the contextual relationship features and local detail features of the molecular data. HAE's channel attention module obtains global features of molecular data. Furthermore, to address the issue of missing information within modalities, we propose an asymmetrically masked triplet masked autoencoder to reconstruct lost information within modalities. Extensive experiments demonstrate the superiority of our method over state-of-the-art methods on four benchmark datasets in both complete and missing settings.

Data irregularity in cancer genomics studies has been widely observed in the form of outliers and heavy-tailed distributions in the complex traits. In the past decade, robust variable selection methods have emerged as powerful alternatives to the non-robust ones to identify important genes associated with heterogeneous disease traits and build superior predictive models. In this study, to keep the remarkable features of the quantile LASSO and fully Bayesian regularized quantile regression while overcoming their disadvantage in the analysis of high-dimensional genomics data, we propose the spike-and-slab quantile LASSO through a fully Bayesian spike-and-slab formulation under the robust likelihood by adopting the asymmetric Laplace distribution (ALD). The proposed robust method has inherited the prominent properties of selective shrinkage and self-adaptivity to the sparsity pattern from the spike-and-slab LASSO (Ro\v{c}kov\'a and George, 2018). Furthermore, the spike-and-slab quantile LASSO has a computational advantage to locate the posterior modes via soft-thresholding rule guided Expectation-Maximization (EM) steps in the coordinate descent framework, a phenomenon rarely observed for robust regularization with non-differentiable loss functions. We have conducted comprehensive simulation studies with a variety of heavy-tailed errors in both homogeneous and heterogeneous model settings to demonstrate the superiority of the spike-and-slab quantile LASSO over its competing methods. The advantage of the proposed method has been further demonstrated in case studies of the lung adenocarcinomas (LUAD) and skin cutaneous melanoma (SKCM) data from The Cancer Genome Atlas (TCGA).

Survival prediction is an important branch of cancer prognosis analysis. The model that predicts survival risk through TCGA genomics data can discover genes related to cancer and provide diagnosis and treatment recommendations based on patient characteristics. We found that deep learning models based on Cox proportional hazards often suffer from overfitting when dealing with high-throughput data. Moreover, we found that as the number of network layers increases, the experimental results will not get better, and network degradation will occur. Based on this problem, we propose a new framework based on Deep Residual Learning. Combine the ideas of Cox proportional hazards and Residual. And name it ResSurv. First, ResSurv is a feed-forward deep learning network stacked by multiple basic ResNet Blocks. In each ResNet Block, we add a Normalization Layer to prevent gradient disappearance and gradient explosion. Secondly, for the loss function of the neural network, we inherited the Cox proportional hazards methods, applied the semi-parametric of the CPH model to the neural network, combined with the partial likelihood model, established the loss function, and performed backpropagation and gradient update. Finally, we compared ResSurv networks of different depths and found that we can effectively extract high-dimensional features. Ablation experiments and comparative experiments prove that our model has reached SOTA(state of the art) in the field of deep learning, and our network can effectively extract deep information.

Multi-relation Question Answering is a challenging task, due to the requirement of elaborated analysis on questions and reasoning over multiple fact triples in knowledge base. In this paper, we present a novel model called Interpretable Reasoning Network that employs an interpretable, hop-by-hop reasoning process for question answering. The model dynamically decides which part of an input question should be analyzed at each hop; predicts a relation that corresponds to the current parsed results; utilizes the predicted relation to update the question representation and the state of the reasoning process; and then drives the next-hop reasoning. Experiments show that our model yields state-of-the-art results on two datasets. More interestingly, the model can offer traceable and observable intermediate predictions for reasoning analysis and failure diagnosis.