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DUAL-BLADE: Dual-Path NVMe-Direct KV-Cache Offloading for Edge LLM Inference Progressive Semantic Communication for Efficient Edge-Cloud Vision-Language Models Efficient, VRAM-Constrained xLM Inference on Clients Folding Tensor and Sequence Parallelism for Memory-Efficient Transformer Training & Inference DORA: A Scalable Asynchronous Reinforcement Learning System for Language Model Training AMMA: A Multi-Chiplet Memory-Centric Architecture for Low-Latency 1M Context Attention Serving RaMP: Runtime-Aware Megakernel Polymorphism for Mixture-of-Experts Spark Policy Toolkit: Semantic Contracts and Scalable Execution for Policy Learning in Spark Internet of Everything in the 6G Era: Paradigms, Enablers, Potentials and Future Directions PolyKV: A Shared Asymmetrically-Compressed KV Cache Pool for Multi-Agent LLM Inference A Survey on Split Learning for LLM Fine-Tuning: Models, Systems, and Privacy Optimizations ITAS: A Multi-Agent Architecture for LLM-Based Intelligent Tutoring Latency and Cost of Multi-Agent Intelligent Tutoring at Scale TACO: Efficient Communication Compression of Intermediate Tensors for Scalable Tensor-Parallel LLM Training FreeScale: Distributed Training for Sequence Recommendation Models with Minimal Scaling Cost CommFuse: Hiding Tail Latency via Communication Decomposition and Fusion for Distributed LLM Training A Taxonomy and Resolution Strategy for Client-Level Disagreements in Federated Learning Usable Agent Discovery for Decentralized AI Systems Cloud to Edge: Benchmarking LLM Inference On Hardware-Accelerated Single-Board Computers Data-Free Contribution Estimation in Federated Learning using Gradient von Neumann Entropy Shard the Gradient, Scale the Model: Serverless Federated Aggregation via Gradient Partitioning Promoting Simple Agents: Ensemble Methods for Event-Log Prediction GraphLeap: Decoupling Graph Construction and Convolution for Vision GNN Acceleration on FPGA AGNT2: Autonomous Agent Economies on Interaction-Optimized Layer 2 Infrastructure FedSIR: Spectral Client Identification and Relabeling for Federated Learning with Noisy Labels Stream-CQSA: Avoiding Out-of-Memory in Attention Computation via Flexible Workload Scheduling A Delta-Aware Orchestration Framework for Scalable Multi-Agent Edge Computing Federated Learning over Blockchain-Enabled Cloud Infrastructure Optimal Routing for Federated Learning over Dynamic Satellite Networks: Tractable or Not? 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ConfigSpec: Profiling-Based Configuration Selection for Distributed Edge--Cloud Speculative LLM Serving OpenCLAW-P2P v7.0-P2PCLAW: Resilient Multi-Layer Persistence, Live Reference Verification, and Production-Scale Evaluation of Decentralized AI Peer Review v7.0 -- Mathematical Corrections & Ecosystem Developments Edition DarwinNet: An Evolutionary Network Architecture for Agent-Driven Protocol Synthesis RoboECC: Multi-Factor-Aware Edge-Cloud Collaborative Deployment for VLA Models Hardware Utilization and Inference Performance of Edge Object Detection Under Fault Injection HearthNet: Edge Multi-Agent Orchestration for Smart Homes Token-Budget-Aware Pool Routing for Cost-Efficient LLM Inference Cornserve: A Distributed Serving System for Any-to-Any Multimodal Models Characterizing Performance-Energy Trade-offs of Large Language Models in Multi-Request Workflows ECHO: Elastic Speculative Decoding with Sparse Gating for High-Concurrency Scenarios Duration-Informed Workload Scheduler Domain-Adaptive Model Merging Across Disconnected Modes Why Smaller Is Slower? Dimensional Misalignment in Compressed LLMs veScale-FSDP: Flexible and High-Performance FSDP at Scale AEG: A Baremetal Framework for AI Acceleration via Direct Hardware Access in Heterogeneous Accelerators ACE-Bench: A Lightweight Benchmark for Evaluating Azure SDK Usage Correctness StreamServe: Adaptive Speculative Flows for Low-Latency Disaggregated LLM Serving Emergent Social Structures in Autonomous AI Agent Networks: A Metadata Analysis of 626 Agents on the Pilot Protocol SPEED-Bench: A Unified and Diverse Benchmark for Speculative Decoding Para-B&B: Load-Balanced Deterministic Parallelization of Solving MIP Rashomon Sets and Model Multiplicity in Federated Learning Characterizing WebGPU Dispatch Overhead for LLM Inference Across Four GPU Vendors, Three Backends, and Three Browsers Scalable Explainability-as-a-Service (XaaS) for Edge AI Systems NPU Design for Diffusion Language Model Inference PRAXIS: Integrating Program Analysis with Observability for Root-Cause Analysis BitFlipScope: Scalable Fault Localization and Recovery for Bit-Flip Corruptions in LLMs Cornfigurator: Automated Planning for Any-to-Any Multimodal Model Serving SHARe-KAN: Post-Training Vector Quantization for Cache-Resident KAN Inference Spira: Exploiting Voxel Data Structural Properties for Efficient Sparse Convolution in Point Cloud Networks Power to the Clients: Federated Learning in a Dictatorship Setting From Tokens to Layers: Redefining Stall-Free Scheduling for MoE Serving with Layered Prefill Speculative Actions: A Lossless Framework for Faster Agentic Systems InfiniPipe: Elastic Pipeline Parallelism for Efficient Variable-Length Long-Context LLM Training DPQuant: Efficient and Differentially-Private Model Training via Dynamic Quantization Scheduling HFX: Joint Design of Algorithms and Systems for Multi-SLO Serving and Fast Scaling Reliable Microservice Tail Latency Prediction via Decoupled Dual-Stream Learning and Gradient Modulation On the Surprising Effectiveness of a Single Global Merging in Decentralized Learning FedRef: Bayesian Fine-Tuning using a Reference Model to Mitigate Catastrophic Forgetting for Heterogeneous Federated Learning Sandwich: Joint Configuration Search and Hot-Switching for Efficient CPU LLM Serving MegaScale-Data: Scaling Dataloader for Multisource Large Foundation Model Training RESFL: An Uncertainty-Aware Framework for Responsible Federated Learning by Balancing Privacy, Fairness and Utility BatchLLM: Optimizing Large Batched LLM Inference with Global Prefix Sharing and Throughput-oriented Token Batching Deep Optimizer States: Towards Scalable Training of Transformer Models Using Interleaved Offloading CoreGuard: Safeguarding Foundational Capabilities of LLMs Against Model Stealing in Edge Deployment Cloudless-Training: A Framework to Improve Efficiency of Geo-Distributed ML Training
SW# - GPU enabled exact alignments on genome scale
Matija Korpar, Mile Sikic · 2013-04-22 · via cs.DC updates on arXiv.org

Sequence alignment is one of the oldest and the most famous problems in bioinformatics. Even after 45 years, for one reason or another, this problem is still actual; current solutions are trade-offs between execution time, memory consumption and accuracy. We purpose SW#, a new CUDA GPU enabled and memory efficient implementation of dynamic programming algorithms for local alignment. In this implementation indels are treated using the affine gap model. Although there are other GPU implementations of the Smith-Waterman algorithm, SW# is the only publicly available implementation that can produce sequence alignments on genome-wide scale. For long sequences, our implementation is at least a few hundred times faster than a CPU version of the same algorithm.

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