Daily Papers

Efficient computation or approximation of Levenshtein distance, a widely-used metric for evaluating sequence similarity, has attracted significant attention with the emergence of DNA storage and other biological applications. Sequence embedding, which maps Levenshtein distance to a conventional distance between embedding vectors, has emerged as a promising solution. In this paper, a novel neural network-based sequence embedding technique using Poisson regression is proposed. We first provide a theoretical analysis of the impact of embedding dimension on model performance and present a criterion for selecting an appropriate embedding dimension. Under this embedding dimension, the Poisson regression is introduced by assuming the Levenshtein distance between sequences of fixed length following a Poisson distribution, which naturally aligns with the definition of Levenshtein distance. Moreover, from the perspective of the distribution of embedding distances, Poisson regression approximates the negative log likelihood of the chi-squared distribution and offers advancements in removing the skewness. Through comprehensive experiments on real DNA storage data, we demonstrate the superior performance of the proposed method compared to state-of-the-art approaches.

Storing information in DNA molecules is of great interest because of its advantages in longevity, high storage density, and low maintenance cost. A key step in the DNA storage pipeline is to efficiently cluster the retrieved DNA sequences according to their similarities. Levenshtein distance is the most suitable metric on the similarity between two DNA sequences, but it is inferior in terms of computational complexity and less compatible with mature clustering algorithms. In this work, we propose a novel deep squared Euclidean embedding for DNA sequences using Siamese neural network, squared Euclidean embedding, and chi-squared regression. The Levenshtein distance is approximated by the squared Euclidean distance between the embedding vectors, which is fast calculated and clustering algorithm friendly. The proposed approach is analyzed theoretically and experimentally. The results show that the proposed embedding is efficient and robust.

Animal vocalizations contain sequential structures that carry important communicative information, yet most computational bioacoustics studies average the extracted frame-level features across the temporal axis, discarding the order of the sub-units within a vocalization. This paper investigates whether discrete acoustic token sequences, derived through vector quantization and gumbel-softmax vector quantization of extracted self-supervised speech model representations can effectively capture and leverage temporal information. To that end, pairwise distance analysis of token sequences generated from HuBERT embeddings shows that they can discriminate call-types and callers across four bioacoustics datasets. Sequence classification experiments using k-Nearest Neighbour with Levenshtein distance show that the vector-quantized token sequences yield reasonable call-type and caller classification performances, and hold promise as alternative feature representations towards leveraging sequential information in animal vocalizations.

Motivation: The activity of the adaptive immune system is governed by T-cells and their specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent advances in experimental techniques have enabled sequencing of TCRs and their antigenic targets (epitopes), allowing to research the missing link between TCR sequence and epitope binding specificity. Scarcity of data and a large sequence space make this task challenging, and to date only models limited to a small set of epitopes have achieved good performance. Here, we establish a k-nearest-neighbor (K-NN) classifier as a strong baseline and then propose TITAN (Tcr epITope bimodal Attention Networks), a bimodal neural network that explicitly encodes both TCR sequences and epitopes to enable the independent study of generalization capabilities to unseen TCRs and/or epitopes. Results: By encoding epitopes at the atomic level with SMILES sequences, we leverage transfer learning and data augmentation to enrich the input data space and boost performance. TITAN achieves high performance in the prediction of specificity of unseen TCRs (ROC-AUC 0.87 in 10-fold CV) and surpasses the results of the current state-of-the-art (ImRex) by a large margin. Notably, our Levenshtein-distance-based K-NN classifier also exhibits competitive performance on unseen TCRs. While the generalization to unseen epitopes remains challenging, we report two major breakthroughs. First, by dissecting the attention heatmaps, we demonstrate that the sparsity of available epitope data favors an implicit treatment of epitopes as classes. This may be a general problem that limits unseen epitope performance for sufficiently complex models. Second, we show that TITAN nevertheless exhibits significantly improved performance on unseen epitopes and is capable of focusing attention on chemically meaningful molecular structures.

Textual overlays are often used in social media videos as people who watch them without the sound would otherwise miss essential information conveyed in the audio stream. This is why extraction of those overlays can serve as an important meta-data source, e.g. for content classification or retrieval tasks. In this work, we present a robust method for extracting textual overlays from videos that builds up on multiple neural network architectures. The proposed solution relies on several processing steps: keyframe extraction, text detection and text recognition. The main component of our system, i.e. the text recognition module, is inspired by a convolutional recurrent neural network architecture and we improve its performance using synthetically generated dataset of over 600,000 images with text prepared by authors specifically for this task. We also develop a filtering method that reduces the amount of overlapping text phrases using Levenshtein distance and further boosts system's performance. The final accuracy of our solution reaches over 80A% and is au pair with state-of-the-art methods.

Object Recognition and Document Skew Estimation have come a long way in terms of performance and efficiency. New models follow one of two directions: improving performance using larger models, and improving efficiency using smaller models. However, real-time document detection and rectification is a niche that is largely unexplored by the literature, yet it remains a vital step for automatic information retrieval from visual documents. In this work, we strive towards an efficient document detection pipeline that is satisfactory in terms of Optical Character Recognition (OCR) retrieval and faster than other available solutions. We adapt IWPOD-Net, a license plate detection network, and train it for detection on NBID, a synthetic ID card dataset. We experiment with data augmentation and cross-dataset validation with MIDV (another synthetic ID and passport document dataset) to find the optimal scenario for the model. Other methods from both the Object Recognition and Skew Estimation state-of-the-art are evaluated for comparison with our approach. We use each method to detect and rectify the document, which is then read by an OCR system. The OCR output is then evaluated using a novel OCR quality metric based on the Levenshtein distance. Since the end goal is to improve automatic information retrieval, we use the overall OCR quality as a performance metric. We observe that with a promising model, document rectification does not have to be perfect to attain state-of-the-art performance scores. We show that our model is smaller and more efficient than current state-of-the-art solutions while retaining a competitive OCR quality metric. All code is available at https://github.com/BOVIFOCR/iwpod-doc-corners.git

Recent advances in persona-centric memory have revealed the powerful capability of multi-agent systems in managing persona memory, especially in conversational scenarios. However, these complex frameworks often suffer from information loss and are fragile across varying scenarios, resulting in suboptimal performance. In this paper, we propose DeltaMem, an agentic memory management system that formulates persona-centric memory management as an end-to-end task within a single-agent setting. To further improve the performance of our agentic memory manager, we draw inspiration from the evolution of human memory and synthesize a user-assistant dialogue dataset along with corresponding operation-level memory updating labels. Building on this, we introduce a novel Memory-based Levenshtein Distance to formalize the memory updating reward, and propose a tailored reinforcement learning framework to further enhance the management capabilities of DeltaMem. Extensive experiments show that both training-free and RL-trained DeltaMem outperform all product-level baselines across diverse long-term memory benchmarks, including LoCoMo, HaluMem, and PersonaMem.

Turning static slides into engaging video lectures takes considerable time and effort, requiring presenters to record explanations and visually guide their audience through the material. We introduce an end-to-end system designed to automate this process entirely. Given a slide deck, this system synthesizes a video lecture featuring AI-generated narration synchronized precisely with dynamic visual highlights. These highlights automatically draw attention to the specific concept being discussed, much like an effective presenter would. The core technical contribution is a novel highlight alignment module. This module accurately maps spoken phrases to locations on a given slide using diverse strategies (e.g., Levenshtein distance, LLM-based semantic analysis) at selectable granularities (line or word level) and utilizes timestamp-providing Text-to-Speech (TTS) for timing synchronization. We demonstrate the system's effectiveness through a technical evaluation using a manually annotated slide dataset with 1000 samples, finding that LLM-based alignment achieves high location accuracy (F1 > 92%), significantly outperforming simpler methods, especially on complex, math-heavy content. Furthermore, the calculated generation cost averages under $1 per hour of video, offering potential savings of two orders of magnitude compared to conservative estimates of manual production costs. This combination of high accuracy and extremely low cost positions this approach as a practical and scalable tool for transforming static slides into effective, visually-guided video lectures.

This paper presents a spell checker and correction tool specifically designed for Wolof, an under-represented spoken language in Africa. The proposed spell checker leverages a combination of a trie data structure, dynamic programming, and the weighted Levenshtein distance to generate suggestions for misspelled words. We created novel linguistic resources for Wolof, such as a lexicon and a corpus of misspelled words, using a semi-automatic approach that combines manual and automatic annotation methods. Despite the limited data available for the Wolof language, the spell checker's performance showed a predictive accuracy of 98.31% and a suggestion accuracy of 93.33%. Our primary focus remains the revitalization and preservation of Wolof as an Indigenous and spoken language in Africa, providing our efforts to develop novel linguistic resources. This work represents a valuable contribution to the growth of computational tools and resources for the Wolof language and provides a strong foundation for future studies in the automatic spell checking and correction field.

This paper presents a novel approach to calculating the Levenshtein (edit) distance within the framework of Fully Homomorphic Encryption (FHE), specifically targeting third-generation schemes like TFHE. Edit distance computations are essential in applications across finance and genomics, such as DNA sequence alignment. We introduce an optimised algorithm that significantly reduces the cost of edit distance calculations called Leuvenshtein. This algorithm specifically reduces the number of programmable bootstraps (PBS) needed per cell of the calculation, lowering it from approximately 94 operations -- required by the conventional Wagner-Fisher algorithm -- to just 1. Additionally, we propose an efficient method for performing equality checks on characters, reducing ASCII character comparisons to only 2 PBS operations. Finally, we explore the potential for further performance improvements by utilising preprocessing when one of the input strings is unencrypted. Our Leuvenshtein achieves up to 278times faster performance compared to the best available TFHE implementation and up to 39times faster than an optimised implementation of the Wagner-Fisher algorithm. Moreover, when offline preprocessing is possible due to the presence of one unencrypted input on the server side, an additional 3times speedup can be achieved.

Assessing the extent of human edits on texts generated by Large Language Models (LLMs) is crucial to understanding the human-AI interactions and improving the quality of automated text generation systems. Existing edit distance metrics, such as Levenshtein, BLEU, ROUGE, and TER, often fail to accurately measure the effort required for post-editing, especially when edits involve substantial modifications, such as block operations. In this paper, we introduce a novel compression-based edit distance metric grounded in the Lempel-Ziv-77 algorithm, designed to quantify the amount of post-editing applied to LLM-generated texts. Our method leverages the properties of text compression to measure the informational difference between the original and edited texts. Through experiments on real-world human edits datasets, we demonstrate that our proposed metric is highly correlated with actual edit time and effort. We also show that LLMs exhibit an implicit understanding of editing speed, that aligns well with our metric. Furthermore, we compare our metric with existing ones, highlighting its advantages in capturing complex edits with linear computational efficiency. Our code and data are available at: https://github.com/NDV-tiime/CompressionDistance