arXiv subjects

Alkin Kaz

Publications and source records attributed to Alkin Kaz.

3 recordsLinked to original sources

arXiv2026

A meta-algorithm for ab initio reconstruction of complex mixtures in cryo-EM

We describe a systematic approach for spawning and aggregating multi-class cryo-EM reconstruction jobs. This approach formalizes standard ad hoc strategies of iterative classification and filtering typically used by practitioners to sort impure, heterogeneous samples. To our knowledge, this is the first method that can successfully perform ab initio reconstruction on datasets containing dozens of distinct species. We obtain 97% accuracy on ab initio reconstruction of a 45-class subset of Tomotwin-100, 75% accuracy on the full Tomotwin-100 dataset, and demonstrate recovery of ribosomal assembly states from an unfiltered experimental cryo-EM dataset. Our approach's capability scales with compute and lays the foundation for automated cryo-EM workflows in modern experimental settings.

q-bio.BM↗

arXiv2025

Are Robust LLM Fingerprints Adversarially Robust?

Model fingerprinting has emerged as a promising paradigm for claiming model ownership. However, robustness evaluations of these schemes have mostly focused on benign perturbations such as incremental fine-tuning, model merging, and prompting. Lack of systematic investigations into {\em adversarial robustness} against a malicious model host leaves current systems vulnerable. To bridge this gap, we first define a concrete, practical threat model against model fingerprinting. We then take a critical look at existing model fingerprinting schemes to identify their fundamental vulnerabilities. Based on these, we develop adaptive adversarial attacks tailored for each vulnerability, and demonstrate that these can bypass model authentication completely for ten recently proposed fingerprinting schemes while maintaining high utility of the model for the end users. Our work encourages fingerprint designers to adopt adversarial robustness by design. We end with recommendations for future fingerprinting methods.

cs.CR↗

arXiv2024

CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural variability has spurred the development of heterogeneous reconstruction algorithms that can infer distributions of 3D structures from noisy, unlabeled imaging data. Despite the growing number of advanced methods, progress in the field is hindered by the lack of standardized benchmarks with ground truth information and reliable validation metrics. Here, we introduce CryoBench, a suite of datasets, metrics, and benchmarks for heterogeneous reconstruction in cryo-EM. CryoBench includes five datasets representing different sources of heterogeneity and degrees of difficulty. These include conformational heterogeneity generated from designed motions of antibody complexes or sampled from a molecular dynamics simulation, as well as compositional heterogeneity from mixtures of ribosome assembly states or 100 common complexes present in cells. We then analyze state-of-the-art heterogeneous reconstruction tools, including neural and non-neural methods, assess their sensitivity to noise, and propose new metrics for quantitative evaluation. We hope that CryoBench will be a foundational resource for accelerating algorithmic development and evaluation in the cryo-EM and machine learning communities. Project page: https://cryobench.cs.princeton.edu.

cs.CV↗