arXiv Machine Learning

VESTIGE: A Knowledge-Guided Masking Strategy for Corruption-Aware Fine-Tuning of Genomic Transformers, Validated on Ancient DNA Reconstruction

arXiv:2607. 27712v1 Announce Type: new Abstract: Standard masked-language-model fine-tuning applies a uniform masking probability across every token position, assuming reconstruction difficulty is position-agnostic.

arXiv AI

Jun 19

Calibration Without Comprehension: Diagnosing the Limits of Fine-Tuning LLMs for Vulnerability Detection in Systems Software

arXiv:2606. 20502v1 Announce Type: cross Abstract: Whether LLMs scoring well on vulnerability benchmarks genuinely reason about security or merely pattern-match on contaminated data remains unresolved.

By Arastoo Zibaeirad, Marco Vieira

llms fine-tuning benchmarks

arXiv AI

Aug 5

Making Single-Cell Data Distillation Auditable: Traceable Real-Cell Coresets via Discrete Min--Max Selection

arXiv:2607. 19426v2 Announce Type: replace-cross Abstract: Large single-cell datasets are expensive to store, curate, and repeatedly reuse for model training.

By Yaodi Luo, Peize He, Lingbei Meng, Bowen Han, Zheng Lu, Jianqing Zhu, Lian Zhang

rag efficiency benchmarks

arXiv AI

Jul 23

Making Single-Cell Data Distillation Auditable: Traceable Real-Cell Coresets via Discrete Min-Max Selection

arXiv:2607. 19426v1 Announce Type: cross Abstract: Single-cell datasets are increasingly costly to store, audit, and reuse for model training.

By Yaodi Luo, Peize He, Bowen Han, Lingbei Mengg

efficiency

arXiv Machine Learning

Jul 16

Screening of Biosecurity Features in Metagenomic Data with Evo 2 Probes

arXiv:2607. 14070v1 Announce Type: cross Abstract: Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored.

By Jeremy Guntoro, Alexander Dack, Dylan Danno, Michaela Jan\v{c}ovi\v{c}ov\'a, Kri\v{z}an Jurinovi\'c, Vanessa Smilansky

rag fine-tuning

arXiv AI

Jun 10

Alignment Collapse Under KV Cache Quantization: Diagnosis and Mitigation

arXiv:2606. 09864v1 Announce Type: cross Abstract: Key-value (KV) cache quantization is widely used to reduce Large Language Model (LLM) inference memory, yet existing evaluations solely focus on measuring perplexity and accuracy without assessing the safety impact.

By Bruce Changlong Xu, Adarsh Kumarappan, Mu Zhou

llms efficiency benchmarks safety

arXiv Machine Learning

Jun 9

Scaling Laws for Masked-Reconstruction Transformers on Single-Cell Transcriptomics

arXiv:2602. 15253v2 Announce Type: replace Abstract: Neural scaling laws -- power-law relationships between loss, model size, and data -- have been extensively documented for language and vision transformers, yet their existence in single-cell genomics remains largely unexplored.

By Ihor Kendiukhov

llms nlp

arXiv AI

Jun 16

CRC-Screen: Certified DNA-Synthesis Hazard Screening Under Taxonomic Shift

arXiv:2605. 00074v2 Announce Type: replace-cross Abstract: DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists.

By Najmul Hasan

llms rag

arXiv Machine Learning

Jun 3

Reading the Finetuning Prior: Verbatim Content Recovery via Contrastive Decoding Diffing

arXiv:2605. 25902v2 Announce Type: replace Abstract: Narrowly finetuned language models memorize implanted content verbatim, but auditing what a deployed model has been taught, without access to its weights or training data, remains an open challenge.

By Micha{\l} Brzozowski, Zuzanna Dubanowska, Enrico Cassano, Neo Christopher Chung

llms fine-tuning benchmarks data-engineering

arXiv AI

Aug 5

MalariAI: A Label-Resilient Decoupled Framework for Annotation-Agnostic Cell Segmentation and Explainable Stage Classification in Dense Malaria Blood Smears

arXiv:2607. 00385v2 Announce Type: replace-cross Abstract: Automated malaria diagnosis from blood smear microscopy is a critical global health AI challenge; expert scarcity remains the primary diagnostic bottleneck.

By Kaysarul Anas Apurba, Md Hasibul Hasan, Mohammed Ali, Tanzilur Rahman

computer-vision

arXiv Machine Learning

Jul 28

MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model

arXiv:2607. 23607v1 Announce Type: new Abstract: Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry.

By Xin Zhao, Yumin Liu, Zhuo Li, Weichu Zheng, Feng Zhu, Xiaokang Yang, Yaohui Jin, Yanyan Xu

llms fine-tuning safety

arXiv AI

Aug 5

Surrogate Substitution Preserves PHI Detectability: A Multi-Detector Equivalence Study

arXiv:2608. 03172v1 Announce Type: new Abstract: Structure-preserving de-identification replaces protected health information (PHI) with realistic same-type surrogates -- "Anna S.

By Qiming Bao, Sherry J. H. Feng, Kim Chester Eugenio, Meng Fon

benchmarks

arXiv Machine Learning

Jul 21

GeneSpeak-FP: Target and Compound Retrieval from Observed Cell-Level Perturbation Signatures

arXiv:2607. 17671v1 Announce Type: new Abstract: Large-scale single-cell perturbation atlases make it possible to ask an inverse question: given an observed transcriptional response, which annotated targets and compounds in a fixed library are most consistent with that response?

By Kseniia Vaniushkina, Jeongmin Lim, Jinyong Park

llms rag safety

Related stories