The paper introduces EditJumps, the first open implementation of the Edit Flows and EvoFlows framework for antibody lead optimization. EditJumps trains a single generalist antibody editor on 1.66 M homolog pairs to generate homolog‑like variants of a seed sequence, enabling zero‑shot editing of unseen leads without per‑family retraining. The authors demonstrate that both Edit Flows and EvoFlows operate by sequentially applying edits at learned rates in continuous time, and they highlight the importance of open code for reproducing generative biology results, noting that published evaluation metrics can be highly sensitive to reference sample size.
arXiv:2609.01409v1 Announce Type: new Abstract: Vision-language models (VLMs) have shown strong performance in generating scientific figures from text or images. However, producing publication-ready...
AutoIndexer is a generative model that trains causal models on chains of edits, enabling flexible post‑generation modifications such as token insertions, substitutions, and deletions. It introduces marker tokens for opening and closing edits and moves a cursor through the token sequence, mimicking a text editor. By perturbing ground‑truth labels with inverse edit operations during training, AutoIndexer becomes robust to erroneous context and can perform editing tasks like code correction while maintaining performance on standard LLM benchmarks.
arXiv:2607. 28947v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly used to solve complex problems by searching over program space, offering a general paradigm for scientific problems that can be naturally represented and solved as programs.
The paper compares two output regimes for code-editing language models: direct generation, where the model outputs the entire modified file, and iterative diff-based generation, where the model emits a sequence of localized edits. Experiments on Flutter/Dart tasks show that direct generation consistently outperforms diff-based generation across metrics such as compilation success, token efficiency, and quality judgments. However, diff-based generation can be competitive for short, spatially localized edits, particularly in refactoring and error-handling tasks with few edit steps.
arXiv:2511. 05852v4 Announce Type: replace-cross Abstract: Knowledge editing (KE) offers a lightweight alternative to retraining for updating large language models (LLMs).
The paper investigates the problem of over‑editing by large language models when repairing code, showing that even state‑of‑the‑art models like GPT‑5.5 frequently rewrite more code than necessary. Using a benchmark of 400 BigCodeBench problems with controlled AST corruptions, the authors quantify excess edits and demonstrate that a simple preservation instruction can reduce unnecessary changes and improve pass rates. They further explore training strategies, finding that reinforcement learning yields the best balance between edit fidelity and performance retention, highlighting edit fidelity as a distinct, measurable dimension of code‑repair quality.
The paper investigates how tokenization can undermine post‑release guarantees that sensitive knowledge has been edited or unlearned from open‑weight large language models. By showing that alternative valid tokenizations can bypass localized modifications, the authors introduce Toketive, a reference‑free attack that detects modified knowledge and reconstructs pre‑edit responses using only the released model. Experiments on five LLMs, six datasets, and six editing techniques reveal that 38.6% of alternative tokenizations recover suppressed information, with Toketive achieving high detection and reconstruction accuracy.
arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.
arXiv:2607. 25130v1 Announce Type: cross Abstract: Imperfections in AI-generated code require that software developers modify the generated code manually, or by re-prompting an AI programming assistant.
arXiv:2609.38510v1 Announce Type: new Abstract: Speculative decoding accelerates autoregressive LLMs by having a lightweight drafter propose tokens that the target model verifies in parallel. Diffusi...
The paper investigates the problem of over‑editing by large language models (LLMs) when repairing code, showing that even state‑of‑the‑art models like GPT‑5.5 often rewrite more code than necessary. Using a benchmark of 400 BigCodeBench problems with controlled AST‑level corruptions, the authors quantify over‑editing and demonstrate that a simple preservation instruction can significantly reduce excess edits and cognitive complexity while improving Pass@1. They further explore post‑training strategies, finding that reinforcement learning yields the best balance between edit fidelity and performance retention, thereby establishing edit fidelity as a distinct, measurable dimension of code‑repair quality.
arXiv:2607. 20433v1 Announce Type: cross Abstract: While language models remain frozen at their training state, the world evolves continuously.