When Edit Flows are Edit Jumps: replicating Edit Flows and EvoFlows
Authors: Gabriel Bénédict, Melanie Buechler, Gerard Riera-Solà, Chloé de Ancos, Yves Gaetan Nana Teukam, Moritz Freidank
Abstract
Antibody lead optimization calls for a small, bounded set of edits to an existing candidate: substitutions, but also insertions and deletions. Edit-based generative models are the only ones that allocate such an edit budget without fixing the edit positions, the edit count, or the output length in advance. However, the existing approaches Edit Flows and EvoFlows did not release code or complete training specifications. Here, we show that both methods follow the same underlying process -- edits firing one at a time, at learned rates, in continuous time -- the pure-jump case of generator matching over finite sequences. With EditJumps we introduce the first open implementation of this framework, with a single generalist antibody editor trained on 1.66M Observed Antibody Space homolog pairs to propose homolog-like variants of a seed sequence, editing unseen leads zero-shot, without the per-family retraining original approaches require. Replicating this system from scratch exposes why open code is essential for generative biology: reconciling published edit distributions required reverse-engineering an undocumented rate-scaling hyperparameter that dictates realized mutation counts. Moreover, we show that published evaluation metrics are highly sensitive to reference sample size, frequently flipping method rankings. We release our full codebase, automated test suite, and configurations at: https://github.com/VisiumCH/editjumps
Data editing with generative methods typically requires differentiable objectives and gradient-based search. However, these assumptions break down in flow-based settings, where edits are performed through forward and backward integration and often involve non-differentiable or black-box objectives. We introduce residual-space evolutionary optimization, a model-agnostic framework that addresses this gap by combining flow-based generative editing with evolutionary algorithms. Building on the observation that conditional flow matching (CFM) can disentangle condition-controlled factors from instance-specific residuals, our framework directly operates in residual space and separates two complementary search regimes: self-pollination performs local exploitation through feature-preserving residual refinement, and cross-pollination promotes broader exploration by recombining residuals across heterogeneous samples. As a proof of concept, we validate on MorphoMNIST, a benchmark dataset for counterfactual generation, and on crystal data, demonstrating that this exploration--exploitation decomposition provides a useful mechanism for balancing target alignment, instance preservation, and diversity, and extends beyond images to real-world scientific domains.
Designing functional biological sequences requires navigating vast discrete spaces under strict evolutionary and biophysical constraints. Discrete Flow Matching (DFM) offers a generative framework over such spaces, but existing approaches rely on biologically uninformative couplings and offer limited flexibility for variable-length sequence generation and fine-grained control. We propose a structured coupling that encodes domain-specific preferences among sequence elements, biasing the source distribution toward plausible regions without modifying the flow objective or training procedure. Building on this, we introduce a latent edit-based rate parameterization that models variable-length generation via edit operations conditioned on a shared global latent, akin to a latent variable model, while remaining tractable. We further introduce a latent classifier-free guidance mechanism that steers generation coherently in continuous latent space, along with Dirichlet-prior temperature scaling for test-time control over edit operations. Our method achieves state-of-the-art performance across diverse biological sequence tasks, including density estimation, unconditional and conditional DNA sequence generation, and peptide sequence generation.
We study the application of recent Edit Flows for inference-time reward control for DNA sequence generation. Unlike most reward-guided DNA generation frameworks, which operate on fixed-length sequence spaces, Edit Flows have a potential to generate variable-length DNA through biologically plausible insertion, deletion, and substitution operations. In particular, we propose Local Perturbation Discrete Programming (LPDP), a training-free, intermediate-state and action-aware local re-solving operator for variable-length DNA edit-action generators at inference time. More specifically, at each guided rollout step, LPDP scores one-step root edits, retains a near-best root band, and re-ranks each retained root by solving a bounded local discrete program around its child sequence. This local program uses the typed geometry of edit actions to focus on coherent substitution, insertion, or deletion subgraphs, and aggregates local continuations with either a hard Max backup or a soft log-sum-exponential (LSE) backup. We instantiate LPDP in two regimes: front-loaded reward tilting for enhancer optimization, where early edits are critical for establishing global regulatory sequence structure, and back-loaded reward tilting for exon-intron-exon inpainting, where late edits fine-tune splice-boundary contexts.