MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, in clinical applications such as infectious disease screening and the diagnosis and early detection of diseases such as cancer. A key task in metagenomics is to determine the species present in a sample and their relative abundances. Currently, the field is dominated by either alignment-based tools, which offer high accuracy but are computationally expensive, or alignment-free tools, which are fast but lack the needed accuracy for many applications. In response to this dichotomy, we introduce MetaFast, a tool based on heuristics, to achieve a fundamental improvement in accuracy-runtime tradeoff over existing methods. MetaFast delivers accuracy comparable to the alignment-based and highly accurate tool Metalign but with significantly enhanced efficiency. In MetaFast, we accelerate memory-frugal reference database indexing and filtering. We further employ heuristics to accelerate read mapping. Our evaluation demonstrates that MetaFast achieves a 4x speedup over Metalign without compromising accuracy. MetaFast is publicly available at //github.com/CMU-SAFARI/MetaFast.
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Machine learning models, in particular deep neural networks, are currently an integral part of various applications, from healthcare to finance. However, using sensitive data to train these models raises concerns about privacy and security. One method that has emerged to verify if the trained models are privacy-preserving is Membership Inference Attacks (MIA), which allows adversaries to determine whether a specific data point was part of a model's training dataset. While a series of MIAs have been proposed in the literature, only a few can achieve high True Positive Rates (TPR) in the low False Positive Rate (FPR) region (0.01%~1%). This is a crucial factor to consider for an MIA to be practically useful in real-world settings. In this paper, we present a novel approach to MIA that is aimed at significantly improving TPR at low FPRs. Our method, named learning-based difficulty calibration for MIA(LDC-MIA), characterizes data records by their hardness levels using a neural network classifier to determine membership. The experiment results show that LDC-MIA can improve TPR at low FPR by up to 4x compared to the other difficulty calibration based MIAs. It also has the highest Area Under ROC curve (AUC) across all datasets. Our method's cost is comparable with most of the existing MIAs, but is orders of magnitude more efficient than one of the state-of-the-art methods, LiRA, while achieving similar performance.
The peculiar congestion patterns in data centers are caused by the bursty and composite nature of traffic, the small bandwidth-delay product, and the tiny switch buffers. It is not practical to modify TCP to adapt to data centers, especially in public clouds where multiple congestion control protocols coexist. In this work, we design a switch-based method to address such congestion issues; our approach does not require any modification to TCP, which enables easy and seamless deployment in public data centers via switch software update. We first present a simple analysis to demonstrate the stability and effectiveness of the scheme, and then we discuss a hardware NetFPGA switch-based prototype. The experimental results from real deployments in a small testbed cluster show the effectiveness of our approach.
Flowcharts and mind maps, collectively known as flowmind, are vital in daily activities, with hand-drawn versions facilitating real-time collaboration. However, there's a growing need to digitize them for efficient processing. Automated conversion methods are essential to overcome manual conversion challenges. Existing sketch recognition methods face limitations in practical situations, being field-specific and lacking digital conversion steps. Our paper introduces the Flowmind2digital method and hdFlowmind dataset to address these challenges. Flowmind2digital, utilizing neural networks and keypoint detection, achieves a record 87.3% accuracy on our dataset, surpassing previous methods by 11.9%. The hdFlowmind dataset, comprising 1,776 annotated flowminds across 22 scenarios, outperforms existing datasets. Additionally, our experiments emphasize the importance of simple graphics, enhancing accuracy by 9.3%.
Planning for many manipulation tasks, such as using tools or assembling parts, often requires both symbolic and geometric reasoning. Task and Motion Planning (TAMP) algorithms typically solve these problems by conducting a tree search over high-level task sequences while checking for kinematic and dynamic feasibility. This can be inefficient as the width of the tree can grow exponentially with the number of possible actions and objects. In this paper, we propose a novel approach to TAMP that relaxes discrete-and-continuous TAMP problems into inference problems on a continuous domain. Our method, Stein Task and Motion Planning (STAMP) subsequently solves this new problem using a gradient-based variational inference algorithm called Stein Variational Gradient Descent, by obtaining gradients from a parallelized differentiable physics simulator. By introducing relaxations to the discrete variables, leveraging parallelization, and approaching TAMP as an Bayesian inference problem, our method is able to efficiently find multiple diverse plans in a single optimization run. We demonstrate our method on two TAMP problems and benchmark them against existing TAMP baselines.
Causal inference is a crucial goal of science, enabling researchers to arrive at meaningful conclusions regarding the predictions of hypothetical interventions using observational data. Path models, Structural Equation Models (SEMs), and, more generally, Directed Acyclic Graphs (DAGs), provide a means to unambiguously specify assumptions regarding the causal structure underlying a phenomenon. Unlike DAGs, which make very few assumptions about the functional and parametric form, SEM assumes linearity. This can result in functional misspecification which prevents researchers from undertaking reliable effect size estimation. In contrast, we propose Super Learner Equation Modeling, a path modeling technique integrating machine learning Super Learner ensembles. We empirically demonstrate its ability to provide consistent and unbiased estimates of causal effects, its competitive performance for linear models when compared with SEM, and highlight its superiority over SEM when dealing with non-linear relationships. We provide open-source code, and a tutorial notebook with example usage, accentuating the easy-to-use nature of the method.
This study investigates the complexity of regulatory affairs in the medical device industry, a critical factor influencing market access and patient care. Through qualitative research, we sought expert insights to understand the factors contributing to this complexity. The study involved semi-structured interviews with 28 professionals from medical device companies, specializing in various aspects of regulatory affairs. These interviews were analyzed using open coding and Natural Language Processing (NLP) techniques. The findings reveal key sources of complexity within the regulatory landscape, divided into five domains: (A) Regulatory language complexity, (B) Intricacies within the regulatory process, (C) Global-level complexities, (D) Database-related considerations, and (E) Product-level issues. The participants highlighted the need for strategies to streamline regulatory compliance, enhance interactions between regulatory bodies and industry players, and develop adaptable frameworks for rapid technological advancements. Emphasizing interdisciplinary collaboration and increased transparency, the study concludes that these elements are vital for establishing coherent and effective regulatory procedures in the medical device sector.
Multimodality Representation Learning, as a technique of learning to embed information from different modalities and their correlations, has achieved remarkable success on a variety of applications, such as Visual Question Answering (VQA), Natural Language for Visual Reasoning (NLVR), and Vision Language Retrieval (VLR). Among these applications, cross-modal interaction and complementary information from different modalities are crucial for advanced models to perform any multimodal task, e.g., understand, recognize, retrieve, or generate optimally. Researchers have proposed diverse methods to address these tasks. The different variants of transformer-based architectures performed extraordinarily on multiple modalities. This survey presents the comprehensive literature on the evolution and enhancement of deep learning multimodal architectures to deal with textual, visual and audio features for diverse cross-modal and modern multimodal tasks. This study summarizes the (i) recent task-specific deep learning methodologies, (ii) the pretraining types and multimodal pretraining objectives, (iii) from state-of-the-art pretrained multimodal approaches to unifying architectures, and (iv) multimodal task categories and possible future improvements that can be devised for better multimodal learning. Moreover, we prepare a dataset section for new researchers that covers most of the benchmarks for pretraining and finetuning. Finally, major challenges, gaps, and potential research topics are explored. A constantly-updated paperlist related to our survey is maintained at //github.com/marslanm/multimodality-representation-learning.
Normalization is known to help the optimization of deep neural networks. Curiously, different architectures require specialized normalization methods. In this paper, we study what normalization is effective for Graph Neural Networks (GNNs). First, we adapt and evaluate the existing methods from other domains to GNNs. Faster convergence is achieved with InstanceNorm compared to BatchNorm and LayerNorm. We provide an explanation by showing that InstanceNorm serves as a preconditioner for GNNs, but such preconditioning effect is weaker with BatchNorm due to the heavy batch noise in graph datasets. Second, we show that the shift operation in InstanceNorm results in an expressiveness degradation of GNNs for highly regular graphs. We address this issue by proposing GraphNorm with a learnable shift. Empirically, GNNs with GraphNorm converge faster compared to GNNs using other normalization. GraphNorm also improves the generalization of GNNs, achieving better performance on graph classification benchmarks.
Since real-world objects and their interactions are often multi-modal and multi-typed, heterogeneous networks have been widely used as a more powerful, realistic, and generic superclass of traditional homogeneous networks (graphs). Meanwhile, representation learning (\aka~embedding) has recently been intensively studied and shown effective for various network mining and analytical tasks. In this work, we aim to provide a unified framework to deeply summarize and evaluate existing research on heterogeneous network embedding (HNE), which includes but goes beyond a normal survey. Since there has already been a broad body of HNE algorithms, as the first contribution of this work, we provide a generic paradigm for the systematic categorization and analysis over the merits of various existing HNE algorithms. Moreover, existing HNE algorithms, though mostly claimed generic, are often evaluated on different datasets. Understandable due to the application favor of HNE, such indirect comparisons largely hinder the proper attribution of improved task performance towards effective data preprocessing and novel technical design, especially considering the various ways possible to construct a heterogeneous network from real-world application data. Therefore, as the second contribution, we create four benchmark datasets with various properties regarding scale, structure, attribute/label availability, and \etc.~from different sources, towards handy and fair evaluations of HNE algorithms. As the third contribution, we carefully refactor and amend the implementations and create friendly interfaces for 13 popular HNE algorithms, and provide all-around comparisons among them over multiple tasks and experimental settings.
Recently, neural networks have been widely used in e-commerce recommender systems, owing to the rapid development of deep learning. We formalize the recommender system as a sequential recommendation problem, intending to predict the next items that the user might be interacted with. Recent works usually give an overall embedding from a user's behavior sequence. However, a unified user embedding cannot reflect the user's multiple interests during a period. In this paper, we propose a novel controllable multi-interest framework for the sequential recommendation, called ComiRec. Our multi-interest module captures multiple interests from user behavior sequences, which can be exploited for retrieving candidate items from the large-scale item pool. These items are then fed into an aggregation module to obtain the overall recommendation. The aggregation module leverages a controllable factor to balance the recommendation accuracy and diversity. We conduct experiments for the sequential recommendation on two real-world datasets, Amazon and Taobao. Experimental results demonstrate that our framework achieves significant improvements over state-of-the-art models. Our framework has also been successfully deployed on the offline Alibaba distributed cloud platform.
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