With the advancement of artificial intelligence, molecular design based on generative models offers novel approaches to accelerate drug discovery. However, existing molecular generation methods suffer from inadequate representational capability in geometric structure and discrepancies between topological and geometric structure representations. These challenges result in generating chemically implausible and structurally unstable molecules. Furthermore, existing methods neglect the crucial properties of both quantum and drug-likeness in drug design. To address these challenges, we propose a novel Geometric Structure-Aware Diffusion Model for molecular generation and optimization tasks, named MolGD. First, we designed a Geometric Structure-Aware Network (GSAN) to directly predict structurally stable molecules from noisy inputs. Within GSAN, a Molecular Graph Attention Network (MGAT) is designed to incorporate geometric information during the topological message-passing process. Then, atomic spatial positions are updated by a Geometric Reconstruction Network (GRN) for enabling integrated modeling of molecular structures. Second, MolGD integrates quantum attributes as conditional constraints for precise quantum property regulation. These conditional constraints can guide MolGD to generate molecules with specific quantum properties. Finally, for drug-likeness property optimization, MolGD integrates self-optimization strategies (MolGD-RL) to guide the model toward generating high drug-likeness and easily synthesisable molecules. Experimental results on the quantum chemistry data set QM9 and the molecular conformation data set GEOM-Drugs demonstrate that the MolGD model outperforms existing molecular generation methods in terms of the effectiveness and stability of generated molecules, the generation of specific quantum properties, and high drug-likeness optimization. This validates its efficacy in molecular generation and optimization tasks, offering novel insights for intelligent molecular design.

Learned image compression (LIC) methods surpass traditional algorithms in rate-distortion (RD) performance, but still struggle to optimally balance effectiveness and efficiency. Moreover, many methods often overlook the importance of frequency-domain information. Even the few recent methods that incorporate fixed frequency transforms lack content-adaptive capabilities. Therefore, we propose an efficient spatial-frequency dual-path LIC method. Specifically, for the spatial path, we introduce Cross-Sparse Window Attention, leveraging sparse, window-conditioned global tokens to efficiently model long-range dependencies. It achieves lower computational cost and superior effectiveness than standard Window-based Multi-head Self-attention. For the frequency path, we design a content-adaptive frequency transform, employing a decomposition weight generator and learnable global weights to adaptively process multi-scale frequency components. Furthermore, we propose Denoising-as-Regularizer, a training-only module that structures and smooths the latent representation via a denoising task, enhancing reconstruction quality at zero inference cost. Experiments on the Kodak, CLIC, and Tecnick datasets demonstrate that the proposed method significantly outperforms existing state-of-the-art methods in both RD performance and latency.

Lossless compression has made significant advancements in Genomics Data (GD) storage, sharing and management. Current learning-based methods are non-evolvable with problems of low-level compression modeling, limited adaptability, and user-unfriendly interface. To this end, we propose AgentGC, the first evolutionary Agent-based GD Compressor, consisting of 3 layers with multi-agent named Leader and Worker. Specifically, the 1) User layer provides a user-friendly interface via Leader combined with LLM; 2) Cognitive layer, driven by the Leader, integrates LLM to consider joint optimization of algorithm-dataset-system, addressing the issues of low-level modeling and limited adaptability; and 3) Compression layer, headed by Worker, performs compression decompression via a automated multi-knowledge learning-based compression framework. On top of AgentGC, we design 3 modes to support diverse scenarios: CP for compression-ratio priority, TP for throughput priority, and BM for balanced mode. Compared with 14 baselines on 9 datasets, the average compression ratios gains are 16.66

LLM-driven Anomaly Detection (AD) helps enhance the understanding and explanatory abilities of anomalous behaviors in Time Series (TS). Existing methods face challenges of inadequate reasoning ability, deficient multi-turn dialogue capability, and narrow generalization. To this end, we 1) propose a multi-agent-based TS Evolution algorithm named TSEvol. On top of it, we 2) introduce the AD reasoning and multi-turn dialogue Dataset TSEData-20K and contribute the Chatbot family for AD, including ChatAD-Llama3-8B, Qwen2.5-7B, and Mistral-7B. Furthermore, 3) we propose the TS Kahneman-Tversky Optimization (TKTO) to enhance ChatAD's cross-task generalization capability. Lastly, 4) we propose a LLM-driven Learning-based AD Benchmark LLADBench to evaluate the performance of ChatAD and nine baselines across seven datasets and tasks. Our three ChatAD models achieve substantial gains, up to 34.50

While Learned Data Compression (LDC) has achieved superior compression ratios, balancing precise probability modeling with system efficiency remains challenging. Crucially, uniform single-stream architectures struggle to simultaneously capture micro-syntactic and macro-semantic features, necessitating deep serial stacking that exacerbates latency. Compounding this, heterogeneous systems are constrained by device speed mismatches, where throughput is capped by Amdahl's Law due to serial processing. To this end, we propose a Dual-Stream Multi-Scale Decoupler that disentangles local and global contexts to replace deep serial processing with shallow parallel streams, and incorporate a Hierarchical Gated Refiner for adaptive feature refinement and precise probability modeling. Furthermore, we design a Concurrent Stream-Parallel Pipeline, which overcomes systemic bottlenecks to achieve full-pipeline parallelism. Extensive experiments demonstrate that our method achieves state-of-the-art performance in both compression ratio and throughput, while maintaining the lowest latency and memory usage. The code is available at https://github.com/huidong-ma/FADE.

As various types of data grow explosively, large-scale data storage, backup, and transmission become challenging, which motivates many researchers to propose efficient universal compression algorithms for multi-source data. In recent years, due to the emergence of hardware acceleration devices such as GPUs, TPUs, DPUs, and FPGAs, the performance bottleneck of neural networks (NN) has been overcome, making NN-based compression algorithms increasingly practical and popular. However, the research survey for the NN-based universal lossless compressors has not been conducted yet, and there is also a lack of unified evaluation metrics. To address the above problems, in this paper, we present a holistic survey as well as benchmark evaluations. Specifically, i) we thoroughly investigate NN-based lossless universal compression algorithms toward multi-source data and classify them into 3 types: static pre-training, adaptive, and semi-adaptive. ii) We unify 19 evaluation metrics to comprehensively assess the compression effect, resource consumption, and model performance of compressors. iii) We conduct experiments more than 4600 CPU/GPU hours to evaluate 17 state-of-the-art compressors on 28 real-world datasets across data types of text, images, videos, audio, etc. iv) We also summarize the strengths and drawbacks of NN-based lossless data compressors and discuss promising research directions. We summarize the results as the NN-based Lossless Compressors Benchmark (NNLCB, See fahaihi.github.io/NNLCB website), which will be updated and maintained continuously in the future.

Learning-based lossless compressors play a crucial role in large-scale genomic database backup, storage, transmission, and management. However, their 1) inadequate compression ratio, 2) low compression & decompression throughput, and 3) poor compression robustness limit their widespread adoption and application in both industry and academia. To solve those challenges, we propose a novel Parallel Multi-Knowledge Learning-based Compressor (PMKLC) with four crucial designs: 1) We propose an automated multi-knowledge learning-based compression framework as compressors' backbone to enhance compression ratio and robustness; 2) we design a GPU-accelerated (s,k)-mer encoder to optimize compression throughput and computing resource usage; 3) we introduce data block partitioning and Step-wise Model Passing (SMP) mechanisms for parallel acceleration; 4) We design two compression modes PMKLC-S and PMKLC-M to meet the complex application scenarios, where the former runs on a resource-constrained single GPU and the latter is multi-GPU accelerated. We benchmark PMKLC-S/M and 14 baselines (7 traditional and 7 leaning-based) on 15 real-world datasets with different species and data sizes. Compared to baselines on the testing datasets, PMKLC-S/M achieve the average compression ratio improvement up to 73.609% and 73.480%, the average throughput improvement up to 3.036X and 10.710X, respectively. Besides, PMKLC-S/M also achieve the best robustness and competitive memory cost, indicating its greater stability against datasets with different probability distribution perturbations, and its strong ability to run on memory-constrained devices. Overall, PMKLC is a balanced compression solution that optimizes compression ratio, throughput, robustness, and resource consumption. PMKLC and linkages of datasets are available at https://github.com/dingyanfeng/PMKLC.

With the rapid development of the Internet, the huge amount of multi-source data (MSD) brings challenges in data sharing and storing. Lossless data compression is the major way to solve those problems. Nowadays, neural-network technologies bring significant advantages in data modeling, making learning-based lossless compressors (LLCs) for multi-source data have emerged continuously. Compared with traditional compressors, the LLCs are more useful to catch complex redundancy patterns in MSD, and thus have great potential in enhancing compression ratio. However, existing LLCs still suffer from unsatisfactory compression ratios and lower throughput. To solve those problems, we propose a novel universal MSD lossless compressor called MSDZip via Stepwise-parallel and learning-based prediction technologies, it introduces two major designs: 1) We propose a Local-Global-Deep Mixing block in the learning-based prediction module to establish dependencies for MSD symbols, where designed Deep Mixing block solves the problem of unstable weights in the perceptual layers caused by cold-start problem to enhance the compression ratio significantly. 2) We design a Stepwise-parallel multi-GPU-accelerated compression strategy to address the compression speed and graphics memory constraints of single GPU in the face of large-scale data. The Stepwise-parallel module passes the source MSD to learning-based prediction model through the data chunking strategy, where the model of the previous chunk is used to guide the compression of the next chunk in parallel. We compare MSDZip with 5 classical learning-based and 6 traditional compressors on 12 well-studied real-world datasets. The experimental results demonstrate that MSDZip optimizes 3.418%-69.874% in terms of compression ratio and 31.171%-495.649% in terms of throughput compared to advanced LLCs. The source code of MSDZip and the linkages of the experimental datasets are available at https://anonymous.4open.science/r/MSDZip-0E4E/.

Learning-based lossless compressors have been validated to have competitive advantages in genomics data (GD) compression. However, learning-based GD-dedicated compressors typically need to be pre-trained on multi-source data and then are directly used to compress another target data, we denote them as static compressors, and they often face two challenges: limited compression ratios and bad-performed generalization due to data distribution variations. To solve these problems, we propose AGDLC, a novel Adaptive Genomics Data Lossless Compressor. It includes two critical designs: 1) We design a multiple (s, k)-mer mixer for extracting GD redundancy from multiple dimensions to improve compression ratios. 2) We introduce a recently popular XLSTM model as the backbone, which adaptively compresses GD while updating parameters, without pre-training, improving compression ratios and compression generalization at the same time. We compare AGDLC with 13 baselines on 7 real-world datasets, and the experimental results demonstrate that it achieves the best compression ratio with an average improvement of 2.162%-69.436%. The codes can be found at https://github.com/dingyanfeng/AGDLC.

Explosive growth of multi-source data (MSD) poses challenges in data transmitting and storing. Neural Network (NN)-based lossless compressors are an important type of compression approaches to alleviate these problems. However, existing NN-based lossless compressors suffer from poor compression ratio and high time cost at the same time. To address these issues, we propose a novel MSD Lossless Compressor (MSDLC) with two compression stages: 1) We propose a Parallel Expansion Mapper (PEM) to map redundant pieces in MSD into unused alphabet values, which not only compresses MSD but also saves time for the next stage's NN-based lossless compression. 2) With the mapped MSD as input, we design a NN -based lossless compressor to further improve compression ratio, where we introduce the state-of-the-art xLSTM model and design a Deep Spatial Gating Module (DSGM) as the backbone of NN. We compare MSDLC with 11 baselines on 6 real-world datasets and the results validate that MSDLC obtains the best average compression ratio and time cost. Compared with baselines, compression ratios are improved by 1.103 % similar to 113.897%, and the time costs are improved by 41367% similar to 73.891 %. The codes can be available at https://github.com/mhuidong/MSDLC.

Learning-based compression shows competitive compression ratios for genomics data. It often includes three types of compressors: static, adaptive and semi-adaptive. However, these existing compressors suffer from inferior compression ratios or throughput, and adaptive compressors also faces model cold-start problems. To address these issues, we propose DeepGeCo, a novel genomics data lossless adaptive compression framework with (s,k)-mer encoding and deep neural networks, involving three compression modes (MINI for static, PLUS for adaptive, ULTRA for semi-adaptive) for flexible requirements of compression ratios or throughput. In DeepGeCo, (1) we develop BiGRU and Transformer as the backbone to build Warm-Start and Supporter models in terms of cold-start problems. (2) We introduce (s,k)-mer encoding to pre-process genomics data before feeding it into the DNN model for improve model throughput, and we propose a new metric - Ranking of Throughput and Compression Ratio (RTCR) for effective encoding parameters selection. (3) We design a threshold controller and a probabilistic mixer within the backbone to balance compression ratios and model throughput. Experiments on 10 real-world datasets show that DeepGeCo's three compression modes improve up to a 22.949X average throughput and up to a 31.095% average compression ratio improvement while occupying low CPU or GPU memory.

The mobile element variant is a very important structural variant, accounting for a quarter of structural variants, and it is closely related to many issues such as genetic diseases and species diversity. However, few detection algorithms of mobile element variants have been developed on third-generation sequencing data. We propose an algorithm ricME that combines sequence realignment and identity calculation for detecting mobile element variants. The ricME first performs an initial detection to obtain the positions of insertions and deletions, and extracts the variant sequences; then applies sequence realignment and identity calculation to obtain the transposon classes related to the variant sequences; finally, adopts a multi-level judgment rule to achieve accurate detection of mobile element variants based on the transposon classes and identities. Compared with a representative long-read based mobile element variant detection algorithm rMETL, the ricME improves the F1-score by 11.5 and 21.7% on simulated datasets and real datasets, respectively.