Block Sparse Attention with Log-Linear Complexity

Modern large language models increasingly require long contexts for reasoning and multi-document tasks, but attention's quadratic complexity creates a severe computational bottleneck. We present Block Sparse Flash Attention (BSFA), a drop-in replacement that accelerates long-context inference while preserving model quality. Unlike methods that predict importance before computing scores, BSFA computes exact query-key similarities to select the top-k most important value blocks for each query. By comparing per-block maximum scores against calibrated thresholds, we skip approximately 50% of the computation and memory transfers for pruned blocks. Our training-free approach requires only a one-time threshold calibration on a small dataset to learn the per-layer and per-head attention score distributions. We provide a CUDA kernel implementation that can be used as a drop-in replacement for FlashAttention. On Llama-3.1-8B, BSFA achieves up to 1.13x end-to-end speedup on LongBench with only a 1.1% accuracy drop, and up to 1.24x on Needle-in-a-Haystack retrieval at a 1% accuracy drop. The attention kernel itself accelerates by up to 1.38x. We compare BSFA against five recent sparse attention baselines (SpargeAttention, MInference, FlexPrefill, XAttention, and BLASST), and verify the method on Qwen2.5-7B and on A6000 and H100 GPUs. The implementation is available at https://github.com/Danielohayon/Block-Sparse-Flash-Attention.

Block sparse attention is a hardware friendly way to alleviate the key-value (KV) cache read bottleneck in large language models (LLMs). However, it is not prevalent among leading open-weight LLMs, which rely instead on dense attention or fine-grained selection, thereby motivating our analysis. We study DeepSeek's Native Sparse Attention (NSA) as a representative method, whose three-branch design lets us isolate block selection, the most challenging and consequential stage. We formalize selection and reduce it to ranking blocks by a single quantity, the attention mass: the sum of a block's attention scores. We show that if selection retrieves the blocks with the largest attention mass, block sparse attention can match the quality of dense attention. However, computing the exact attention mass requires reading every key, so the problem of block selection ultimately reduces to approximating this mass from a compact summary instead of the full keys. Via a cumulant expansion, we show why existing methods falter: their selection strategies attempt to estimate the attention mass, but are confined to a first-order approximation. Therefore, we propose COBS (Cumulant Order Block Sparse Attention), an attention method that builds on NSA, incorporating a novel selector that stores a compressed second-order statistic per block. On the 32k RULER long-context retrieval benchmark, COBS raises the NSA baseline's mean score from 0.2999 to 0.8195, approaching dense attention at 0.9040 and closing about 86% of the gap, while using only 1.21x the KV cache read traffic of the NSA baseline and 15.15x less read traffic than dense. The same model preserves short-context behavior and attains lower position-wise negative log-likelihood (NLL) than dense attention in our comparison.

Token-level sparse attention mechanisms, exemplified by DeepSeek Sparse Attention (DSA), achieve fine-grained key selection by scoring every historical key for each query through a lightweight indexer, then computing attention only on the selected subset. While the downstream sparse attention itself scales favorably, the indexer must still scan the entire prefix for every query, introducing an per-layer bottleneck that grows prohibitively with context length. We propose HISA (Hierarchical Indexed Sparse Attention), a plug-and-play replacement for the indexer that rewrites the search path from a flat token scan into a two-stage hierarchical procedure: (1) a block-level coarse filtering stage that scores pooled block representations to discard irrelevant regions, followed by (2) a token-level refinement stage that applies the original indexer exclusively within the retained candidate blocks. HISA preserves the identical token-level top-sparse pattern consumed by the downstream Sparse MLA operator and requires no additional training. On kernel-level benchmarks, HISA achieves up to speedup at 64K context. On Needle-in-a-Haystack and LongBench, we directly replace the indexer in DeepSeek-V3.2 and GLM-5 with our HISA indexer, without any finetuning. HISA closely matches the original DSA in quality, while substantially outperforming block-sparse baselines.