Sequence Alignment

AlphaFold 3 predicts protein structures with remarkable accuracy, yet how structural information emerges within the model remains poorly understood. Here, through causal interventions on internal representations and direct probing of every Pairformer block, we trace the formation of global protein geometry and identify the multiple sequence alignment (MSA) as a structural shortcut to the fold. Removing the MSA largely preserves local secondary structure while disrupting the long-range relationships that define global topology. Restoring the MSA-enriched pair representation at only forty residues recovers most of this lost organization, including at pairs never directly modified. This contribution depends on the detailed direction of the MSA module's output rather than its magnitude. The Pairformer rapidly converts this signal into global geometry: the final fold becomes recoverable by approximately block 9 of 48 for a majority of proteins, roughly twenty-seven blocks before the model's decoder can render it, whereas without the MSA it remains inaccessible for most proteins throughout the pass. Which homologs are supplied shapes this trajectory more strongly than which query is supplied; it persists for a designed query that never evolved but collapses for a shuffled sequence. Most importantly, an alignment built for a different protein that shares the fold, supplied only at the structurally corresponding columns, raises the median TM-score against experiment from 0.44 to 0.72, while the same alignment shifted a few residues along the chain performs worse than supplying no alignment at all. What AlphaFold 3 reads from an alignment is therefore a description of the fold itself, transferable between proteins that share one, rather than the query's own evolutionary history. This explains both its accuracy and the limits of what it has solved.

Classical texts aligned with their translations support machine translation, retrieval and computational research, but evidence comparing alignment workflows is scattered. This study compares seven systems on 452 texts in Pali, Sanskrit, Mishnaic Hebrew and Tibetan, comprising 9,833 human-aligned units: four embedding pipelines, a direct LLM call, an autonomous agent, and the agent revised by an independent auditor. Generative workflows recover 93-94% of reference correspondences, against at most 77% for embeddings. A ceiling analysis shows that sentence boundaries make some references unrepresentable by the embedding pipelines. Reference recovery is similar across generative workflows: the agent's advantage is 0.5 percentage points (95% CI -0.02 to 1.17), and auditing adds no established benefit. Agents nevertheless produce structurally valid output for all 452 texts, against 437 for direct calls. A blinded three-LLM panel assesses every generative mismatch against the source and human reference. Most mismatches are labelled defensible editorial variation; consensus major-error labels cover only 0.06-0.14% of units. The panel labels significantly fewer residual defects for agents than direct calls (0.7% versus 1.4%), suggesting that reference recovery alone understates alignment quality. On ten long Pali discourses taken as published online, agents and audited agents raise recovery from the direct call's 71% to 84% and 92%. Identical reference-located chunks bring all three to 93%. Agents thus improve structural reliability and reduce judged defects on short passages, while their large recovery advantage on long documents disappears after chunking. In this setting, independent auditing offers little measurable additional benefit on prepared passages.

Bharatanatyam is the oldest Indian Classical Dance (ICD) which is learned and practiced across India and the world. Adavu is the core of this dance form. There exist 15 Adavus and 58 variations. Each Adavu variation comprises a well-defined set of motions and postures (called dance steps) that occur in a particular order. So, while learning Adavus, students not only learn the dance steps but also take care of its sequence of occurrences. This paper proposed a method to recognize these sequences. In this work, firstly, we recognize the involved Key Postures (KPs) and motions in the Adavu using Convolutional Neural Network (CNN) and Support Vector Machine (SVM), respectively. In this, CNN achieves 99% and SVM's recognition accuracy becomes 84%. Next, we compare these KP and motion sequences with the ground truth to find the best match using the Edit Distance algorithm with an accuracy of 98%. The paper contributes hugely to the state-of-the-art in the form of digital heritage, dance tutoring system, and many more. The paper addresses three novelties; (a) Recognizing the sequences based on the KPs and motions rather than only KPs as reported in the earlier works. (b) The performance of the proposed work is measured by analyzing the prediction time per sequence. We also compare our proposed approach with the previous works that deal with the same problem statement. (c) It tests the scalability of the proposed approach by including all the Adavu variations, unlike the earlier literature, which uses only one/two variations.

We present string2string Studio, an interactive in-browser platform for string-to-string analysis across natural language processing, computational biology, and the digital humanities. The system integrates six main modules (alignment, distance, similarity, search, generation metrics, and BLAST homology search), operating at character, word, token, line, and residue levels. Its C++-based algorithms compile to WebAssembly, so core operations run locally by default without any installation or data upload. The interface reports scores with their "evidence" (alignments, edit paths, metric matches, search hits, and homology traces), making methods inspectable, debuggable, and comparable on shared inputs. Internal benchmarks show speedups of up to 2,500x over the Python predecessor, faster global/local alignment than a general-purpose native C aligner, and exact agreement with independent references under declared settings. For homology search, the scoped client-side blastn path closely matches NCBI BLAST+ rankings and statistics under matched parameters. A curated showcase and Learn mode present canonical algorithms and metrics as reusable demonstrations. string2string Studio is open-source and freely available at string2string.org.

Scene Text Recognition (STR) models are trained almost exclusively on word crops of at most 25 characters, yet real deployments (signage, product labels, dense captions) require reading much longer text. This paper diagnoses that failure and then closes it. The diagnosis separates out-of-length failure into two simultaneously extrapolating axes (the encoder's width axis and the decoder's time axis) and shows that encoder width, not decoder length, is the dominant failure mode. Representation-side fixes bring only partial relief: training-free rotary rescalings recover at most 2-4 points of character error rate (CER), and a weighted fine-tuning recipe recovers 6-8 points while improving standard-benchmark accuracy, yet word accuracy on the Long Text Benchmark (LTB) stays near zero, because the residual gap lies in the decoding mechanism rather than the representation. We then close that gap at inference time, on an unmodified word-level checkpoint: the long image is sliced into overlapping crops at the model's training width, each decoded independently and in-distribution, and the reads stitched by geometry-anchored edit-distance alignment. This procedure reaches 42.79-43.05% bucket-average word accuracy on LTB across two base checkpoints, matching the published state of the art (41.57%) and beating it by 11-12 points on the hardest bucket, at wall-clock parity with plain decoding; applied unchanged to the public PARSeq checkpoint it reaches 47.11%. Once chunking is applied fine-tuning no longer helps: the decoding-side fix alone matches purpose-built architectures. We release the diagnosis harness and implementation.

Multiple Sequence Alignments (MSAs) provide protein language models with explicit evolutionary context, but their large depth makes subsampling unavoidable under limited token budgets. Existing strategies, including random selection, identity-based filtering, and diversity-driven sampling, are effective heuristics, yet provide limited control over the evolutionary signals retained in the subset. In this work, we recast MSA subsampling as an explicit optimization problem, where key evolutionary measures, including query identity and diversity, are treated as controllable objectives. Building on this view, we introduce AP-REASONER, an Affinity-Propagation-based factor-graph approach. With evolution-aware unary factors, exemplar-consistency factors, and two control knobs, AP-REASONER performs factor-graph reasoning through message passing to infer a fixed-budget MSA subset. Experiments on long-range contact prediction and conformational ensemble prediction show that AP-REASONER outperforms baseline subsamplers on structure-sensitive downstream tasks and enables controllable recovery of alternative protein conformations. These results highlight the value of modeling MSA subsampling as a controllable optimization problem, where factor-graph reasoning offers an effective alternative to heuristic selection.

This paper explores a way to verify that audio has not been maliciously tampered in a specific context: short viral videos taken from news recordings. Rather than trying to detect artifacts of tampering (internal inconsistency), we focus on positively verifying a query against a trusted source such as a news recording (external consistency). We propose a method for cross verifying a short audio query against a reference recording from which it was taken. Our approach is to define two hypotheses (non-tampered vs tampered), calculate the most likely alignment between query and reference for each hypothesis, and then perform a likelihood ratio test on the two alignments. We show that this method is fast to compute, much more robust than using MFCC features with Euclidean distance, and has the key benefit of explainability. Our cross verification approach provides an alternative perspective and complementary tool to existing tampering detection methods.

Evolved sequences can be used to infer the rules of evolution. Orally transmitted folk melodies are evolved sequences whose similarity to protein sequences (one-dimensional, drawn from a limited alphabet) invites application of bioinformatics methods to study cultural evolution. A major obstacle is that melodies encode rhythm, which breaks some assumptions of standard sequence-alignment algorithms. We develop a rhythm-aware alignment method and apply it to \num{40000} Irish dance tune variants, enabling the first large-scale automated melodic alignment. Four canonical bioinformatics analyses -- mutability, substitution matrices, positional conservation, and covariance -- reveal patterns distinct from those of molecular evolution, revealing the forces that shape each domain: biochemical and biophysical constraints for proteins; memory, motor, and social biases for melodies. Together the results show that bioinformatics provides a powerful framework -- conceptual as much as algorithmic -- for studying cultural evolution. Although the cultural transmission of music has been discussed for centuries, here we show how to analyze it at large scale.

Aligner-Encoders are recently proposed seq2seq end-to-end ASR models that replace decoder attention by predicting the uth token directly from the u-th encoder position, so the encoder must learn the alignment internally without cross-attention or a transducer lattice. In practice, this alignment often forms abruptly in the upper layers, making training sensitive and brittle on long utterances. We propose InterAligner, which adds an intermediate Aligner objective so alignment can form progressively across depth, together with an intermediate CTC loss (InterCTC) to stabilize optimization. On LibriSpeech with a 17-layer Conformer, a final-only Aligner reaches 5.0/7.8 WER (test-clean/other). InterCTC improves to 3.4/6.0, and InterAligner further reduces WER to 3.1/5.6 with the largest gains on long utterances.

In recent years, thanks to advances in automatic music transcription (AMT), several large-scale datasets of automatically transcribed piano solo music have been released. While these datasets undoubtedly offer extensive material for performance studies, they vary substantially in quality. In the case of classical music, performances often differ not only in expressive aspects such as tempo, but also in their structural interpretation of the score (including repeat patterns and edition-specific variants). To meaningfully use large-scale transcribed datasets for performance research, transcriptions of the same piece must be grouped according to their underlying structural realisation to support valid comparison. We address this by applying sequence-to-sequence alignment followed by hierarchical clustering: we create pairwise alignments for all pairs of transcriptions of a given piece, and use the alignment cost and (dis)similarity of performed sequence lengths to resolve structural mismatches as features for grouping. We propose this approach as a first step towards automatically evaluating large-scale transcribed datasets that lack ground-truth score and/or audio, shifting the evaluation criterion from truth-based accuracy to musical coherence and plausibility. We demonstrate our score-agnostic approach on around 1,500 transcriptions of 88 compositions from a recently published large-scale transcribed piano performance dataset.

Aligning structured data is a fundamental problem in computer vision and machine learning, underlying tasks such as time series analysis, human action recognition, and visual representation learning. Existing alignment methods, including Dynamic Time Warping (DTW) and its differentiable variants, rely on deterministic similarity measures and are therefore sensitive to heterogeneous and noisy features. In this work, we introduce uncertainty-aware alignment, a probabilistic framework that models pairwise correspondences with heteroscedastic uncertainty and performs structured matching along alignment paths. Our formulation, uncertainty-DTW (uDTW), assigns each correspondence a Normal distribution and parametrizes each alignment path by a Maximum Likelihood Estimate objective consisting of (i) a precision-weighted matching term that suppresses unreliable features, and (ii) a log-variance regularization that prevents degenerate solutions. This yields a probabilistic alignment mechanism that is robust to noise and interpretable, as uncertainty directly reflects the reliability of matches. We further generalize this framework from temporal sequences to tokenized visual representations, enabling structured matching over sets of visual tokens. The learned uncertainty can be interpreted as a reverse-attention: semantically relevant regions exhibit low uncertainty and dominate the alignment, while ambiguous/noisy regions have high uncertainty. This provides a connection between alignment, attention, and uncertainty modeling. We evaluate the proposed framework across diverse domains. The results demonstrate consistent improvements over state-of-the-art methods and show that learned uncertainty correlates with semantic importance. These findings establish uncertainty-aware alignment as a general, robust, and interpretable framework for learning from structured data.

Audio-to-score alignment is a long-standing challenge in music information retrieval and arguably the most widely applicable alignment task for music research. Alignment algorithms match two versions of a piece of music, and for this to work these versions need to be in comparable formats. Audio-to-audio alignment matches audio features; when matching audio files to scores, they must either synthesize the score or derive audio-like features by means of piano rolls or similar feature sequences. Symbolic alignment, by contrast, matches symbolically encoded notes; in an audio-to-score scenario these would be obtained by a transcription of the audio file. In this article, we present an algorithm that bridges audio-like and symbol-level features directly. Sequential audio features encoding onset and spectral activation are matched to score positions by a bespoke dynamic programming-based matching algorithm derived from symbolic alignment methods. The resulting method is both precise - surpassing widely used audio-to-audio approaches based on synthesized scores -, and remains flexible in its digital signal processing components, i.e., the method is adaptable to diverse timbral characteristics without requiring a separate transcription model. Furthermore it inherits some of the symbolic alignment runtime advantages with an algorithmic complexity that is at worst linear in the length of the (typically short) symbolic score and (typically long) audio feature sequence. In the following sections, we provide a detailed algorithm description and evaluate its alignment quality on a large-scale dataset of solo piano recordings.

Contextual Automatic Speech Recognition (ASR) faces challenges with large-scale keyword dictionaries, as excessive irrelevant candidates introduce noise that degrades accuracy. To address this, dynamic filtering typically uses a base ASR model to generate preliminary hypotheses, followed by semantic text retrievers to fetch a concise subset of relevant keywords. However, this approach frequently fails in Chinese ASR. Base models often produce homophonic or near-homophonic errors that preserve the phonetic cues of the target keywords but severely distort their semantic meaning, rendering standard semantic retrievers ineffective. To resolve this, we propose a filtering framework that jointly integrates Semantic, Pinyin, and Glyph features (JSPG). Pinyin effectively retrieves targets based on phonetic similarity, while glyph provides complementary structural cues to filter out numerous irrelevant homophones inherent in Chinese. To bridge the gap between character-level pinyin/glyph metrics and sequence-level filtering, we introduce an extended Smith-Waterman algorithm that computes similarity scores between the N-best hypothesis sequences and keywords. Experiments on the Aishell-1 and RWCS-NER datasets demonstrate that JSPG significantly outperforms single-feature baselines. Furthermore, downstream contextual ASR models guided by JSPG achieve substantial improvements in keyword recognition accuracy.

Elastic distances like dynamic time warping (DTW) are central to time series machine learning because they compare sequences under local temporal misalignment. Soft-DTW is an adaptation of DTW that can be used as a gradient-based loss by replacing the hard minimum in its dynamic-programming recursion with a smooth relaxation. However, this approach does not directly extend to elastic distances whose transition costs depend on the local alignment context. Move-Split-Merge (MSM) is one such distance: it uses context-aware split and merge penalties and has often outperformed DTW in supervised and unsupervised time series machine learning tasks such as classification and clustering. We introduce Soft-MSM, a smooth relaxation of MSM and an elastic alignment loss with context-aware transition costs. Central to the formulation is a smooth gated surrogate for MSM's piecewise split/merge cost, which enables gradients through both the dynamic-programming recursion and the local transition structure. We derive the forward recursion, backward recursion, soft alignment matrix, closed-form gradient, limiting behaviour, and divergence-corrected formulation. Experiments on 112 UCR datasets show that Soft-MSM gives lower MSM barycentre loss than existing MSM barycentre methods, and yields significantly better clustering and nearest-centroid classification performance than Soft-DTW-based alternatives. An implementation is available in the open-source \texttt{aeon} toolkit.

Current open-source prompt-injection detectors converge on two architectural choices: regular-expression pattern matching and fine-tuned transformer classifiers. Both share failure modes that recent work has made concrete. Regular expressions miss paraphrased attacks. Fine-tuned classifiers are vulnerable to adaptive adversaries: a 2025 NAACL Findings study reported that eight published indirect-injection defenses were bypassed with greater than fifty percent attack success rates under adaptive attacks. This work proposes seven detection techniques that each port a specific mechanism from a discipline outside large-language-model security: forensic linguistics, materials-science fatigue analysis, deception technology from network security, local-sequence alignment from bioinformatics, mechanism design from economics, spectral signal analysis from epidemiology, and taint tracking from compiler theory. Three of the seven techniques are implemented in the prompt-shield v0.4.1 release (Apache 2.0) and evaluated in a four-configuration ablation across six datasets including deepset/prompt-injections, NotInject, LLMail-Inject, AgentHarm, and AgentDojo. The local-alignment detector lifts F1 on deepset from 0.033 to 0.378 with zero additional false positives. The stylometric detector adds 11.1 percentage points of F1 on an indirect-injection benchmark. The fatigue tracker is validated via a probing-campaign integration test. All code, data, and reproduction scripts are released under Apache 2.0.