arXiv subjects

Constance Ferragu

Publications and source records attributed to Constance Ferragu.

3 recordsLinked to original sources

arXiv2026

EvoFlows: Evolutionary Edit-Based Flow-Matching for Protein Engineering

We introduce EvoFlows, a variable-length protein sequence-to-sequence modeling approach designed for protein engineering. Existing protein language models are poorly suited for optimization tasks: autoregressive models require full sequence generation, masked language and discrete diffusion models rely on pre-specified mutation locations, and no existing methods naturally support insertions and deletions relative to a template sequence. EvoFlows learns mutational trajectories between evolutionarily related protein sequences via edit flows, allowing it to perform a controllable number of mutations (insertions, deletions, and substitutions) on a template sequence, predicting not only _which_ mutation to perform, but also _where_ it should occur. Through extensive _in silico_ evaluation on diverse protein families from UniRef and OAS, we show that EvoFlows generates variants that remain consistent with natural protein families while exploring farther from template sequences than leading baselines.

cs.LG↗

arXiv2025

g-DPO: Scalable Preference Optimization for Protein Language Models

Direct Preference Optimization (DPO) is an effective approach for aligning protein language models with experimental design goals. However, DPO faces a scalability bottleneck: the number of possible training pairs grows quadratically with the number of labeled sequences, leading to prohibitive training times even for modestly sized datasets. We introduce g-DPO, a framework that (i) uses sequence space clustering to prune redundant pairs while preserving training signal, and (ii) amortizes likelihood computations with group-based approximations. Across three protein engineering tasks, g-DPO maintains in silico and in vitro performance that is statistically indistinguishable from standard DPO, while converging 1.7x to 5.4x times faster, with speedups that scale with dataset size and the structure of the underlying mutational landscape.

cs.LG↗

arXiv2024

Multimodal CLIP Inference for Meta-Few-Shot Image Classification

In recent literature, few-shot classification has predominantly been defined by the N-way k-shot meta-learning problem. Models designed for this purpose are usually trained to excel on standard benchmarks following a restricted setup, excluding the use of external data. Given the recent advancements in large language and vision models, a question naturally arises: can these models directly perform well on meta-few-shot learning benchmarks? Multimodal foundation models like CLIP, which learn a joint (image, text) embedding, are of particular interest. Indeed, multimodal training has proven to enhance model robustness, especially regarding ambiguities, a limitation frequently observed in the few-shot setup. This study demonstrates that combining modalities from CLIP's text and image encoders outperforms state-of-the-art meta-few-shot learners on widely adopted benchmarks, all without additional training. Our results confirm the potential and robustness of multimodal foundation models like CLIP and serve as a baseline for existing and future approaches leveraging such models.

cs.CV↗