Protein language models (PLMs) have transferred the latest advances from natural language processing to computational biology. These models, trained on large corpora of protein sequence data, are widely used to translate amino acid sequences into latent-space embeddings, ready for use in diverse downstream tasks (DTs).
arXiv:2608. 12090v1 Announce Type: new Abstract: Protein language models (PLMs) have transferred the latest advances from natural language processing to computational biology.
arXiv:2512. 15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality.
arXiv:2607. 22777v1 Announce Type: cross Abstract: Protein language models learn transferable sequence representations.
arXiv:2608. 06111v1 Announce Type: cross Abstract: Positional embeddings (PE) in Transformers encode token distance and order but are largely agnostic to \textit{syntactic structure}.
arXiv:2512. 10092v2 Announce Type: replace Abstract: Analyzing large-scale text corpora is a core challenge in machine learning, crucial for tasks like identifying undesirable model behaviors or biases in training data.
arXiv:2608. 05980v1 Announce Type: new Abstract: We investigate whether simple transformations can translate representations across heterogeneous text embedding models.
arXiv:2602. 17162v3 Announce Type: replace Abstract: Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature".
arXiv:2606. 27242v1 Announce Type: new Abstract: Training-free source selection for LLM families with shared vocabularies arises in scientific string domains such as SMILES, protein, and genomic sequences, where candidate corpora share a tokenizer but differ in prediction targets.
arXiv:2604. 04287v2 Announce Type: replace Abstract: Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing.
arXiv:2509. 15676v2 Announce Type: replace-cross Abstract: In-context learning (ICL) has emerged as a powerful paradigm for adapting large language models (LLMs) to new and data-scarce tasks using only a few carefully selected task-specific examples presented in the prompt.
Zero-shot learning (ZSL) for inertial measurement unit (IMU)-based human activity recognition (HAR) faces a central challenge: bridging the gap between sensor embeddings and semantic class representations. We systematically evaluate seven configurations combining three inference methods with two training pipelines on the PAMAP2 dataset, using 14 seen and 4 unseen activity classes with subjects 108 and 109 held out for testing.
arXiv:2606. 15521v1 Announce Type: cross Abstract: Tokenization introduces representational redundancy: under a fixed token vocabulary, every byte string admits many valid token encodings, or segmentations, that decode to the same surface string.