PLM
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Related Articles from SNS
Polynomial Trajectory Compression for Protein Language Model Embeddings
Protein language models (PLMs) generate rich, layer-wise embeddings that capture diverse biological information but are expensive in terms of storage and computation at scale. In this work, we propose a compact surrogate representation for PLM embeddings across transformer layers using low-dimensional PCA projections and cubic polynomial trajectories. This approach enables efficient storage and on-demand reconstruction of these protein-level embeddings at any layer without rerunning the PLM.
AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design
arXiv:2606.02386v1 Announce Type: new Abstract: Protein language models (PLMs) are passive oracles: they generate sequences in a single forward pass with no mechanism to consult external biophysical feedback or redirect generation when a candidate violates thermodynamic or structural constraints. We introduce AgentPLM, which addresses this by equipping a pre-trained PLM with i) Reasoning-Augmented Decoding (RAD), which interleaves autoregressive generation with tool calls (ESMFold, FoldX,...
Disentangling Similarity and Relatedness in Topic Models
Announce Type: replace Abstract: The recent success of large pre-trained language models (PLMs) has motivated their integration into topic modeling. However, PLM-augmented topic models differ from classical co-occurrence models such as Latent Dirichlet Allocation (LDA) not only in performance, but also in the type of semantic structure they capture. We formalize this distinction along two psycholinguistic axes: thematic relatedness (dog/bone) and taxonomic similarity (dog/wolf).
Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators
Announce Type: replace-cross Abstract: Molecular dynamics (MD) is a central computational tool in physics, chemistry, and biology, enabling quantitative prediction of experimental observables as expectations over high-dimensional molecular distributions such as Boltzmann distributions and transition densities. However, conventional MD is fundamentally limited by the high computational cost required to generate independent samples. Generative molecular dynamics (GenMD) has recently emerged as...
Bridging the Gap: Transfer Learning from English PLMs to Malaysian English
arXiv:2407.01374v2 Announce Type: replace Abstract: Malaysian English is a low resource creole language, where it carries the elements of Malay, Chinese, and Tamil languages, in addition to Standard English. Named Entity Recognition (NER) models underperform when capturing entities from Malaysian English text due to its distinctive morphosyntactic adaptations, semantic features and code-switching (mixing English and Malay). Considering these gaps, we introduce MENmBERT and MENBERT, a...
Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators
Announce Type: replace Abstract: Molecular dynamics (MD) is a central computational tool in physics, chemistry, and biology, enabling quantitative prediction of experimental observables as expectations over high-dimensional molecular distributions such as Boltzmann distributions and transition densities. However, conventional MD is fundamentally limited by the high computational cost required to generate independent samples. Generative molecular dynamics (GenMD) has recently emerged as an...