Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes is challenging, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that $k$-mers are a crucial stepping stone to bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of $k$-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different $k$-mer-based measures of genetic variation behave in population genetic simulations according to the choice of $k$, depth of sequencing coverage, and degree of data compression. Overall, we find that $k$-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity ($\pi$) up to values of about $\pi = 0.025$ ($R^2 = 0.97$) for neutrally evolving populations. For populations with even more variation, using shorter $k$-mers will maintain the scalability up to at least $\pi = 0.1$. Furthermore, in our simulated populations, $k$-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of $k$-mer based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using $k$-mers.
Over the last decade, deep learning has shown great success at performing computer vision tasks, including classification, super-resolution, and style transfer. Now, we apply it to data compression to help build the next generation of multimedia codecs. This thesis provides three primary contributions to this new field of learned compression. First, we present an efficient low-complexity entropy model that dynamically adapts the encoding distribution to a specific input by compressing and transmitting the encoding distribution itself as side information. Secondly, we propose a novel lightweight low-complexity point cloud codec that is highly specialized for classification, attaining significant reductions in bitrate compared to non-specialized codecs. Lastly, we explore how motion within the input domain between consecutive video frames is manifested in the corresponding convolutionally-derived latent space.
The rapid growth of Internet of Things (IoT) devices necessitates efficient data compression techniques to handle the vast amounts of data generated by these devices. Chemiresistive sensor arrays (CSAs), a simple-to-fabricate but crucial component in IoT systems, generate large volumes of data due to their simultaneous multi-sensor operations. Classical principal component analysis (cPCA) methods, a common solution to the data compression challenge, face limitations in preserving critical information during dimensionality reduction. In this study, we present self-adaptive quantum kernel (SAQK) PCA as a superior alternative to enhance information retention. Our findings demonstrate that SAQK PCA outperforms cPCA in various back-end machine-learning tasks, especially in low-dimensional scenarios where access to quantum bits is limited. These results highlight the potential of noisy intermediate-scale quantum (NISQ) computers to revolutionize data processing in real-world IoT applications by improving the efficiency and reliability of CSA data compression and readout, despite the current constraints on qubit availability.
Quantization is a common approach to mitigate the communication cost of federated learning (FL). In practice, the quantized local parameters are further encoded via an entropy coding technique, such as Huffman coding, for efficient data compression. In this case, the exact communication overhead is determined by the bit rate of the encoded gradients. Recognizing this fact, this work deviates from the existing approaches in the literature and develops a novel quantized FL framework, called \textbf{r}ate-\textbf{c}onstrained \textbf{fed}erated learning (RC-FED), in which the gradients are quantized subject to both fidelity and data rate constraints. We formulate this scheme, as a joint optimization in which the quantization distortion is minimized while the rate of encoded gradients is kept below a target threshold. This enables for a tunable trade-off between quantization distortion and communication cost. We analyze the convergence behavior of RC-FED, and show its superior performance against baseline quantized FL schemes on several datasets.
Scientific applications in fields such as high energy physics, computational fluid dynamics, and climate science generate vast amounts of data at high velocities. This exponential growth in data production is surpassing the advancements in computing power, network capabilities, and storage capacities. To address this challenge, data compression or reduction techniques are crucial. These scientific datasets have underlying data structures that consist of structured and block structured multidimensional meshes where each grid point corresponds to a tensor. It is important that data reduction techniques leverage strong spatial and temporal correlations that are ubiquitous in these applications. Additionally, applications such as CFD, process tensors comprising hundred plus species and their attributes at each grid point. Reduction techniques should be able to leverage interrelationships between the elements in each tensor. In this paper, we propose an attention-based hierarchical compression method utilizing a block-wise compression setup. We introduce an attention-based hyper-block autoencoder to capture inter-block correlations, followed by a block-wise encoder to capture block-specific information. A PCA-based post-processing step is employed to guarantee error bounds for each data block. Our method effectively captures both spatiotemporal and inter-variable correlations within and between data blocks. Compared to the state-of-the-art SZ3, our method achieves up to 8 times higher compression ratio on the multi-variable S3D dataset. When evaluated on single-variable setups using the E3SM and XGC datasets, our method still achieves up to 3 times and 2 times higher compression ratio, respectively.
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction is resource intensive and hard to be parallelized, and many methods for querying large full-text indices only report exact matches or their simple extensions. These limitations have hampered the biological applications of full-text indices. Results: We developed ropebwt3 for efficient BWT construction and query. Ropebwt3 indexed 320 assembled human genomes in 65 hours and indexed 7.3 terabases of commonly studied bacterial assemblies in 26 days. This was achieved using up to 170 gigabytes of memory at the peak without working disk space. Ropebwt3 can find maximal exact matches and inexact alignments under affine-gap penalties, and can retrieve similar local haplotypes matching a query sequence. It demonstrates the feasibility of full-text indexing at the terabase scale. Availability and implementation: https://github.com/lh3/ropebwt3
Large language models (LLMs) trained on next-token prediction (NTP) paradigm have demonstrated powerful capabilities. However, the existing NTP paradigm contains several limitations, particularly related to planned task complications and error propagation during inference. In our work, we extend the critique of NTP, highlighting its limitation also due to training with a narrow objective: the prediction of a sub-optimal one-hot distribution. To support this critique, we conducted a pre-experiment treating the output distribution from powerful LLMs as efficient world data compression. By evaluating the similarity between the $n$-gram distribution and the one-hot distribution with LLMs, we observed that the $n$-gram distributions align more closely with the output distribution of LLMs. Based on this insight, we introduce Next Distribution Prediction (NDP), which uses $n$-gram distributions to replace the one-hot targets, enhancing learning without extra online training time. We conducted experiments across translation, general task, language transfer, and medical domain adaptation. Compared to NTP, NDP can achieve up to +2.97 COMET improvement in translation tasks, +0.61 average improvement in general tasks, and incredible +10.75 average improvement in the medical domain. This demonstrates the concrete benefits of addressing the target narrowing problem, pointing to a new direction for future work on improving NTP.
Current data compression methods, such as sparsification in Federated Averaging (FedAvg), effectively enhance the communication efficiency of Federated Learning (FL). However, these methods encounter challenges such as the straggler problem and diminished model performance due to heterogeneous bandwidth and non-IID (Independently and Identically Distributed) data. To address these issues, we introduce a bandwidth-aware compression framework for FL, aimed at improving communication efficiency while mitigating the problems associated with non-IID data. First, our strategy dynamically adjusts compression ratios according to bandwidth, enabling clients to upload their models at a close pace, thus exploiting the otherwise wasted time to transmit more data. Second, we identify the non-overlapped pattern of retained parameters after compression, which results in diminished client update signals due to uniformly averaged weights. Based on this finding, we propose a parameter mask to adjust the client-averaging coefficients at the parameter level, thereby more closely approximating the original updates, and improving the training convergence under heterogeneous environments. Our evaluations reveal that our method significantly boosts model accuracy, with a maximum improvement of 13% over the uncompressed FedAvg. Moreover, it achieves a $3.37\times$ speedup in reaching the target accuracy compared to FedAvg with a Top-K compressor, demonstrating its effectiveness in accelerating convergence with compression. The integration of common compression techniques into our framework further establishes its potential as a versatile foundation for future cross-device, communication-efficient FL research, addressing critical challenges in FL and advancing the field of distributed machine learning.
The Variational Bayesian method (VB) is used to solve the probability distributions of latent variables with the minimum free energy criterion. This criterion is not easy to understand, and the computation is complex. For these reasons, this paper proposes the Semantic Variational Bayes' method (SVB). The Semantic Information Theory the author previously proposed extends the rate-distortion function R(D) to the rate-fidelity function R(G), where R is the minimum mutual information for given semantic mutual information G. SVB came from the parameter solution of R(G), where the variational and iterative methods originated from Shannon et al.'s research on the rate-distortion function. The constraint functions SVB uses include likelihood, truth, membership, similarity, and distortion functions. SVB uses the maximum information efficiency (G/R) criterion, including the maximum semantic information criterion for optimizing model parameters and the minimum mutual information criterion for optimizing the Shannon channel. For the same tasks, SVB is computationally simpler than VB. The computational experiments in the paper include 1) using a mixture model as an example to show that the mixture model converges as G/R increases; 2) demonstrating the application of SVB in data compression with a group of error ranges as the constraint; 3) illustrating how the semantic information measure and SVB can be used for maximum entropy control and reinforcement learning in control tasks with given range constraints, providing numerical evidence for balancing control's purposiveness and efficiency. Further research is needed to apply SVB to neural networks and deep learning.
The key to effective point cloud compression is to obtain a robust context model consistent with complex 3D data structures. Recently, the advancement of large language models (LLMs) has highlighted their capabilities not only as powerful generators for in-context learning and generation but also as effective compressors. These dual attributes of LLMs make them particularly well-suited to meet the demands of data compression. Therefore, this paper explores the potential of using LLM for compression tasks, focusing on lossless point cloud geometry compression (PCGC) experiments. However, applying LLM directly to PCGC tasks presents some significant challenges, i.e., LLM does not understand the structure of the point cloud well, and it is a difficult task to fill the gap between text and point cloud through text description, especially for large complicated and small shapeless point clouds. To address these problems, we introduce a novel architecture, namely the Large Language Model-based Point Cloud Geometry Compression (LLM-PCGC) method, using LLM to compress point cloud geometry information without any text description or aligning operation. By utilizing different adaptation techniques for cross-modality representation alignment and semantic consistency, including clustering, K-tree, token mapping invariance, and Low Rank Adaptation (LoRA), the proposed method can translate LLM to a compressor/generator for point cloud. To the best of our knowledge, this is the first structure to employ LLM as a compressor for point cloud data. Experiments demonstrate that the LLM-PCGC outperforms the other existing methods significantly, by achieving -40.213% bit rate reduction compared to the reference software of MPEG Geometry-based Point Cloud Compression (G-PCC) standard, and by achieving -2.267% bit rate reduction compared to the state-of-the-art learning-based method.
In hierarchical cognitive radio networks, edge or cloud servers utilize the data collected by edge devices for modulation classification, which, however, is faced with problems of the computation load, transmission overhead, and data privacy. In this article, an edge learning (EL) based framework jointly mobilizing the edge device and the edge server for intelligent co-inference is proposed to realize the collaborative automatic modulation classification (C-AMC) between them. A spectrum semantic compression neural network is designed for the edge device to compress the collected raw data into a compact semantic embedding that is then sent to the edge server via the wireless channel. On the edge server side, a modulation classification neural network combining the bidirectional long-short term memory and attention structures is elaborated to determine the modulation type from the noisy semantic embedding. The C-AMC framework decently balances the computation resources of both sides while avoiding the high transmission overhead and data privacy leakage. Both the offline and online training procedures of the C-AMC framework are elaborated. The compression strategy of the C-AMC framework is also developed to further facilitate the deployment, especially for the resource-constrained edge device. Simulation results show the superiority of the EL-based C-AMC framework in terms of the classification accuracy, computational complexity, and the data compression rate as well as reveal useful insights paving the practical implementation.
Empirically-determined scaling laws have been broadly successful in predicting the evolution of large machine learning models with training data and number of parameters. As a consequence, they have been useful for optimizing the allocation of limited resources, most notably compute time. In certain applications, storage space is an important constraint, and data format needs to be chosen carefully as a consequence. Computer vision is a prominent example: images are inherently analog, but are always stored in a digital format using a finite number of bits. Given a dataset of digital images, the number of bits $L$ to store each of them can be further reduced using lossy data compression. This, however, can degrade the quality of the model trained on such images, since each example has lower resolution. In order to capture this trade-off and optimize storage of training data, we propose a `storage scaling law' that describes the joint evolution of test error with sample size and number of bits per image. We prove that this law holds within a stylized model for image compression, and verify it empirically on two computer vision tasks, extracting the relevant parameters. We then show that this law can be used to optimize the lossy compression level. At given storage, models trained on optimally compressed images present a significantly smaller test error with respect to models trained on the original data. Finally, we investigate the potential benefits of randomizing the compression level.
NASA's Solar Dynamics Observatory (SDO) mission collects extensive data to monitor the Sun's daily activity. In the realm of space mission design, data compression plays a crucial role in addressing the challenges posed by limited telemetry rates. The primary objective of data compression is to facilitate efficient data management and transmission to work within the constrained bandwidth, thereby ensuring that essential information is captured while optimizing the utilization of available resources. This paper introduces a neural video compression technique that achieves a high compression ratio for the SDO's image data collection. The proposed approach focuses on leveraging both temporal and spatial redundancies in the data, leading to a more efficient compression. In this work, we introduce an architecture based on the Transformer model, which is specifically designed to capture both local and global information from input images in an effective and efficient manner. Additionally, our network is equipped with an entropy model that can accurately model the probability distribution of the latent representations and improves the speed of the entropy decoding step. The entropy model leverages a channel-dependent approach and utilizes checkerboard-shaped local and global spatial contexts. By combining the Transformer-based video compression network with our entropy model, the proposed compression algorithm demonstrates superior performance over traditional video codecs like H.264 and H.265, as confirmed by our experimental results.
To fill the gap of traditional GS compression method, in this paper, we first propose a simple and effective GS data compression anchor called Graph-based GS Compression (GGSC). GGSC is inspired by graph signal processing theory and uses two branches to compress the primitive center and attributes. We split the whole GS sample via KDTree and clip the high-frequency components after the graph Fourier transform. Followed by quantization, G-PCC and adaptive arithmetic coding are used to compress the primitive center and attribute residual matrix to generate the bitrate file. GGSS is the first work to explore traditional GS compression, with advantages that can reveal the GS distortion characteristics corresponding to typical compression operation, such as high-frequency clipping and quantization. Second, based on GGSC, we create a GS Quality Assessment dataset (GSQA) with 120 samples. A subjective experiment is conducted in a laboratory environment to collect subjective scores after rendering GS into Processed Video Sequences (PVS). We analyze the characteristics of different GS distortions based on Mean Opinion Scores (MOS), demonstrating the sensitivity of different attributes distortion to visual quality. The GGSC code and the dataset, including GS samples, MOS, and PVS, are made publicly available at https://github.com/Qi-Yangsjtu/GGSC.
The training process of foundation models as for other classes of deep learning systems is based on minimizing the reconstruction error over a training set. For this reason, they are susceptible to the memorization and subsequent reproduction of training samples. In this paper, we introduce a training-as-compressing perspective, wherein the model's weights embody a compressed representation of the training data. From a copyright standpoint, this point of view implies that the weights can be considered a reproduction or, more likely, a derivative work of a potentially protected set of works. We investigate the technical and legal challenges that emerge from this framing of the copyright of outputs generated by foundation models, including their implications for practitioners and researchers. We demonstrate that adopting an information-centric approach to the problem presents a promising pathway for tackling these emerging complex legal issues.
A language is made up of an infinite/finite number of sentences, which in turn is composed of a number of words. The Electrocardiogram (ECG) is the most popular noninvasive medical tool for studying heart function and diagnosing various irregular cardiac rhythms. Intuitive inspection of the ECG reveals a marked similarity between ECG signals and the spoken language. As a result, the ECG signal may be thought of as a series of heartbeats (similar to sentences in a spoken language), with each heartbeat consisting of a collection of waves (similar to words in a sentence) with varying morphologies. Just as natural language processing (NLP) is used to help computers comprehend and interpret human natural language, it is conceivable to create NLP-inspired algorithms to help computers comprehend the electrocardiogram data more efficiently. In this study, we propose a novel ECG analysis technique, based on embedding and self attention, to capture the spatial as well as the temporal dependencies of the ECG data. To generate the embedding, an encoder-decoder network was proposed to capture the temporal dependencies of the ECG signal and perform data compression. The compressed and encoded data was fed to the embedding layer as its weights. Finally, the proposed CNN-LSTM-Self Attention classifier works on the embedding layer and classifies the signal as normal or anomalous. The approach was tested using the PTB-xl dataset, which is severely imbalanced. Our emphasis was to appropriately recognise the disease classes present in minority numbers, in order to limit the detection of False Negative cases. An accuracy of 91% was achieved with a good F1-score for all the disease classes. Additionally, the the size of the model was reduced by 34% due to compression, making it suitable for deployment in real time applications
Modern data compression methods are slowly reaching their limits after 80 years of research, millions of papers, and wide range of applications. Yet, the extravagant 6G communication speed requirement raises a major open question for revolutionary new ideas of data compression. We have previously shown all understanding or learning are compression, under reasonable assumptions. Large language models (LLMs) understand data better than ever before. Can they help us to compress data? The LLMs may be seen to approximate the uncomputable Solomonoff induction. Therefore, under this new uncomputable paradigm, we present LMCompress. LMCompress shatters all previous lossless compression algorithms, doubling the lossless compression ratios of JPEG-XL for images, FLAC for audios, and H.264 for videos, and quadrupling the compression ratio of bz2 for texts. The better a large model understands the data, the better LMCompress compresses.
Deep learning recommendation models (DLRMs) are at the heart of the current e-commerce industry. However, the amount of training data used to train these large models is growing exponentially, leading to substantial training hurdles. The training dataset contains two primary types of information: content-based information (features of users and items) and collaborative information (interactions between users and items). One approach to reduce the training dataset is to remove user-item interactions. But that significantly diminishes collaborative information, which is crucial for maintaining accuracy due to its inclusion of interaction histories. This loss profoundly impacts DLRM performance. This paper makes an important observation that if one can capture the user-item interaction history to enrich the user and item embeddings, then the interaction history can be compressed without losing model accuracy. Thus, this work, Collaborative Aware Data Compression (CADC), takes a two-step approach to training dataset compression. In the first step, we use matrix factorization of the user-item interaction matrix to create a novel embedding representation for both the users and items. Once the user and item embeddings are enriched by the interaction history information the approach then applies uniform random sampling of the training dataset to drastically reduce the training dataset size while minimizing model accuracy drop. The source code of CADC is available at \href{https://anonymous.4open.science/r/DSS-RM-8C1D/README.md}{https://anonymous.4open.science/r/DSS-RM-8C1D/README.md}.
Low-discrepancy points (also called Quasi-Monte Carlo points) are deterministically and cleverly chosen point sets in the unit cube, which provide an approximation of the uniform distribution. We explore two methods based on such low-discrepancy points to reduce large data sets in order to train neural networks. The first one is the method of Dick and Feischl [4], which relies on digital nets and an averaging procedure. Motivated by our experimental findings, we construct a second method, which again uses digital nets, but Voronoi clustering instead of averaging. Both methods are compared to the supercompress approach of [14], which is a variant of the K-means clustering algorithm. The comparison is done in terms of the compression error for different objective functions and the accuracy of the training of a neural network.
Data is the cornerstone of large language models (LLMs), but not all data is useful for model learning. Carefully selected data can better elicit the capabilities of LLMs with much less computational overhead. Most methods concentrate on evaluating the quality of individual samples in data selection, while the combinatorial effects among samples are neglected. Even if each sample is of perfect quality, their combinations may be suboptimal in teaching LLMs due to their intrinsic homogeneity or contradiction. In this paper, we aim to uncover the underlying relationships between LLM performance and data selection. Inspired by the information compression nature of LLMs, we uncover an ``entropy law'' that connects LLM performance with data compression ratio and first-epoch training loss, which reflect the information redundancy of a dataset and the mastery of inherent knowledge encoded in this dataset, respectively. Through both theoretical deduction and empirical evaluation, we find that model performance is negatively correlated to the compression ratio of training data, which usually yields a lower training loss. Based on the findings of the entropy law, we propose a quite efficient and universal data selection method named \textbf{ZIP} for training LLMs, which aim to prioritize data subsets exhibiting a low compression ratio. Based on a multi-stage algorithm that selects diverse data in a greedy manner, we can obtain a good data subset with satisfactory diversity. Extensive experiments have been conducted to validate the entropy law and the superiority of ZIP across different LLM backbones and alignment stages. We also present an interesting application of entropy law that can detect potential performance risks at the beginning of model training.