We present COBS, a compact bit-sliced signature index, which is a cross-over between an inverted index and Bloom filters. Our target application is to index @math -mers of DNA samples or @math -grams from text documents and process approximate pattern matching queries on the corpus with a user-chosen coverage threshold. Query results may contain a number of false positives which decreases exponentially with the query length and the false positive rate of the index determined at construction time. We compare COBS to seven other index software packages on 100 000 microbial DNA samples. COBS' compact but simple data structure outperforms the other indexes in construction time and query performance with Mantis by on second place. However, different from Mantis and other previous work, COBS does not need the complete index in RAM and is thus designed to scale to larger document sets.
In the original SBT @cite_16 a simple greedy clustering method is used, the bit union is stored in each inner node, and all nodes are RRR compressed @cite_3 using SDSL @cite_24 . The first improvement, the Split Sequence Bloom Tree (SSBT) @cite_12 , splits the inner nodes into two Bloom filters: a filter and a filter, where the first contains all bits in both child filters and the second those set in either child minus the filter. Simultaneously, Sun, Harris, Chikhi, and Medvedev proposed the AllSome Sequence Bloom Tree (AllSome-SBT) @cite_7 , which splits each inner node into an and a subfilter. The filter contains bits in all leaves below the node, excluding those already set in the parent node, and the filter all bits in some leaves but not all. The currently smallest SBT variant is called HowDe-SBT by Harris and Medvedev @cite_20 . It decomposes the Bloom filters in each inner node into two bit vectors: the vector signals if a particular bit is at this inner node, meaning that it is equal in all descendant leaves, and a vector signaling if it is determined as zero or one. All determined bits can be omitted from any children.
@cite_7 @cite_3 @cite_24 @cite_16 @cite_20 @cite_12
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Recently there has been a lot of work on pruning filters from deep convolutional neural networks (CNNs) with the intention of reducing computations. The key idea is to rank the filters based on a certain criterion (say, l1-norm, average percentage of zeros, etc) and retain only the top ranked filters. Once the low scoring filters are pruned away the remainder of the network is fine tuned and is shown to give performance comparable to the original unpruned network. In this work, we report experiments which suggest that the comparable performance of the pruned network is not due to the specific criterion chosen but due to the inherent plasticity of deep neural networks which allows them to recover from the loss of pruned filters once the rest of the filters are fine-tuned. Specifically, we show counter-intuitive results wherein by randomly pruning 25-50 filters from deep CNNs we are able to obtain the same performance as obtained by using state of the art pruning methods. We empirically validate our claims by doing an exhaustive evaluation with VGG-16 and ResNet-50. Further, we also evaluate a real world scenario where a CNN trained on all 1000 ImageNet classes needs to be tested on only a small set of classes at test time (say, only animals). We create a new benchmark dataset from ImageNet to evaluate such class specific pruning and show that even here a random pruning strategy gives close to state of the art performance. Lastly, unlike existing approaches which mainly focus on the task of image classification, in this work we also report results on object detection. We show that using a simple random pruning strategy we can achieve significant speed up in object detection (74 improvement in fps) while retaining the same accuracy as that of the original Faster RCNN model. Convolutional neural networks (CNNs) have state-of-the-art performance on many problems in machine vision. However, networks with superior performance often have millions of weights so that it is difficult or impossible to use CNNs on computationally limited devices or to humanly interpret them. A myriad of CNN compression approaches have been proposed and they involve pruning and compressing the weights and filters. In this article, we introduce a greedy structural compression scheme that prunes filters in a trained CNN. We define a filter importance index equal to the classification accuracy reduction (CAR) of the network after pruning that filter (similarly defined as RAR for regression). We then iteratively prune filters based on the CAR index. This algorithm achieves substantially higher classification accuracy in AlexNet compared to other structural compression schemes that prune filters. Pruning half of the filters in the first or second layer of AlexNet, our CAR algorithm achieves 26 and 20 higher classification accuracies respectively, compared to the best benchmark filter pruning scheme. Our CAR algorithm, combined with further weight pruning and compressing, reduces the size of first or second convolutional layer in AlexNet by a factor of 42, while achieving close to original classification accuracy through retraining (or fine-tuning) network. Finally, we demonstrate the interpretability of CAR-compressed CNNs by showing that our algorithm prunes filters with visually redundant functionalities. In fact, out of top 20 CAR-pruned filters in AlexNet, 17 of them in the first layer and 14 of them in the second layer are color-selective filters as opposed to shape-selective filters. To our knowledge, this is the first reported result on the connection between compression and interpretability of CNNs. Consider an ordered, static tree T where each node has a label from alphabet Σ. Tree T may be of arbitrary degree and shape. Our goal is designing a compressed storage scheme of T that supports basic navigational operations among the immediate neighbors of a node (i.e. parent, ith child, or any child with some label,…) as well as more sophisticated path-based search operations over its labeled structure. We present a novel approach to this problem by designing what we call the XBW-transform of the tree in the spirit of the well-known Burrows-Wheeler transform for strings [1994]. The XBW-transform uses path-sorting to linearize the labeled tree T into two coordinated arrays, one capturing the structure and the other the labels. For the first time, by using the properties of the XBW-transform, our compressed indexes go beyond the information-theoretic lower bound, and support navigational and path-search operations over labeled trees within (near-)optimal time bounds and entropy-bounded space. Our XBW-transform is simple and likely to spur new results in the theory of tree compression and indexing, as well as interesting application contexts. As an example, we use the XBW-transform to design and implement a compressed index for XML documents whose compression ratio is significantly better than the one achievable by state-of-the-art tools, and its query time performance is order of magnitudes faster. Abstract Bloom filters are probabilistic data structures commonly used for approximate membership problems in many areas of Computer Science (networking, distributed systems, databases, etc.). With the increase in data size and distribution of data, problems arise where a large number of Bloom filters are available, and all of them need to be searched for potential matches. As an example, in a federated cloud environment, each cloud provider could encode the information using Bloom filters and share the Bloom filters with a central coordinator. The problem of interest is not only whether a given element is in any of the sets represented by the Bloom filters, but also which of the existing sets contain the given element. This problem cannot be solved by just constructing a Bloom filter on the union of all the sets. Instead, we effectively have a multidimensional Bloom filter problem: given an element, we wish to receive a list of candidate sets where the element might be. To solve this problem, we consider three alternatives. Firstly, we can naively check many Bloom filters. Secondly, we propose to organize the Bloom filters in a hierarchical index structure akin to a B+ tree that we call Bloofi. Finally, we propose another data structure that packs the Bloom filters in such a way as to exploit bit-level parallelism, which we call Flat-Bloofi. Our theoretical and experimental results show that Bloofi and Flat-Bloofi provide scalable and efficient solutions alternatives to search through a large number of Bloom filters.