GPU-Accelerated BWT Construction for Large Collection of Short Reads

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many state-of-the-art aligners, at their core, have used the Burrows-Wheeler transform (BWT) as a main-memory index of a reference genome (typical example, NCBI human genome). Recently, BWT has also found its use in string-graph assembly, for indexing the reads (i.e., raw data from DNA sequencers). In a typical data set, the volume of reads is tens of times of the sequenced genome and can be up to 100 Gigabases. Note that a reference genome is relatively stable and computing the index is not a frequent task. For reads, the index has to computed from scratch for each given input. The ability of efficient BWT construction becomes a much bigger concern than before. In this paper, we present a practical method called CX1 for constructing the BWT of very large string collections. CX1 is the first tool that can take advantage of the parallelism given by a graphics processing unit (GPU, a relative cheap device providing a thousand or more primitive cores), as well as simultaneously the parallelism from a multi-core CPU and more interestingly, from a cluster of GPU-enabled nodes. Using CX1, the BWT of a short-read collection of up to 100 Gigabases can be constructed in less than 2 hours using a machine equipped with a quad-core CPU and a GPU, or in about 43 minutes using a cluster with 4 such machines (the speedup is almost linear after excluding the first 16 minutes for loading the reads from the hard disk). The previously fastest tool BRC is measured to take 12 hours to process 100 Gigabases on one machine; it is non-trivial how BRC can be parallelized to take advantage a cluster of machines, let alone GPUs.Comment: 11 page

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., it avoids pre-processing like partitioning and normalization, which might compromise on result integrity. MEGAHIT generates 3 times larger assembly, with longer contig N50 and average contig length than the previous assembly. 55.8% of the reads were aligned to the assembly, which is 4 times higher than the previous. The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license.Comment: 2 pages, 2 tables, 1 figure, submitted to Oxford Bioinformatics as an Application Not

Hidden Trends in 90 Years of Harvard Business Review

In this paper, we demonstrate and discuss results of our mining the abstracts of the publications in Harvard Business Review between 1922 and 2012. Techniques for computing n-grams, collocations, basic sentiment analysis, and named-entity recognition were employed to uncover trends hidden in the abstracts. We present findings about international relationships, sentiment in HBR's abstracts, important international companies, influential technological inventions, renown researchers in management theories, US presidents via chronological analyses.Comment: 6 pages, 14 figures, Proceedings of 2012 International Conference on Technologies and Applications of Artificial Intelligenc

Explicit Visual Prompting for Universal Foreground Segmentations

Foreground segmentation is a fundamental problem in computer vision, which includes salient object detection, forgery detection, defocus blur detection, shadow detection, and camouflage object detection. Previous works have typically relied on domain-specific solutions to address accuracy and robustness issues in those applications. In this paper, we present a unified framework for a number of foreground segmentation tasks without any task-specific designs. We take inspiration from the widely-used pre-training and then prompt tuning protocols in NLP and propose a new visual prompting model, named Explicit Visual Prompting (EVP). Different from the previous visual prompting which is typically a dataset-level implicit embedding, our key insight is to enforce the tunable parameters focusing on the explicit visual content from each individual image, i.e., the features from frozen patch embeddings and high-frequency components. Our method freezes a pre-trained model and then learns task-specific knowledge using a few extra parameters. Despite introducing only a small number of tunable parameters, EVP achieves superior performance than full fine-tuning and other parameter-efficient fine-tuning methods. Experiments in fourteen datasets across five tasks show the proposed method outperforms other task-specific methods while being considerably simple. The proposed method demonstrates the scalability in different architectures, pre-trained weights, and tasks. The code is available at: https://github.com/NiFangBaAGe/Explicit-Visual-Prompt.Comment: arXiv admin note: substantial text overlap with arXiv:2303.1088

AdaBrowse: Adaptive Video Browser for Efficient Continuous Sign Language Recognition

Raw videos have been proven to own considerable feature redundancy where in many cases only a portion of frames can already meet the requirements for accurate recognition. In this paper, we are interested in whether such redundancy can be effectively leveraged to facilitate efficient inference in continuous sign language recognition (CSLR). We propose a novel adaptive model (AdaBrowse) to dynamically select a most informative subsequence from input video sequences by modelling this problem as a sequential decision task. In specific, we first utilize a lightweight network to quickly scan input videos to extract coarse features. Then these features are fed into a policy network to intelligently select a subsequence to process. The corresponding subsequence is finally inferred by a normal CSLR model for sentence prediction. As only a portion of frames are processed in this procedure, the total computations can be considerably saved. Besides temporal redundancy, we are also interested in whether the inherent spatial redundancy can be seamlessly integrated together to achieve further efficiency, i.e., dynamically selecting a lowest input resolution for each sample, whose model is referred to as AdaBrowse+. Extensive experimental results on four large-scale CSLR datasets, i.e., PHOENIX14, PHOENIX14-T, CSL-Daily and CSL, demonstrate the effectiveness of AdaBrowse and AdaBrowse+ by achieving comparable accuracy with state-of-the-art methods with 1.44$\times$ throughput and 2.12$\times$ fewer FLOPs. Comparisons with other commonly-used 2D CNNs and adaptive efficient methods verify the effectiveness of AdaBrowse. Code is available at \url{https://github.com/hulianyuyy/AdaBrowse}.Comment: ACMMM202

Graph based Label Enhancement for Multi-instance Multi-label learning

Multi-instance multi-label (MIML) learning is widely applicated in numerous domains, such as the image classification where one image contains multiple instances correlated with multiple logic labels simultaneously. The related labels in existing MIML are all assumed as logical labels with equal significance. However, in practical applications in MIML, significance of each label for multiple instances per bag (such as an image) is significant different. Ignoring labeling significance will greatly lose the semantic information of the object, so that MIML is not applicable in complex scenes with a poor learning performance. To this end, this paper proposed a novel MIML framework based on graph label enhancement, namely GLEMIML, to improve the classification performance of MIML by leveraging label significance. GLEMIML first recognizes the correlations among instances by establishing the graph and then migrates the implicit information mined from the feature space to the label space via nonlinear mapping, thus recovering the label significance. Finally, GLEMIML is trained on the enhanced data through matching and interaction mechanisms. GLEMIML (AvgRank: 1.44) can effectively improve the performance of MIML by mining the label distribution mechanism and show better results than the SOTA method (AvgRank: 2.92) on multiple benchmark datasets.Comment: 7 pages,2 figure

Lymph Node Metastasis in Differentiated Thyroid Cancers

Lymph node metastasis is common in differentiated thyroid cancers. Therapeutic neck dissection removes macroscopic nodal metastasis, reduces local recurrence, and facilitates cancer surveillance. On the other hand, microscopic nodal metastasis is also increasingly recognized as a potential cause of persistent disease or early recurrences. Prophylactic neck dissection, by removing microscopic nodal metastasis, has been proposed to reduce recurrence and prevent future reoperation. When cancer recurs, regional nodal recurrence is most common, and the management should be individualized. We hereby present a narrative review on the management of nodal metastasis in differentiated thyroid cancers

D-Unet: A Dual-encoder U-Net for Image Splicing Forgery Detection and Localization

Recently, many detection methods based on convolutional neural networks (CNNs) have been proposed for image splicing forgery detection. Most of these detection methods focus on the local patches or local objects. In fact, image splicing forgery detection is a global binary classification task that distinguishes the tampered and non-tampered regions by image fingerprints. However, some specific image contents are hardly retained by CNN-based detection networks, but if included, would improve the detection accuracy of the networks. To resolve these issues, we propose a novel network called dual-encoder U-Net (D-Unet) for image splicing forgery detection, which employs an unfixed encoder and a fixed encoder. The unfixed encoder autonomously learns the image fingerprints that differentiate between the tampered and non-tampered regions, whereas the fixed encoder intentionally provides the direction information that assists the learning and detection of the network. This dual-encoder is followed by a spatial pyramid global-feature extraction module that expands the global insight of D-Unet for classifying the tampered and non-tampered regions more accurately. In an experimental comparison study of D-Unet and state-of-the-art methods, D-Unet outperformed the other methods in image-level and pixel-level detection, without requiring pre-training or training on a large number of forgery images. Moreover, it was stably robust to different attacks.Comment: 13 pages, 13 figure