The evolution of biological sequences, such as proteins or DNAs, is driven by the three basic edit operations: substitution, insertion, and deletion. Motivated by the recent progress of neural network models for biological tasks, we implement two neural network architectures that can treat such edit operations. The first proposal is the edit invariant neural networks, based on differentiable Needleman-Wunsch algorithms. The second is the use of deep CNNs with concatenations. Our analysis shows that CNNs can recognize star-free regular expressions, and that deeper CNNs can recognize more complex regular expressions including the insertion/deletion of characters. The experimental results for the protein secondary structure prediction task suggest the importance of insertion/deletion. The test accuracy on the widely-used CB513 dataset is 71.5%, which is 1.2-points better than the current best result on non-ensemble models.

We design a system that learns how to edit visual programs. Our edit network consumes a complete input program and a visual target. From this input, we task our network with predicting a local edit operation that could be applied to the input program to improve its similarity to the target.

Computing such neural set divergence require aligning nodes and edges of the two graphs.

Graph Edit Distance (GED) measures the (dis-)similarity between two given graphs in terms of the minimum-cost edit sequence, which transforms one graph to the other.GED is related to other notions of graph similarity, such as graph and subgraph isomorphism, maximum common subgraph, etc. However, the computation of exact GED is NP-Hard, which has recently motivated the design of neural models for GED estimation.However, they do not explicitly account for edit operations with different costs. In response, we propose $\texttt{GraphEdX}$, a neural GED estimator that can work with general costs specified for the four edit operations, viz., edge deletion, edge addition, node deletion, and node addition.We first present GED as a quadratic assignment problem (QAP) that incorporates these four costs.Then, we represent each graph as a set of node and edge embeddings and use them to design a family of neural set divergence surrogates. We replace the QAP terms corresponding to each operation with their surrogates. Computing such neural set divergence requires aligning nodes and edges of the two graphs.We learn these alignments using a Gumbel-Sinkhorn permutation generator, additionally ensuring that the node and edge alignments are consistent with each other. Moreover, these alignments are cognizant of both the presence and absence of edges between node pairs.Through extensive experiments on several datasets, along with a variety of edit cost settings, we show that $\texttt{GraphEdX}$ consistently outperforms state-of-the-art methods and heuristics in terms of prediction error.

Autoregressive generative models naturally generate variable-length sequences, while non-autoregressive models struggle, often imposing rigid, token-wise structures. We propose Edit Flows, a non-autoregressive model that overcomes these limitations by defining a discrete flow over sequences through edit operations$\unicode{x2013}$insertions, deletions, and substitutions. By modeling these operations within a Continuous-time Markov Chain over the sequence space, Edit Flows enable flexible, position-relative generation that aligns more closely with the structure of sequence data. Our training method leverages an expanded state space with auxiliary variables, making the learning process efficient and tractable. Empirical results show that Edit Flows outperforms both autoregressive and mask models on image captioning and significantly outperforms the mask construction in text and code generation.

We design a system that learns how to edit visual programs. Our edit network consumes a complete input program and a visual target. From this input, we task our network with predicting a local edit operation that could be applied to the input program to improve its similarity to the target.

Temporal point processes (TPPs) are a fundamental tool for modeling event sequences in continuous time, but most existing approaches rely on autoregressive parameterizations that are limited by their sequential sampling. Recent non-autoregressive, diffusion-style models mitigate these issues by jointly interpolating between noise and data through event insertions and deletions in a discrete Markov chain. In this work, we generalize this perspective and introduce an Edit Flow process for TPPs that transports noise to data via insert, delete, and substitute edit operations. By learning the instantaneous edit rates within a continuous-time Markov chain framework, we attain a flexible and efficient model that effectively reduces the total number of necessary edit operations during generation. Empirical results demonstrate the generative flexibility of our unconditionally trained model in a wide range of unconditional and conditional generation tasks on benchmark TPPs.

Prompt engineering has proven to be a crucial step in leveraging pretrained large language models (LLMs) in solving various real-world tasks. Numerous solutions have been proposed that seek to automate prompt engineering by using the model itself to edit prompts. However, the majority of state-of-the-art approaches are evaluated on tasks that require minimal prompt templates and on very large and highly capable LLMs. In contrast, solving complex tasks that require detailed information to be included in the prompt increases the amount of text that needs to be optimised. Furthermore, smaller models have been shown to be more sensitive to prompt design. To address these challenges, we propose an evolutionary search approach to automated discrete prompt optimisation consisting of two phases. In the first phase, grammar-guided genetic programming is invoked to synthesise prompt-creating programmes by searching the space of programmes populated by function compositions of syntactic, dictionary-based and LLM-based prompt-editing functions. In the second phase, local search is applied to explore the neighbourhoods of best-performing programmes in an attempt to further fine-tune their performance. Our approach outperforms three state-of-the-art prompt optimisation approaches, PromptWizard, OPRO, and RL-Prompt, on three relatively small general-purpose LLMs in four domain-specific challenging tasks. We also illustrate several examples where these benchmark methods suffer relatively severe performance degradation, while our approach improves performance in almost all task-model combinations, only incurring minimal degradation when it does not.

Graph Edit Distance (GED) measures the (dis-)similarity between two given graphs in terms of the minimum-cost edit sequence, which transforms one graph to the other.GED is related to other notions of graph similarity, such as graph and subgraph isomorphism, maximum common subgraph, etc. However, the computation of exact GED is NP-Hard, which has recently motivated the design of neural models for GED estimation.However, they do not explicitly account for edit operations with different costs. In response, we propose \texttt{GraphEdX}, a neural GED estimator that can work with general costs specified for the four edit operations, viz., edge deletion, edge addition, node deletion, and node addition.We first present GED as a quadratic assignment problem (QAP) that incorporates these four costs.Then, we represent each graph as a set of node and edge embeddings and use them to design a family of neural set divergence surrogates. We replace the QAP terms corresponding to each operation with their surrogates. Computing such neural set divergence requires aligning nodes and edges of the two graphs.We learn these alignments using a Gumbel-Sinkhorn permutation generator, additionally ensuring that the node and edge alignments are consistent with each other. Moreover, these alignments are cognizant of both the presence and absence of edges between node pairs.Through extensive experiments on several datasets, along with a variety of edit cost settings, we show that \texttt{GraphEdX} consistently outperforms state-of-the-art methods and heuristics in terms of prediction error.