Authors: Benjamin K. Johnson, Thomas Goralski, Ayush Semwal, Hui Shen, H. Josh Jang
Organizations: Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, 49503, MI, USA. · Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, 49503, MI, USA.
Abstract
Semi-Markov Conditional Random Fields (semi-CRFs) assign labels to segments of a sequence rather than to individual positions, enabling exact inference over segment-level features and principled uncertainty estimates at their boundaries. However, existing implementations must materialize a large edge potential tensor whose size grows with sequence length, maximum segment length, and label count, becoming prohibitive for speech-scale state spaces and intractable at genomic scales where sequences can exceed 100,000 positions. This memory bottleneck has limited the adoption of exact segment-level inference for long sequences and large label sets. We identify that the core inefficiency is materializing edge potentials that can instead be evaluated on-the-fly from a compact prefix-sum array, and make several improvements. First, replacing the stored edge tensor with prefix-sum lookup reduces the memory footprint by a factor proportional to the product of segment length and label count. Second, a streaming forward-backward pass with checkpoint-boundary normalization keeps working memory sublinear in sequence length while preserving exact gradients. Third, zero-centered cumulative scores control numerical drift and induce an adaptive duration prior under label imbalance. We integrate these ideas into Flash-SemiCRF, a fused Triton kernel that enables exact semi-CRF inference on previously intractable problem sizes. Available at https://github.com/biobenkj/flash-semicrf.
Sequence labelling, a core task of Natural Language Processing (NLP), consists in assigning each token of an input sentence a label. From a Machine Learning point of view, sequence labelling is often cast as a Linear-Chain Conditional Random Field (CRF) parametrised by a neural network. While this approach gives good empirical results, CRFs assume a finite decision span (eg label bigrams) which can limit their expressivity and hurt performance when long-range dependencies are required. We show we can leverage diffusion to train a CRF conditioned on an entire label sequence, with the caveat that the condition is on a noisy version of labels. We show experimentally that this method, in conjunction with approximate CRF inference, improves label accuracy with a 16.5% error reduction for POS-tagging.
Transformer-based large language models face severe scalability challenges in long-context generation due to the computational and memory costs of full-context attention. Under practical computation and memory constraints, many inference-efficient long-context methods improve efficiency by adopting bounded-context or segment-level execution only during inference, while continuing to train models under full-context attention, resulting in a mismatch between training and inference execution and state-transition semantics. Based on this insight, we propose a training-inference consistent segment-level generation framework, in which training and inference follow the same segment-level forward execution semantics. During training, consistency with inference is enforced by restricting gradient propagation to KV states carried over from the immediately preceding segment, while permitting head-specific access to past KV states during the forward pass without involving them in gradient propagation. Across long-context benchmarks, our approach achieves performance comparable to full-context attention, while achieving competitive latency-memory trade-offs against strong inference-efficient baselines, and substantially improving scalability at very long context lengths (e.g., approximately 6x lower peak prefill memory at 128K compared to full-context attention with FlashAttention).
Long-form automatic speech recognition (ASR) requires both high accuracy and low latency, but existing systems force a trade-off between the two. Chunk-based pipelines process audio in parallel windows for low latency, but lose cross-chunk context and need brittle heuristics to align speakers and timestamps at boundaries. Long-context ASR models resolve everything in a single pass for better accuracy, but are an order of magnitude slower. We propose Murmur, an inference system that overcomes this trade-off by operating at two levels. At the inter-chunk level, we revisit the chunk-based pipeline for modern long-context ASR, treating chunk size as a tunable hyperparameter, and show that intermediate chunk sizes strike a good balance of accuracy and latency. At the intra-chunk level, we exploit attention sparsity through a sliding window KV cache eviction policy applied to both output and speech tokens. On AMI-IHM, Murmur matches single-pass accuracy while reducing latency by 4.2x, with further gains from token eviction at less than 1% relative tcpWER degradation. The code of Murmur is available at https://github.com/uw-syfi/Murmur.