When do cheap embeddings beat protein language models? A theoretically-grounded hashing sketch for biological sequence classification
Updated 5 h ago · first seen 11 Sept 2026
paper_01M294FRWR7A08EN1ET44KTK8R
- Published
- 11 Sept 2026
- T1 · 5 h ago
- arXiv
- 2512.10147
- T1 · 5 h ago
- Category
- cs.LG
- T1 · 5 h ago
Abstract
\textbf{Motivation:} Pre-trained protein language models (PLMs) such as ESM-2 have become the default representation for biological sequence tasks, but they are computationally heavy and require GPUs both for embedding and for fine-tuning. Whether they are actually necessary for sequence \emph{classification}, as opposed to structure prediction, is rarely tested against strong, principled, lightweight alternatives. This question has direct practical stakes for large-scale genomic surveillance, where embedding millions of sequences on commodity hardware is a recurring bottleneck.\\ \textbf{Results:} We introduce Murmur2Vec, an alignment-free, training-free embedding that aggregates $k$-mer counts into a small hash table via the deterministic MurmurHash function, and we cast it as a randomized sketch of the classical $k$-mer spectrum kernel. We provide a complete theoretical treatment: closed-form bias/variance of the inner product, an unbiased signed variant with a Johnson--Lindenstrauss-type concentration bound, an excess-risk bound for downstream linear classifiers that makes the bias--variance trade-off in the hash-table size explicit, and an implicit-regularization mechanism by which collisions damage frequent non-discriminative $k$-mers more than rare lineage-defining ones. Across four classification tasks, SARS-CoV-2 spike lineage (22 classes), HIV-1 Env subtype (8 classes), and two protein-family benchmarks (8 and 6 classes), Murmur2Vec matches a LoRA-fine-tuned 650M-parameter ESM-2 model on the two tasks for which LoRA fine-tuning was run to convergence (SARS-CoV-2 and HIV-1) and ties frozen ESM-2 on the two protein-family tasks, and it \emph{outperforms} the fine-tuned model on the hardest task (SARS-CoV-2 lineage: $0.854$ vs.\ $0.807$ accuracy; macro-F1 $0.684$ vs.\ $0.401$).
Authors 4
Sarwan Ali, Taslim Murad, Imdadullah Khan, Safi Faizullah
Specification
- Official page
Source:arXiv (Atom API + RSS)T1observed 5 h agohigh
- Arxiv announce type
- replace
Source:arXiv (Atom API + RSS)T1observed 5 h agohigh
- arXiv id
- 2512.10147
Source:arXiv (Atom API + RSS)T1observed 5 h agohigh
- Categories
- cs.LG, q-bio.GN
Source:arXiv (Atom API + RSS)T1observed 5 h agohigh
Source:arXiv (Atom API + RSS)T1observed 5 h agohigh
- Primary category
- cs.LG
Source:arXiv (Atom API + RSS)T1observed 5 h agohigh
- Published
- 11 Sept 2026
Source:arXiv (Atom API + RSS)T1observed 5 h agohigh
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T19
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5 h ago
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- Authors
- Sarwan Ali, Taslim Murad, Imdadullah Khan
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Claim history · Abstract
Abstractabstract1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| \textbf{Motivation:} Pre-trained protein language models (PLMs) such as ESM-2 have become the default representation for biological sequence tasks, but they are computationally heavy and require GPUs both for embedding and for fine-tuning. Whether they are actually necessary for sequence \emph{classification}, as opposed to structure prediction, is rarely tested against strong, principled, lightweight alternatives. This question has direct practical stakes for large-scale genomic surveillance, where embedding millions of sequences on commodity hardware is a recurring bottleneck.\\ \textbf{Results:} We introduce Murmur2Vec, an alignment-free, training-free embedding that aggregates $k$-mer counts into a small hash table via the deterministic MurmurHash function, and we cast it as a randomized sketch of the classical $k$-mer spectrum kernel. We provide a complete theoretical treatment: closed-form bias/variance of the inner product, an unbiased signed variant with a Johnson--Lindenstrauss-type concentration bound, an excess-risk bound for downstream linear classifiers that makes the bias--variance trade-off in the hash-table size explicit, and an implicit-regularization mechanism by which collisions damage frequent non-discriminative $k$-mers more than rare lineage-defining ones. Across four classification tasks, SARS-CoV-2 spike lineage (22 classes), HIV-1 Env subtype (8 classes), and two protein-family benchmarks (8 and 6 classes), Murmur2Vec matches a LoRA-fine-tuned 650M-parameter ESM-2 model on the two tasks for which LoRA fine-tuning was run to convergence (SARS-CoV-2 and HIV-1) and ties frozen ESM-2 on the two protein-family tasks, and it \emph{outperforms} the fine-tuned model on the hardest task (SARS-CoV-2 lineage: $0.854$ vs.\ $0.807$ accuracy; macro-F1 $0.684$ vs.\ $0.401$). | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Claims are temporal and append-only: a new observation closes the previous claim (valid_to) instead of overwriting it. Conflicting claims from different sources are kept side by side and flagged — never averaged. Methodology →
New paper: When do cheap embeddings beat protein language models? A theoretically-grounded hashing sketch for biological sequence classification
arxiv
| Source | Document | Type | Tier | Last observed | Snapshots |
|---|---|---|---|---|---|
| arXiv (Atom API + RSS) | rss.arxiv.org/rss/cs.LG | feed | T1· Official | 3 h ago | 1 |
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