Human perception is at the core of lossy video compression and yet, it is challenging to collect data that is sufficiently dense to drive compression. In perceptual quality assessment, human feedback is typically collected as a single scalar quality score indicating preference of one distorted video over another. In reality, some videos may be better in some parts but not in others. We propose an approach for collecting finer-grained user feedback through an interactive tool that allows direct optimization of perceptual quality given a fixed bitrate. To this end, we built a novel web-tool which allows users to paint spatio-temporal importance maps over videos. The tool allows for interactive successive refinement: we iteratively re-encode the original video according to the painted importance maps, while maintaining the same bitrate, thus allowing the user to visually see the trade-off of assigning higher importance to one spatio-temporal part of the video at the cost of others. We use this tool to collect data in-the-wild (10 videos, 17 users) and utilize the obtained importance maps in the context of x264 coding to demonstrate that the tool can indeed be used to generate videos which, at the same bitrate, look perceptually better through a subjective study (n = 26) - and are 1.9 times more likely to be preferred by viewers. We plan on collecting a large-scale dataset using the tool for automated perceptual compression in the future. The code for the tool and dataset can be found at https://github.com/jenyap/video-annotation-tool.git.

We consider lossless compression based on statistical data modeling followed by prediction-based encoding, where an accurate statistical model for the input data leads to substantial improvements in compression. We propose DZip, a general-purpose compressor for sequential data that exploits the well-known modeling capabilities of neural networks (NNs) for prediction, followed by arithmetic coding. DZip uses a novel hybrid architecture based on adaptive and semi-adaptive training. Unlike most NN-based compressors, DZip does not require additional training data and is not restricted to specific data types. The proposed compressor outperforms general-purpose compressors such as Gzip (29% size reduction on average) and 7zip (12% size reduction on average) on a variety of real datasets, achieves near-optimal compression on synthetic datasets, and performs close to specialized compressors for large sequence lengths, without any human input. While the main limitation of NN-based compressors is generally the encoding/decoding speed, we empirically demonstrate that DZip achieves comparable compression ratio to other NN-based compressors while being several times faster. The source code for DZip and links to the datasets are available at https://github.com/mohit1997/Dzip-torch.

COVID-19 has made video communication one of the most important modes of information exchange. While extensive research has been conducted on the optimization of the video streaming pipeline, in particular the development of novel video codecs, further improvement in the video quality and latency is required, especially under poor network conditions. This paper proposes an alternative to the conventional codec through the implementation of a keypoint-centric encoder relying on the transmission of keypoint information from within a video feed, as shown in Figure 1. The decoder uses the streamed keypoints to generate a reconstruction preserving the semantic features in the input feed. Focusing on video calling applications, we detect and transmit the body pose and face mesh information through the network, which are displayed at the receiver in the form of animated puppets. Using efficient pose and face mesh detection in conjunction with skeleton-based animation, we demonstrate a prototype requiring lower than 35 kbps bandwidth, an order of magnitude reduction over typical video calling systems. The added computational latency due to the mesh extraction and animation is below 120ms on a standard laptop, showcasing the potential of this framework for real-time applications. The code for this work is available at https://github.com/shubhamchandak94/digital-puppetry/ and the full version is available on arXiv [1].

While learned video codecs have demonstrated great promise, they have yet to achieve sufficient efficiency for practical deployment. In this work, we propose several novel ideas for learned video compression which allow for improved performance for the low-latency mode (I- and P-frames only) along with a considerable increase in computational efficiency. In this setting, for natural videos our approach compares favorably across the entire R-D curve under metrics PSNR, MS-SSIM and VMAF against all mainstream video standards (H.264, H.265, AV1) and all ML codecs. At the same time, our approach runs at least 5x faster and has fewer parameters than all ML codecs which report these figures.Our contributions include a flexible-rate framework allowing a single model to cover a large and dense range of bitrates, at a negligible increase in computation and parameter count; an efficient backbone optimized for ML-based codecs; and a novel in-loop flow prediction scheme which leverages prior information towards more efficient compression.We benchmark our method, which we call ELF-VC (Efficient, Learned and Flexible Video Coding) on popular video test sets UVG and MCL-JCV under metrics PSNR, MS-SSIM and VMAF. For example, on UVG under PSNR, it reduces the BD-rate by 44% against H.264, 26% against H.265, 15% against AV1, and 35% against the current best ML codec. At the same time, on an NVIDIA Titan V GPU our approach encodes/decodes VGA at 49/91 FPS, HD 720 at 19/35 FPS, and HD 1080 at 10/18 FPS.

MOTIVATION: Nanopore sequencing provides a real-time and portable solution to genomic sequencing, enabling better assembly, structural variant discovery and modified base detection than second generation technologies. The sequencing process generates a huge amount of data in the form of raw signal contained in fast5 files, which must be compressed to enable efficient storage and transfer. Since the raw data is inherently noisy, lossy compression has potential to significantly reduce space requirements without adversely impacting performance of downstream applications. RESULTS: We explore the use of lossy compression for nanopore raw data using two state-of-the-art lossy time-series compressors, and evaluate the tradeoff between compressed size and basecalling/consensus accuracy. We test several basecallers and consensus tools on a variety of datasets at varying depths of coverage, and conclude that lossy compression can provide 35-50% further reduction in compressed size of raw data over the state-of-the-art lossless compressor with negligible impact on basecalling accuracy (≲0.2% reduction) and consensus accuracy (≲0.002% reduction). In addition, we evaluate the impact of lossy compression on methylation calling accuracy and observe that this impact is minimal for similar reductions in compressed size, although further evaluation with improved benchmark datasets is required for reaching a definite conclusion. The results suggest the possibility of using lossy compression, potentially on the nanopore sequencing device itself, to achieve significant reductions in storage and transmission costs while preserving the accuracy of downstream applications. AVAILABILITYAND IMPLEMENTATION: The code is available at https://github.com/shubhamchandak94/lossy_compression_evaluation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We study common randomness generation problems where$n$players aim to generatesamesequences of random coin flips where some subsets of the players share an independent common coin which can be tossed multiple times, and there is a publicly seen blackboard through which the players communicate with each other. We provide a tight representation of the optimal communication rates via linear programming, and more importantly, propose explicit algorithms for the optimal distributed simulation for a wide class of hypergraphs. In particular, the optimal communication rate in complete hypergraphs is still achievable in sparser hypergraphs containing a path-connected cycle-free cluster of topologically connected components. Some key steps in analyzing the upper bounds rely on two different definitions of connectivity in hypergraphs, which may be of independent interest.

Time series data compression is emerging as an important problem with the growth in IoT devices and sensors. Due to the presence of noise in these datasets, lossy compression can often provide significant compression gains without impacting the performance of downstream applications. In this work, we propose an error-bounded lossy compressor, LFZip, for multivariate floating-point time series data that provides guaranteed reconstruction up to user-specified maximum absolute error. The compressor is based on the prediction-quantization-entropy coder framework and benefits from improved prediction using linear models and neural networks. We evaluate the compressor on several time series datasets where it outperforms the existing state-of-the-art error-bounded lossy compressors. The code and data are available at https://github.com/shubhamchandak94/LFZip.

We consider lossless compression based on statistical data modeling followed by prediction-based encoding, where an accurate statistical model for the input data leads to substantial improvements in compression. We propose DZip, a general-purpose compressor for sequential data that exploits the well-known modeling capabilities of neural networks (NNs) for prediction, followed by arithmetic coding. DZip uses a novel hybrid architecture based on adaptive and semi-adaptive training. Unlike most NN based compressors, DZip does not require additional training data and is not restricted to specific data types, only needing the alphabet size of the input data. The proposed compressor outperforms general-purpose compressors such as Gzip (on average 26% reduction) on a variety of real datasets, achieves near-optimal compression on synthetic datasets, and performs close to specialized compressors for large sequence lengths, without any human input. The main limitation of DZip in its current implementation is the encoding/decoding time, which limits its practicality. Nevertheless, the results showcase the potential of developing improved general-purpose compressors based on neural networks and hybrid modeling.

As magnetization and semiconductor based storage technologies approach their limits, bio-molecules, such as DNA, have been identified as promising media for future storage systems, due to their high storage density (petabytes/gram) and long-term durability (thousands of years). Furthermore, nanopore DNA sequencing enables high-throughput sequencing using devices as small as a USB thumb drive and thus is ideally suited for DNA storage applications. Due to the high insertion/deletion error rates associated with base-called nanopore reads, current approaches rely heavily on consensus among multiple reads and thus incur very high reading costs. We propose a novel approach which overcomes the high error rates in basecalled sequences by integrating a Viterbi error correction decoder with the basecaller, enabling the decoder to exploit the soft information available in the deep learning based basecaller pipeline. Using convolutional codes for error correction, we experimentally observed 3x lower reading costs than the state-of-the-art techniques at comparable writing costs.The code, data and Supplementary Material is available at https://github.com/shubhamchandak94/nanopore_dna_storage.

Lossy image compression has been studied extensively in the context of typical loss functions such as RMSE, MS-SSIM, etc. However, it is not well understood what loss function might be most appropriate for human perception. Furthermore, the availability of massive public image datasets appears to have hardly been exploited in image compression. In this work, we perform compression experiments in which one human describes images to another, using publicly available images and text instructions. These image reconstructions are rated by human scorers on the Amazon Mechanical Turk platform and compared to reconstructions obtained by existing image compressors. In our experiments, the humans outperform the state of the art compressor WebP in the MTurk survey on most images, which shows that there is significant room for improvement in image compression for human perception. The images, results and additional data is available at https://compression.stanford.edu/human-compression.

Sequential data is being generated at an unprecedented pace in various forms, including text and genomic data. This creates the need for efficient compression mechanisms to enable better storage, transmission and processing of such data. To solve this problem, many of the existing compressors attempt to learn models for the data and perform prediction-based compression. Since neural networks are known as universal function approximators with the capability to learn arbitrarily complex mappings, and in practice show excellent performance in prediction tasks, we explore and devise methods to compress sequential data using neural network predictors. We combine recurrent neural network predictors with an arithmetic coder and losslessly compress a variety of synthetic, text and genomic datasets. The proposed compressor outperforms Gzip on the real datasets and achieves near-optimal compression for the synthetic datasets. The results also help understand why and where neural networks are good alternatives for traditional finite context models.

For reliable transmission across a noisy communication channel, classical results from information theory show that it is asymptotically optimal to separate out the source and channel coding processes. However, this decomposition can fall short in the finite bit-length regime, as it requires non-trivial tuning of hand-crafted codes and assumes infinite computational power for decoding. In this work, we propose to jointly learn the encoding and decoding processes using a new discrete variational autoencoder model. By adding noise into the latent codes to simulate the channel during training, we learn to both compress and error-correct given a fixed bit-length and computational budget. We obtain codes that are not only competitive against several separation schemes, but also learn useful robust representations of the data for downstream tasks such as classification. Finally, inference amortization yields an extremely fast neural decoder, almost an order of magnitude faster compared to standard decoding methods based on iterative belief propagation.

MOTIVATION: High-Throughput Sequencing technologies produce huge amounts of data in the form of short genomic reads, associated quality values and read identifiers. Because of the significant structure present in these FASTQ datasets, general-purpose compressors are unable to completely exploit much of the inherent redundancy. Although there has been a lot of work on designing FASTQ compressors, most of them lack in support of one or more crucial properties, such as support for variable length reads, scalability to high coverage datasets, pairing-preserving compression and lossless compression. RESULTS: In this work, we propose SPRING, a reference-free compressor for FASTQ files. SPRING supports a wide variety of compression modes and features, including lossless compression, pairing-preserving compression, lossy compression of quality values, long read compression and random access. SPRING achieves substantially better compression than existing tools, for example, SPRING compresses 195 GB of 25× whole genome human FASTQ from Illumina's NovaSeq sequencer to less than 7 GB, around 1.6× smaller than previous state-of-the-art FASTQ compressors. SPRING achieves this improvement while using comparable computational resources. AVAILABILITY AND IMPLEMENTATION: SPRING can be downloaded from https://github.com/shubhamchandak94/SPRING. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

In new applications of data compression, it is desired to have random access to any block of the compressed dataset (without the need to decompress the entire compressed sequence and thus accessing all the stored bits in memory). In this work, we analyze the problem of universal data compression with random access. Building on the work of Mazumdar, Chandar, and Wornell (2015), we discuss a systematic scheme to achieve close to optimal compression with finite random access. We first analyze the performance of the scheme for i.i.d sources. Using the gained intuition, for the more general class of Markov sources, we show the existence of finite random access compression schemes. Finally, we discuss a generic scheme which can be used to convert any universal compressor (e.g., Lempel-Ziv based schemes) into a finite random access universal compressor.

For any Markov source, there exist universal codes whose normalized codelength approaches the Shannon limit asymptotically as the number of samples goes to infinity. This paper investigates how fast the gap between the normalized codelength of the “best” universal compressor and the Shannon limit (i.e. the compression redundancy) vanishes non-asymptotically in terms of the alphabet size and mixing time of the Markov source. We show that, for Markov sources whose relaxation time is at least 1+ [((2+c))/(√k)], where k is the state space size (and c > 0 is a constant), the phase transition for the number of samples required to achieve vanishing compression redundancy is precisely Θ(k2).

Motivation: New Generation Sequencing (NGS) technologies for genome sequencing produce large amounts of short genomic reads per experiment, which are highly redundant and compressible. However, general-purpose compressors are unable to exploit this redundancy due to the special structure present in the data. Results: We present a new algorithm for compressing reads both with and without preserving the read order. In both cases, it achieves 1.4×-2× compression gain over state-of-the-art read compression tools for datasets containing as many as 3 billion Illumina reads. Our tool is based on the idea of approximately reordering the reads according to their position in the genome using hashed substring indices. We also present a systematic analysis of the read compression problem and compute bounds on fundamental limits of read compression. This analysis sheds light on the dynamics of the proposed algorithm (and read compression algorithms in general) and helps understand its performance in practice. The algorithm compresses only the read sequence, works with unaligned FASTQ files, and does not require a reference. Contact: [email protected]. Supplementary information: Supplementary material are available at Bioinformatics online. The proposed algorithm is available for download at https://github.com/shubhamchandak94/HARC.

MOTIVATION: The dramatic decrease in the cost of sequencing has resulted in the generation of huge amounts of genomic data, as evidenced by projects such as the UK10K and the Million Veteran Project, with the number of sequenced genomes ranging in the order of 10 K to 1 M. Due to the large redundancies among genomic sequences of individuals from the same species, most of the medical research deals with the variants in the sequences as compared with a reference sequence, rather than with the complete genomic sequences. Consequently, millions of genomes represented as variants are stored in databases. These databases are constantly updated and queried to extract information such as the common variants among individuals or groups of individuals. Previous algorithms for compression of this type of databases lack efficient random access capabilities, rendering querying the database for particular variants and/or individuals extremely inefficient, to the point where compression is often relinquished altogether. RESULTS: We present a new algorithm for this task, called GTRAC, that achieves significant compression ratios while allowing fast random access over the compressed database. For example, GTRAC is able to compress a Homo sapiens dataset containing 1092 samples in 1.1 GB (compression ratio of 160), while allowing for decompression of specific samples in less than a second and decompression of specific variants in 17 ms. GTRAC uses and adapts techniques from information theory, such as a specialized Lempel-Ziv compressor, and tailored succinct data structures. AVAILABILITY AND IMPLEMENTATION: The GTRAC algorithm is available for download at: https://github.com/kedartatwawadi/GTRAC CONTACT: : [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.