About

Dr. Albert Gu is broadly interested in theoretical and empirical aspects of deep learning. His research involves understanding and developing approaches that can be practically useful for modern large-scale machine learning models, with a current focus on deep sequence models.

Research topics

• Computer Science
• Artificial Intelligence
• Theoretical computer science
• Machine Learning
• Mathematics
• Algorithm
• Discrete mathematics
• Engineering
• Computer engineering

Selected publications

• Retrieval-Aware Distillation for Transformer-SSM Hybrids

  Open MIND · 2026-02-11

  preprintSenior author

  State-space models (SSMs) offer efficient sequence modeling but lag behind Transformers on benchmarks that require in-context retrieval. Prior work links this gap to a small set of attention heads, termed Gather-and-Aggregate (G&A), which SSMs struggle to reproduce. We propose *retrieval-aware distillation*, which converts a pretrained Transformer into a hybrid student by preserving only these retrieval-critical heads and distilling the rest into recurrent heads. We identify the essential heads via ablation on a synthetic retrieval task, producing a hybrid with sparse, non-uniform attention placement. We show that preserving **just 2% of attention heads recovers over 95% of teacher performance on retrieval-heavy tasks** (10 heads in a 1B model), requiring far fewer heads than hybrids that retain at least 25%. We further find that large recurrent states often compensate for missing retrieval: once retrieval is handled by these heads, the SSM backbone can be simplified with limited loss, even with an $8\times$ reduction in state dimension. By reducing both the attention cache and the SSM state, the resulting hybrid is $5$--$6\times$ more memory-efficient than comparable hybrids, closing the Transformer--SSM gap at a fraction of the memory cost.

  DOI

• dnaHNet: A Scalable and Hierarchical Foundation Model for Genomic Sequence Learning

  arXiv (Cornell University) · 2026-02-11

  articleOpen accessSenior author

  Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory elements, while nucleotide-level models preserve biological coherence but incur prohibitive computational costs for long contexts. We introduce dnaHNet, a state-of-the-art tokenizer-free autoregressive model that segments and models genomic sequences end-to-end. Using a differentiable dynamic chunking mechanism, dnaHNet compresses raw nucleotides into latent tokens adaptively, balancing compression with predictive accuracy. Pretrained on prokaryotic genomes, dnaHNet outperforms leading architectures including StripedHyena2 in scaling and efficiency. This recursive chunking yields quadratic FLOP reductions, enabling $>3 \times$ inference speedup over Transformers. On zero-shot tasks, dnaHNet achieves superior performance in predicting protein variant fitness and gene essentiality, while automatically discovering hierarchical biological structures without supervision. These results establish dnaHNet as a scalable, interpretable framework for next-generation genomic modeling.

  PublisherOA PDF

• dnaHNet: A Scalable and Hierarchical Foundation Model for Genomic Sequence Learning

  Open MIND · 2026-02-11

  preprintSenior author

  Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory elements, while nucleotide-level models preserve biological coherence but incur prohibitive computational costs for long contexts. We introduce dnaHNet, a state-of-the-art tokenizer-free autoregressive model that segments and models genomic sequences end-to-end. Using a differentiable dynamic chunking mechanism, dnaHNet compresses raw nucleotides into latent tokens adaptively, balancing compression with predictive accuracy. Pretrained on prokaryotic genomes, dnaHNet outperforms leading architectures including StripedHyena2 in scaling and efficiency. This recursive chunking yields quadratic FLOP reductions, enabling $>3 \times$ inference speedup over Transformers. On zero-shot tasks, dnaHNet achieves superior performance in predicting protein variant fitness and gene essentiality, while automatically discovering hierarchical biological structures without supervision. These results establish dnaHNet as a scalable, interpretable framework for next-generation genomic modeling.

  DOI

• Mamba-3: Improved Sequence Modeling using State Space Principles

  arXiv (Cornell University) · 2026-03-16

  preprintOpen accessSenior author

  Scaling inference-time compute has emerged as an important driver of LLM performance, making inference efficiency a central focus of model design alongside model quality. While the current Transformer-based models deliver strong model quality, their quadratic compute and linear memory make inference expensive. This has spurred the development of sub-quadratic models with reduced linear compute and constant memory requirements. However, many recent linear models trade off model quality and capability for algorithmic efficiency, failing on tasks such as state tracking. Moreover, their theoretically linear inference remains hardware-inefficient in practice. Guided by an inference-first perspective, we introduce three core methodological improvements inspired by the state space model (SSM) viewpoint of linear models. We combine: (1) a more expressive recurrence derived from SSM discretization, (2) a complex-valued state update rule that enables richer state tracking, and (3) a multi-input, multi-output (MIMO) formulation for better model performance without increasing decode latency. Together with architectural refinements, our Mamba-3 model achieves significant gains across retrieval, state-tracking, and downstream language modeling tasks. At the 1.5B scale, Mamba-3 improves average downstream accuracy by 0.6 percentage points compared to the next best model (Gated DeltaNet), with Mamba-3's MIMO variant further improving accuracy by another 1.2 points for a total 1.8 point gain. Across state-size experiments, Mamba-3 achieves comparable perplexity to Mamba-2 despite using half of its predecessor's state size. Our evaluations demonstrate Mamba-3's ability to advance the performance-efficiency Pareto frontier.

  PublisherDOI

• Retrieval-Aware Distillation for Transformer-SSM Hybrids

  ArXiv.org · 2026-02-11

  articleOpen accessSenior author

  State-space models (SSMs) offer efficient sequence modeling but lag behind Transformers on benchmarks that require in-context retrieval. Prior work links this gap to a small set of attention heads, termed Gather-and-Aggregate (G&A), which SSMs struggle to reproduce. We propose *retrieval-aware distillation*, which converts a pretrained Transformer into a hybrid student by preserving only these retrieval-critical heads and distilling the rest into recurrent heads. We identify the essential heads via ablation on a synthetic retrieval task, producing a hybrid with sparse, non-uniform attention placement. We show that preserving **just 2% of attention heads recovers over 95% of teacher performance on retrieval-heavy tasks** (10 heads in a 1B model), requiring far fewer heads than hybrids that retain at least 25%. We further find that large recurrent states often compensate for missing retrieval: once retrieval is handled by these heads, the SSM backbone can be simplified with limited loss, even with an $8\times$ reduction in state dimension. By reducing both the attention cache and the SSM state, the resulting hybrid is $5$--$6\times$ more memory-efficient than comparable hybrids, closing the Transformer--SSM gap at a fraction of the memory cost.

  PublisherOA PDF

• Mamba-3: Improved Sequence Modeling using State Space Principles

  arXiv (Cornell University) · 2026-03-16

  articleOpen accessSenior author

  Scaling inference-time compute has emerged as an important driver of LLM performance, making inference efficiency a central focus of model design alongside model quality. While the current Transformer-based models deliver strong model quality, their quadratic compute and linear memory make inference expensive. This has spurred the development of sub-quadratic models with reduced linear compute and constant memory requirements. However, many recent linear models trade off model quality and capability for algorithmic efficiency, failing on tasks such as state tracking. Moreover, their theoretically linear inference remains hardware-inefficient in practice. Guided by an inference-first perspective, we introduce three core methodological improvements inspired by the state space model (SSM) viewpoint of linear models. We combine: (1) a more expressive recurrence derived from SSM discretization, (2) a complex-valued state update rule that enables richer state tracking, and (3) a multi-input, multi-output (MIMO) formulation for better model performance without increasing decode latency. Together with architectural refinements, our Mamba-3 model achieves significant gains across retrieval, state-tracking, and downstream language modeling tasks. At the 1.5B scale, Mamba-3 improves average downstream accuracy by 0.6 percentage points compared to the next best model (Gated DeltaNet), with Mamba-3's MIMO variant further improving accuracy by another 1.2 points for a total 1.8 point gain. Across state-size experiments, Mamba-3 achieves comparable perplexity to Mamba-2 despite using half of its predecessor's state size. Our evaluations demonstrate Mamba-3's ability to advance the performance-efficiency Pareto frontier.

  PublisherOA PDF

• Towards Codec-LM Co-design for Neural Codec Language Models

  2025-01-01 · 2 citations

  articleOpen accessSenior author

  Shih-Lun Wu, Aakash Lahoti, Arjun D Desai, Karan Goel, Chris Donahue, Albert Gu. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 4: Student Research Workshop). 2025.

  PublisherOA PDFDOI

• Llamba: Scaling Distilled Recurrent Models for Efficient Language Processing

  ArXiv.org · 2025-02-20 · 1 citations

  preprintOpen accessSenior author

  We introduce Llamba, a family of efficient recurrent language models distilled from Llama-3.x into the Mamba architecture. The series includes Llamba-1B, Llamba-3B, and Llamba-8B, which achieve higher inference throughput and handle significantly larger batch sizes than Transformer-based models while maintaining comparable benchmark performance. Furthermore, Llamba demonstrates the effectiveness of cross-architecture distillation using MOHAWK (Bick et al., 2024), achieving these results with less than 0.1% of the training data typically used for models of similar size. To take full advantage of their efficiency, we provide an optimized implementation of Llamba for resource-constrained devices such as smartphones and edge platforms, offering a practical and memory-efficient alternative to Transformers. Overall, Llamba improves the tradeoff between speed, memory efficiency, and performance, making high-quality language models more accessible.

  PublisherOA PDFDOI

• Thinking Slow, Fast: Scaling Inference Compute with Distilled Reasoners

  ArXiv.org · 2025-02-27

  preprintOpen access

  Recent advancements have demonstrated that the performance of large language models (LLMs) can be significantly enhanced by scaling computational resources at test time. A common strategy involves generating multiple Chain-of-Thought (CoT) trajectories and aggregating their outputs through various selection mechanisms. This raises a fundamental question: can models with lower complexity leverage their superior generation throughput to outperform similarly sized Transformers for a fixed computational budget? To address this question and overcome the lack of strong subquadratic reasoners, we distill pure and hybrid Mamba models from pretrained Transformers. Trained on only 8 billion tokens, our distilled models show strong performance and scaling on mathematical reasoning datasets while being much faster at inference for large batches and long sequences. Despite the zero-shot performance hit due to distillation, both pure and hybrid Mamba models can scale their coverage and accuracy performance past their Transformer teacher models under fixed time budgets, opening a new direction for scaling inference compute.

  PublisherOA PDFDOI

• HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model

  ArXiv.org · 2025-02-15 · 5 citations

  preprintOpen access

  Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

  PublisherOA PDFDOI

Frequent coauthors

• Christopher Ré

  22 shared

• Atri Rudra

  17 shared

• Tri Dao

  17 shared

• Christopher Ré

  14 shared

• Karan Goel

  Stanford University

  10 shared

• Ines Chami

  5 shared

• Anna Thomas

  Karunya University

  4 shared

• Christopher De

  4 shared

Labs

• Wellness NetworkPI