arXiv:2607. 19618v1 Announce Type: cross Abstract: Genomic language models achieve strong performance across regulatory-genomics tasks, yet what these models internally represent remains opaque, and the field lacks a principled procedure for verifying that an apparent ``concept'' inside a model is real rather than an artifact of sequence composition.
arXiv:2604. 26866v2 Announce Type: replace-cross Abstract: Large language models (LLMs) acquire most of their factual knowledge during the pre-training stage, through next token prediction.
The study investigates whether unusually high‑gain parameters in transformer models—specifically gated feed‑forward network (gated‑FFN) rows—play a critical functional role across both text and genomic foundation models. By computing exact bilinear weight operators and testing structural extremeness, the authors find that high‑gain rows are enriched for functional importance but do not reliably predict causal effect size or severity. The analysis reveals model‑specific causal organizations, including super‑additive interactions in DNABERT‑2 and position‑localized dependencies in GENERator, indicating that structural prominence signals enrichment rather than calibrated criticality.
The paper introduces IDiom, an autoregressive protein language model trained on a large dataset of intrinsically disordered protein regions (IDRs) from AlphaFold, and demonstrates that it can generate sequences matching natural IDR composition, motifs, and disorder. It further presents RL‑SAE, a reinforcement learning approach that uses sparse autoencoder features to steer generation toward specific functional patterns, achieving high activation of targeted features and improved predicted subcellular localization and transcriptional activity. The combination of IDiom and RL‑SAE allows interpretable, composable IDR design by explicitly controlling function‑associated sequence features.
arXiv:2606. 07607v1 Announce Type: new Abstract: Advances in machine learning and computational power have unlocked the predictive potential of the human genome, yet biologists now demand that these models also elucidate the underlying biological mechanisms.
Neural language models trained on large crowdsourced corpora frequently exploit spurious surface patterns tied to target labels without true linguistic or causal relevance, boosting benchmark performance while failing on adversarial or out-of-distribution inputs. Existing approaches either require manual specification of the feature vocabulary or automate discovery only partially, leaving the gap between dataset-level correlation and model-level exploitation unaddressed.
arXiv:2608. 09209v1 Announce Type: cross Abstract: Neural language models trained on large crowdsourced corpora frequently exploit spurious surface patterns tied to target labels without true linguistic or causal relevance, boosting benchmark performance while failing on adversarial or out-of-distribution inputs.
arXiv:2607. 20596v1 Announce Type: new Abstract: Sparse autoencoder (SAE) features are used to interpret and steer large language models, yet whether a feature's causal role is stable across SAE families remains untested.
The paper introduces Murmur2Vec, a lightweight, alignment‑free embedding that uses k‑mer counts hashed with MurmurHash to create a compact representation for biological sequences. It provides a full theoretical analysis, including bias/variance formulas, a Johnson–Lindenstrauss‑style concentration bound, and an excess‑risk bound that clarifies the trade‑off between hash‑table size and classifier performance. Empirically, Murmur2Vec matches or surpasses a fine‑tuned 650M‑parameter ESM‑2 protein language model across several classification tasks, including SARS‑CoV‑2 spike lineage and HIV‑1 Env subtype identification.
arXiv:2607. 12166v1 Announce Type: new Abstract: Sparse autoencoders (SAEs) are the standard for decomposing superposed neural representations into interpretable features, and evaluation relies predominantly on correlational recovery metrics -- cosine similarity between ground-truth directions and decoder atoms.
arXiv:2606. 17516v1 Announce Type: cross Abstract: Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions.
arXiv:2606. 18383v1 Announce Type: new Abstract: Sparse autoencoders (SAEs) are increasingly used to extract interpretable features from language models (LMs), yet a central question remains: when can an SAE-based explanation be treated as a faithful view of an underlying frozen LM We study this through a post-hoc generalization framework that certifies the LM via a sparse proxy, obtained by replacing a native hidden activation with its pretrained SAE reconstruction.
CellMSA introduces a novel single‑cell representation learning framework that leverages a multiple‑sequence‑alignment‑inspired context model. For each target cell, it retrieves relevant cells across batches and related cell types, summarizing cross‑cell patterns into a context‑dependent gene‑pair representation that is fed into a pair‑aware encoder. Pretraining on a massive human single‑cell corpus (≈109 million cells) and subsequent benchmarks demonstrate consistent performance gains over existing methods.