Feature selection using Wasserstein Distance and application to TCGA-LUAD multi-omics data
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Recent advances in GPU-based parallel simulation have enabled practitioners to collect large amounts of data and train complex control policies using deep reinforcement learning (RL), on commodity GPUs. However, such successes for RL in robotics have been limited to tasks sufficiently simulated by fast rigid-body dynamics. Simulation techniques for soft bodies are comparatively several orders of magnitude slower, thereby limiting the use of RL due to sample complexity requirements. To address this challenge, this paper presents both a novel RL algorithm and a simulation platform to enable scaling RL on tasks involving rigid bodies and deformables. We introduce Soft Analytic Policy Optimization (SAPO), a maximum entropy first-order model-based actor-critic RL algorithm, which uses first-order analytic gradients from differentiable simulation to train a stochastic actor to maximize expected return and entropy. Alongside our approach, we develop Rewarped, a parallel differentiable multiphysics simulation platform that supports simulating various materials beyond rigid bodies. We re-implement challenging manipulation and locomotion tasks in Rewarped, and show that SAPO outperforms baselines over a range of tasks that involve interaction between rigid bodies, articulations, and deformables.
Nowadays, most DL frameworks (DLFs) use multilingual programming of Python and C/C++, facilitating the flexibility and performance of the DLF. However, inappropriate interlanguage interaction may introduce design smells involving multiple programming languages (PLs), i.e., Inter-Language Design Smells (ILDS). Despite the negative impact of ILDS on multi-language DLFs, there is a lack of an automated approach for detecting ILDS in multi-language DLFs and a comprehensive understanding on ILDS in such DLFs. This work automatically detects ILDS in multi-language DLFs written in the combination of Python and C/C++, and to obtain a understanding on such ILDS in DLFs. We first developed an approach to automatically detecting ILDS in the multi-language DLFs written in the combination of Python and C/C++, including a number of ILDS and their detection rules defined based on inter-language communication mechanisms and code analysis. We then developed the CPSMELL tool that implements detection rules for automatically detecting such ILDS, and manually validated the accuracy of the tool. Finally, we performed a study to evaluate the ILDS in multi-language DLFs. We proposed seven ILDS and achieved an accuracy of 98.17% in the manual validation of CPSMELL in 5 popular multi-language DLFs. The study results revealed that among the 5 DLFs, TensorFlow, PyTorch, and PaddlePaddle exhibit relatively high prevalence of ILDS; each smelly file contains around 5 ILDS instances on average, with ILDS Long Lambda Function For Inter-language Binding and Unused Native Entity being relatively prominent; throughout the evolution process of the 5 DLFs, some ILDS were resolved to a certain extent, but the overall count of ILDS instances shows an upward trend. The automated detection of the proposed ILDS achieved a high accuracy, and the study provides a comprehensive understanding on ILDS in the multi-language DLFs.
With the increasing availability of high-dimensional data, analysts often rely on exploratory data analysis to understand complex data sets. A key approach to exploring such data is dimensionality reduction, which embeds high-dimensional data in two dimensions to enable visual exploration. However, popular embedding techniques, such as t-SNE and UMAP, typically assume that data points are independent. When this assumption is violated, as in time-series data, the resulting visualizations may fail to reveal important temporal patterns and trends. To address this, we propose a formal extension to existing dimensionality reduction methods that incorporates two temporal loss terms that explicitly highlight temporal progression in the embedded visualizations. Through a series of experiments on both synthetic and real-world datasets, we demonstrate that our approach effectively uncovers temporal patterns and improves the interpretability of the visualizations. Furthermore, the method improves temporal coherence while preserving the fidelity of the embeddings, providing a robust tool for dynamic data analysis.
Active imaging systems sample the Transient Light Transport Matrix (TLTM) for a scene by sequentially illuminating various positions in this scene using a controllable light source, and then measuring the resulting spatiotemporal light transport with time of flight (ToF) sensors. Time-resolved Non-line-of-sight (NLOS) imaging employs an active imaging system that measures part of the TLTM of an intermediary relay surface, and uses the indirect reflections of light encoded within this TLTM to "see around corners". Such imaging systems have applications in diverse areas such as disaster response, remote surveillance, and autonomous navigation. While existing NLOS imaging systems usually measure a subset of the full TLTM, development of customized gated Single Photon Avalanche Diode (SPAD) arrays \cite{riccardo_fast-gated_2022} has made it feasible to probe the full measurement space. In this work, we demonstrate that the full TLTM on the relay surface can be processed with efficient algorithms to computationally focus and detect our illumination in different parts of the hidden scene, turning the relay surface into a second-order active imaging system. These algorithms allow us to iterate on the measured, first-order TLTM, and extract a \textbf{second order TLTM for surfaces in the hidden scene}. We showcase three applications of TLTMs in NLOS imaging: (1) Scene Relighting with novel illumination, (2) Separation of direct and indirect components of light transport in the hidden scene, and (3) Dual Photography. Additionally, we empirically demonstrate that SPAD arrays enable parallel acquisition of photons, effectively mitigating long acquisition times.
We study the Out-of-Distribution (OOD) generalization in machine learning and propose a general framework that establishes information-theoretic generalization bounds. Our framework interpolates freely between Integral Probability Metric (IPM) and $f$-divergence, which naturally recovers some known results (including Wasserstein- and KL-bounds), as well as yields new generalization bounds. Additionally, we show that our framework admits an optimal transport interpretation. When evaluated in two concrete examples, the proposed bounds either strictly improve upon existing bounds in some cases or match the best existing OOD generalization bounds. Moreover, by focusing on $f$-divergence and combining it with the Conditional Mutual Information (CMI) methods, we derive a family of CMI-based generalization bounds, which include the state-of-the-art ICIMI bound as a special instance. Finally, leveraging these findings, we analyze the generalization of the Stochastic Gradient Langevin Dynamics (SGLD) algorithm, showing that our derived generalization bounds outperform existing information-theoretic generalization bounds in certain scenarios.
Language models (LMs) are capable of acquiring elements of human-like syntactic knowledge. Targeted syntactic evaluation tests have been employed to measure how well they form generalizations about syntactic phenomena in high-resource languages such as English. However, we still lack a thorough understanding of LMs' capacity for syntactic generalizations in low-resource languages, which are responsible for much of the diversity of syntactic patterns worldwide. In this study, we develop targeted syntactic evaluation tests for three low-resource languages (Basque, Hindi, and Swahili) and use them to evaluate five families of open-access multilingual Transformer LMs. We find that some syntactic tasks prove relatively easy for LMs while others (agreement in sentences containing indirect objects in Basque, agreement across a prepositional phrase in Swahili) are challenging. We additionally uncover issues with publicly available Transformers, including a bias toward the habitual aspect in Hindi in multilingual BERT and underperformance compared to similar-sized models in XGLM-4.5B.
Large scale Bayesian nonparametrics (BNP) learner such as stochastic variational inference (SVI) can handle datasets with large class number and large training size at fractional cost. Like its predecessor, SVI rely on the assumption of conjugate variational posterior to approximate the true posterior. A more challenging problem is to consider large scale learning on non-conjugate posterior. Recent works in this direction are mostly associated with using Monte Carlo methods for approximating the learner. However, these works are usually demonstrated on non-BNP related task and less complex models such as logistic regression, due to higher computational complexity. In order to overcome the issue faced by SVI, we develop a novel approach based on the recently proposed variational maximization-maximization (VMM) learner to allow large scale learning on non-conjugate posterior. Unlike SVI, our VMM learner does not require closed-form expression for the variational posterior expectatations. Our only requirement is that the variational posterior is differentiable. In order to ensure convergence in stochastic settings, SVI rely on decaying step-sizes to slow its learning. Inspired by SVI and Adam, we propose the novel use of decaying step-sizes on both gradient and ascent direction in our VMM to significantly improve its learning. We show that our proposed methods is compatible with ResNet features when applied to large class number datasets such as MIT67 and SUN397. Finally, we compare our proposed learner with several recent works such as deep clustering algorithms and showed we were able to produce on par or outperform the state-of-the-art methods in terms of clustering measures.
Retrieval-Augmented Generation (RAG) merges retrieval methods with deep learning advancements to address the static limitations of large language models (LLMs) by enabling the dynamic integration of up-to-date external information. This methodology, focusing primarily on the text domain, provides a cost-effective solution to the generation of plausible but incorrect responses by LLMs, thereby enhancing the accuracy and reliability of their outputs through the use of real-world data. As RAG grows in complexity and incorporates multiple concepts that can influence its performance, this paper organizes the RAG paradigm into four categories: pre-retrieval, retrieval, post-retrieval, and generation, offering a detailed perspective from the retrieval viewpoint. It outlines RAG's evolution and discusses the field's progression through the analysis of significant studies. Additionally, the paper introduces evaluation methods for RAG, addressing the challenges faced and proposing future research directions. By offering an organized framework and categorization, the study aims to consolidate existing research on RAG, clarify its technological underpinnings, and highlight its potential to broaden the adaptability and applications of LLMs.
We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.
High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.
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