Multi-layer matrix factorization for cancer subtyping using full and partial multi-omics dataset

Cancer, with its inherent heterogeneity, is commonly categorized into distinct subtypes based on unique traits, cellular origins, and molecular markers specific to each type. However, current studies primarily rely on complete multi-omics datasets for predicting cancer subtypes, often overlooking predictive performance in cases where some omics data may be missing and neglecting implicit relationships across multiple layers of omics data integration. This paper introduces Multi-Layer Matrix Factorization (MLMF), a novel approach for cancer subtyping that employs multi-omics data clustering. MLMF initially processes multi-omics feature matrices by performing multi-layer linear or nonlinear factorization, decomposing the original data into latent feature representations unique to each omics type. These latent representations are subsequently fused into a consensus form, on which spectral clustering is performed to determine subtypes. Additionally, MLMF incorporates a class indicator matrix to handle missing omics data, creating a unified framework that can manage both complete and incomplete multi-omics data. Extensive experiments conducted on 10 multi-omics cancer datasets, both complete and with missing values, demonstrate that MLMF achieves results that are comparable to or surpass the performance of several state-of-the-art approaches.

UTMath: Math Evaluation with Unit Test via Reasoning-to-Coding Thoughts

The evaluation of mathematical reasoning capabilities is essential for advancing Artificial General Intelligence (AGI). While Large Language Models (LLMs) have shown impressive performance in solving mathematical problems, existing benchmarks such as GSM8K and MATH present limitations, including narrow problem definitions with specific numbers and reliance on predetermined rules that hinder accurate assessments of reasoning and adaptability. This paper introduces the UTMath Benchmark, which robustly evaluates the models through extensive unit tests. It consists of 1,053 problems across 9 mathematical domains, with over 68 test cases per problem. We propose an innovative evaluation framework inspired by unit testing in software development, focusing on both accuracy and reliability of results. Furthermore, we introduce the Reasoning-to-Coding of Thoughts (RCoT) approach, which encourages LLMs to perform explicit reasoning before generating code, leading to generating more advanced solution and improved performance. Furthermore, we are releasing not only the UTMath benchmark but also the UTMath-Train training dataset (more than 70k samples), to support the community in further exploring mathematical reasoning.

Learning Interpretable Network Dynamics via Universal Neural Symbolic Regression

Discovering governing equations of complex network dynamics is a fundamental challenge in contemporary science with rich data, which can uncover the mysterious patterns and mechanisms of the formation and evolution of complex phenomena in various fields and assist in decision-making. In this work, we develop a universal computational tool that can automatically, efficiently, and accurately learn the symbolic changing patterns of complex system states by combining the excellent fitting ability from deep learning and the equation inference ability from pre-trained symbolic regression. We conduct intensive experimental verifications on more than ten representative scenarios from physics, biochemistry, ecology, epidemiology, etc. Results demonstrate the outstanding effectiveness and efficiency of our tool by comparing with the state-of-the-art symbolic regression techniques for network dynamics. The application to real-world systems including global epidemic transmission and pedestrian movements has verified its practical applicability. We believe that our tool can serve as a universal solution to dispel the fog of hidden mechanisms of changes in complex phenomena, advance toward interpretability, and inspire more scientific discoveries.

Diffusion Models as Network Optimizers: Explorations and Analysis

Network optimization is a fundamental challenge in the Internet of Things (IoT) network, often characterized by complex features that make it difficult to solve these problems. Recently, generative diffusion models (GDMs) have emerged as a promising new approach to network optimization, with the potential to directly address these optimization problems. However, the application of GDMs in this field is still in its early stages, and there is a noticeable lack of theoretical research and empirical findings. In this study, we first explore the intrinsic characteristics of generative models. Next, we provide a concise theoretical proof and intuitive demonstration of the advantages of generative models over discriminative models in network optimization. Based on this exploration, we implement GDMs as optimizers aimed at learning high-quality solution distributions for given inputs, sampling from these distributions during inference to approximate or achieve optimal solutions. Specifically, we utilize denoising diffusion probabilistic models (DDPMs) and employ a classifier-free guidance mechanism to manage conditional guidance based on input parameters. We conduct extensive experiments across three challenging network optimization problems. By investigating various model configurations and the principles of GDMs as optimizers, we demonstrate the ability to overcome prediction errors and validate the convergence of generated solutions to optimal solutions.We provide code and data at https://github.com/qiyu3816/DiffSG.

Enhancing SNN-based Spatio-Temporal Learning: A Benchmark Dataset and Cross-Modality Attention Model

Spiking Neural Networks (SNNs), renowned for their low power consumption, brain-inspired architecture, and spatio-temporal representation capabilities, have garnered considerable attention in recent years. Similar to Artificial Neural Networks (ANNs), high-quality benchmark datasets are of great importance to the advances of SNNs. However, our analysis indicates that many prevalent neuromorphic datasets lack strong temporal correlation, preventing SNNs from fully exploiting their spatio-temporal representation capabilities. Meanwhile, the integration of event and frame modalities offers more comprehensive visual spatio-temporal information. Yet, the SNN-based cross-modality fusion remains underexplored. In this work, we present a neuromorphic dataset called DVS-SLR that can better exploit the inherent spatio-temporal properties of SNNs. Compared to existing datasets, it offers advantages in terms of higher temporal correlation, larger scale, and more varied scenarios. In addition, our neuromorphic dataset contains corresponding frame data, which can be used for developing SNN-based fusion methods. By virtue of the dual-modal feature of the dataset, we propose a Cross-Modality Attention (CMA) based fusion method. The CMA model efficiently utilizes the unique advantages of each modality, allowing for SNNs to learn both temporal and spatial attention scores from the spatio-temporal features of event and frame modalities, subsequently allocating these scores across modalities to enhance their synergy. Experimental results demonstrate that our method not only improves recognition accuracy but also ensures robustness across diverse scenarios.

Conditional Prediction ROC Bands for Graph Classification

Graph classification in medical imaging and drug discovery requires accuracy and robust uncertainty quantification. To address this need, we introduce Conditional Prediction ROC (CP-ROC) bands, offering uncertainty quantification for ROC curves and robustness to distributional shifts in test data. Although developed for Tensorized Graph Neural Networks (TGNNs), CP-ROC is adaptable to general Graph Neural Networks (GNNs) and other machine learning models. We establish statistically guaranteed coverage for CP-ROC under a local exchangeability condition. This addresses uncertainty challenges for ROC curves under non-iid setting, ensuring reliability when test graph distributions differ from training data. Empirically, to establish local exchangeability for TGNNs, we introduce a data-driven approach to construct local calibration sets for graphs. Comprehensive evaluations show that CP-ROC significantly improves prediction reliability across diverse tasks. This method enhances uncertainty quantification efficiency and reliability for ROC curves, proving valuable for real-world applications with non-iid objects.

Conditional Uncertainty Quantification for Tensorized Topological Neural Networks

Graph Neural Networks (GNNs) have become the de facto standard for analyzing graph-structured data, leveraging message-passing techniques to capture both structural and node feature information. However, recent studies have raised concerns about the statistical reliability of uncertainty estimates produced by GNNs. This paper addresses this crucial challenge by introducing a novel technique for quantifying uncertainty in non-exchangeable graph-structured data, while simultaneously reducing the size of label prediction sets in graph classification tasks. We propose Conformalized Tensor-based Topological Neural Networks (CF-T2NN), a new approach for rigorous prediction inference over graphs. CF-T2NN employs tensor decomposition and topological knowledge learning to navigate and interpret the inherent uncertainty in decision-making processes. This method enables a more nuanced understanding and handling of prediction uncertainties, enhancing the reliability and interpretability of neural network outcomes. Our empirical validation, conducted across 10 real-world datasets, demonstrates the superiority of CF-T2NN over a wide array of state-of-the-art methods on various graph benchmarks. This work not only enhances the GNN framework with robust uncertainty quantification capabilities but also sets a new standard for reliability and precision in graph-structured data analysis.

CoT-ST: Enhancing LLM-based Speech Translation with Multimodal Chain-of-Thought

Speech Language Models (SLMs) have demonstrated impressive performance on speech translation tasks. However, existing research primarily focuses on direct instruction fine-tuning and often overlooks the inherent reasoning capabilities of SLMs. In this paper, we introduce a three-stage training framework designed to activate the chain-of-thought (CoT) capabilities of SLMs. We propose CoT-ST, a speech translation model that utilizes multimodal CoT to decompose speech translation into sequential steps of speech recognition and translation. We validated the effectiveness of our method on two datasets: the CoVoST-2 dataset and MuST-C dataset. The experimental results demonstrate that CoT-ST outperforms previous state-of-the-art methods, achieving higher BLEU scores (CoVoST-2 en-ja: 30.5->30.8, en-zh: 45.2->47.7, MuST-C en-zh: 19.6->21.2). This work is open sourced at https://github.com/X-LANCE/SLAM-LLM/tree/main/examples/st_covost2 .

UAV-Enabled Data Collection for IoT Networks via Rainbow Learning

Unmanned aerial vehicles (UAVs) assisted Internet of things (IoT) systems have become an important part of future wireless communications. To achieve higher communication rate, the joint design of UAV trajectory and resource allocation is crucial. This letter considers a scenario where a multi-antenna UAV is dispatched to simultaneously collect data from multiple ground IoT nodes (GNs) within a time interval. To improve the sum data collection (SDC) volume, i.e., the total data volume transmitted by the GNs, the UAV trajectory, the UAV receive beamforming, the scheduling of the GNs, and the transmit power of the GNs are jointly optimized. Since the problem is non-convex and the optimization variables are highly coupled, it is hard to solve using traditional optimization methods. To find a near-optimal solution, a double-loop structured optimization-driven deep reinforcement learning (DRL) algorithm and a fully DRL-based algorithm are proposed to solve the problem effectively. Simulation results verify that the proposed algorithms outperform two benchmarks with significant improvement in SDC volumes.

Evaluating and Improving the Robustness of LiDAR-based Localization and Mapping

LiDAR is one of the most commonly adopted sensors for simultaneous localization and mapping (SLAM) and map-based global localization. SLAM and map-based localization are crucial for the independent operation of autonomous systems, especially when external signals such as GNSS are unavailable or unreliable. While state-of-the-art (SOTA) LiDAR SLAM systems could achieve 0.5% (i.e., 0.5m per 100m) of errors and map-based localization could achieve centimeter-level global localization, it is still unclear how robust they are under various common LiDAR data corruptions. In this work, we extensively evaluated five SOTA LiDAR-based localization systems under 18 common scene-level LiDAR point cloud data (PCD) corruptions. We found that the robustness of LiDAR-based localization varies significantly depending on the category. For SLAM, hand-crafted methods are in general robust against most types of corruption, while being extremely vulnerable (up to +80% errors) to a specific corruption. Learning-based methods are vulnerable to most types of corruptions. For map-based global localization, we found that the SOTA is resistant to all applied corruptions. Finally, we found that simple Bilateral Filter denoising effectively eliminates noise-based corruption but is not helpful in density-based corruption. Re-training is more effective in defending learning-based SLAM against all types of corruption.