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 on: //github.com/CMU-SAFARI/MetaFast.
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The heightened emphasis on the regulation of deep generative models, propelled by escalating concerns pertaining to privacy and compliance with regulatory frameworks, underscores the imperative need for precise control mechanisms over these models. This urgency is particularly underscored by instances in which generative models generate outputs that encompass objectionable, offensive, or potentially injurious content. In response, machine unlearning has emerged to selectively forget specific knowledge or remove the influence of undesirable data subsets from pre-trained models. However, modern machine unlearning approaches typically assume access to model parameters and architectural details during unlearning, which is not always feasible. In multitude of downstream tasks, these models function as black-box systems, with inaccessible pre-trained parameters, architectures, and training data. In such scenarios, the possibility of filtering undesired outputs becomes a practical alternative. The primary goal of this study is twofold: first, to elucidate the relationship between filtering and unlearning processes, and second, to formulate a methodology aimed at mitigating the display of undesirable outputs generated from models characterized as black-box systems. Theoretical analysis in this study demonstrates that, in the context of black-box models, filtering can be seen as a form of weak unlearning. Our proposed \textbf{\textit{Feature Aware Similarity Thresholding(FAST)}} method effectively suppresses undesired outputs by systematically encoding the representation of unwanted features in the latent space.
In the rapidly advancing field of conditional image generation research, challenges such as limited explainability lie in effectively evaluating the performance and capabilities of various models. This paper introduces VIESCORE, a Visual Instruction-guided Explainable metric for evaluating any conditional image generation tasks. VIESCORE leverages general knowledge from Multimodal Large Language Models (MLLMs) as the backbone and does not require training or fine-tuning. We evaluate VIESCORE on seven prominent tasks in conditional image tasks and found: (1) VIESCORE (GPT4-v) achieves a high Spearman correlation of 0.3 with human evaluations, while the human-to-human correlation is 0.45. (2) VIESCORE (with open-source MLLM) is significantly weaker than GPT-4v in evaluating synthetic images. (3) VIESCORE achieves a correlation on par with human ratings in the generation tasks but struggles in editing tasks. With these results, we believe VIESCORE shows its great potential to replace human judges in evaluating image synthesis tasks.
Identifying speakers of quotations in narratives is an important task in literary analysis, with challenging scenarios including the out-of-domain inference for unseen speakers, and non-explicit cases where there are no speaker mentions in surrounding context. In this work, we propose a simple and effective approach SIG, a generation-based method that verbalizes the task and quotation input based on designed prompt templates, which also enables easy integration of other auxiliary tasks that further bolster the speaker identification performance. The prediction can either come from direct generation by the model, or be determined by the highest generation probability of each speaker candidate. Based on our approach design, SIG supports out-of-domain evaluation, and achieves open-world classification paradigm that is able to accept any forms of candidate input. We perform both cross-domain evaluation and in-domain evaluation on PDNC, the largest dataset of this task, where empirical results suggest that SIG outperforms previous baselines of complicated designs, as well as the zero-shot ChatGPT, especially excelling at those hard non-explicit scenarios by up to 17% improvement. Additional experiments on another dataset WP further corroborate the efficacy of SIG.
We present a neural network for mitigating biased errors in pseudoranges to improve localization performance with data collected from mobile phones. A satellite-wise Multilayer Perceptron (MLP) is designed to regress the pseudorange bias correction from six satellite, receiver, context-related features derived from Android raw Global Navigation Satellite System (GNSS) measurements. To train the MLP, we carefully calculate the target values of pseudorange bias using location ground truth and smoothing techniques and optimize a loss function involving the estimation residuals of smartphone clock bias. The corrected pseudoranges are then used by a model-based localization engine to compute locations. The Google Smartphone Decimeter Challenge (GSDC) dataset, which contains Android smartphone data collected from both rural and urban areas, is utilized for evaluation. Both fingerprinting and cross-trace localization results demonstrate that our proposed method outperforms model-based and state-of-the-art data-driven approaches.
This work proposes a neural network to extensively exploit spatial information for multichannel joint speech separation, denoising and dereverberation, named SpatialNet. In the short-time Fourier transform (STFT) domain, the proposed network performs end-to-end speech enhancement. It is mainly composed of interleaved narrow-band and cross-band blocks to respectively exploit narrow-band and cross-band spatial information. The narrow-band blocks process frequencies independently, and use self-attention mechanism and temporal convolutional layers to respectively perform spatial-feature-based speaker clustering and temporal smoothing/filtering. The cross-band blocks process frames independently, and use full-band linear layer and frequency convolutional layers to respectively learn the correlation between all frequencies and adjacent frequencies. Experiments are conducted on various simulated and real datasets, and the results show that 1) the proposed network achieves the state-of-the-art performance on almost all tasks; 2) the proposed network suffers little from the spectral generalization problem; and 3) the proposed network is indeed performing speaker clustering (demonstrated by attention maps).
This study is concerned with the application of virtual reality (VR) in rehabilitation programs for faulty neck posture which is a primary source of neck pain (NP). The latter is a highly prevalent musculoskeletal disorder that is associated with serious societal and economic burden. VR has been shown to be effective in the physical rehabilitation of various diseases. Specifically, it has been shown to improve the adherence of patients and engagement to carry out physical exercises on a regular basis. Many games have been used to manage NP with different immersion levels. Towards this goal, we present a VR-based system that targets a specific neck problem, the so called forward head posture (FHP), which is a faulty head position that abnormally stresses neck structures. The system can also generalize well to other neck-related disorders and rehabilitation goals. We show the steps for designing and developing the system, and we highlight the aspects of interaction between usability and various game elements. Using a three-point scale for user experience, we also present preliminary insights on the evaluation of the system prototype, and we discuss future enhancement directions based on the feedback from users.
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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