Daily Papers

Modern ASR models trained on heterogeneously annotated data treat transcription style (verbatim vs. intended) as an uncontrolled latent variable, causing measurable decoding instability, evaluation confounding (up to 60% of reported WER attributable to style mismatch), and unreliable word-level timing. We show that models already encode both styles; the challenge is controlled activation. Using coverage-aware decoder task tokens trained on parallel verbatim/intended transcript pairs, we raise German disfluency F1 from 10% to 79% zero-shot, despite English-only training. Full English-only fine-tuning surpasses all baselines in verbatim accuracy, disfluency detection, and intended-mode quality across both languages. We further introduce supervised cross-attention fine-tuning that improves word-level timestamps on disfluent speech beyond forced-alignment baselines. Finally, we propose verbatimize, a new task enabling scalable creation and enrichment of speech corpora with high-quality canonical verbatim transcriptions.

Most music source separation systems require large collections of isolated sources for training, which can be difficult to obtain. In this work, we use musical scores, which are comparatively easy to obtain, as a weak label for training a source separation system. In contrast with previous score-informed separation approaches, our system does not require isolated sources, and score is used only as a training target, not required for inference. Our model consists of a separator that outputs a time-frequency mask for each instrument, and a transcriptor that acts as a critic, providing both temporal and frequency supervision to guide the learning of the separator. A harmonic mask constraint is introduced as another way of leveraging score information during training, and we propose two novel adversarial losses for additional fine-tuning of both the transcriptor and the separator. Results demonstrate that using score information outperforms temporal weak-labels, and adversarial structures lead to further improvements in both separation and transcription performance.

This research addresses the challenge of training an ASR model for personalized voices with minimal data. Utilizing just 14 minutes of custom audio from a YouTube video, we employ Retrieval-Based Voice Conversion (RVC) to create a custom Common Voice 16.0 corpus. Subsequently, a Cross-lingual Self-supervised Representations (XLSR) Wav2Vec2 model is fine-tuned on this dataset. The developed web-based GUI efficiently transcribes and translates input Hindi videos. By integrating XLSR Wav2Vec2 and mBART, the system aligns the translated text with the video timeline, delivering an accessible solution for multilingual video content transcription and translation for personalized voice.

Non-linguistic filler words, such as "uh" or "um", are prevalent in spontaneous speech and serve as indicators for expressing hesitation or uncertainty. Previous works for detecting certain non-linguistic filler words are highly dependent on transcriptions from a well-established commercial automatic speech recognition (ASR) system. However, certain ASR systems are not universally accessible from many aspects, e.g., budget, target languages, and computational power. In this work, we investigate filler word detection system that does not depend on ASR systems. We show that, by using the structured state space sequence model (S4) and neural semi-Markov conditional random fields (semi-CRFs), we achieve an absolute F1 improvement of 6.4% (segment level) and 3.1% (event level) on the PodcastFillers dataset. We also conduct a qualitative analysis on the detected results to analyze the limitations of our proposed system.

Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to converge on best practices and limits the reproducibility of insights across studies. We present BMFM-RNA, an open-source, modular software package that unifies diverse TFM pretraining and fine-tuning objectives within a single framework. Leveraging this capability, we introduce a novel training objective, whole cell expression decoder (WCED), which captures global expression patterns using an autoencoder-like CLS bottleneck representation. In this paper, we describe the framework, supported input representations, and training objectives. We evaluated four model checkpoints pretrained on CELLxGENE using combinations of masked language modeling (MLM), WCED and multitask learning. Using the benchmarking capabilities of BMFM-RNA, we show that WCED-based models achieve performance that matches or exceeds state-of-the-art approaches like scGPT across more than a dozen datasets in both zero-shot and fine-tuning tasks. BMFM-RNA, available as part of the biomed-multi-omics project ( https://github.com/BiomedSciAI/biomed-multi-omic ), offers a reproducible foundation for systematic benchmarking and community-driven exploration of optimal TFM training strategies, enabling the development of more effective tools to leverage the latest advances in AI for understanding cell biology.

This paper presents an overview of rule-based system for automatic accentuation and phonemic transcription of Russian texts for speech connected tasks, such as Automatic Speech Recognition (ASR). Two parts of the developed system, accentuation and transcription, use different approaches to achieve correct phonemic representations of input phrases. Accentuation is based on "Grammatical dictionary of the Russian language" of A.A. Zaliznyak and wiktionary corpus. To distinguish homographs, the accentuation system also utilises morphological information of the sentences based on Recurrent Neural Networks (RNN). Transcription algorithms apply the rules presented in the monograph of B.M. Lobanov and L.I. Tsirulnik "Computer Synthesis and Voice Cloning". The rules described in the present paper are implemented in an open-source module, which can be of use to any scientific study connected to ASR or Speech To Text (STT) tasks. Automatically marked up text annotations of the Russian Voxforge database were used as training data for an acoustic model in CMU Sphinx. The resulting acoustic model was evaluated on cross-validation, mean Word Accuracy being 71.2%. The developed toolkit is written in the Python language and is accessible on GitHub for any researcher interested.

This paper presents a state-of-the-art model for transcribing speech in any language into the International Phonetic Alphabet (IPA). Transcription of spoken languages into IPA is an essential yet time-consuming process in language documentation, and even partially automating this process has the potential to drastically speed up the documentation of endangered languages. Like the previous best speech-to-IPA model (Wav2Vec2Phoneme), our model is based on wav2vec 2.0 and is fine-tuned to predict IPA from audio input. We use training data from seven languages from CommonVoice 11.0, transcribed into IPA semi-automatically. Although this training dataset is much smaller than Wav2Vec2Phoneme's, its higher quality lets our model achieve comparable or better results. Furthermore, we show that the quality of our universal speech-to-IPA models is close to that of human annotators.

Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present single cell, Cell-ontology guided TFM scCello. We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training. The novel loss component guide scCello to learn the cell-type-specific representation and the structural relation between cell types from the cell ontology graph, respectively. We pre-trained scCello on 22 million cells from CellxGene database leveraging their cell-type labels mapped to the cell ontology graph from Open Biological and Biomedical Ontology Foundry. Our TFM demonstrates competitive generalization and transferability performance over the existing TFMs on biologically important tasks including identifying novel cell types of unseen cells, prediction of cell-type-specific marker genes, and cancer drug responses.

Subtitling plays a crucial role in enhancing the accessibility of audiovisual content and encompasses three primary subtasks: translating spoken dialogue, segmenting translations into concise textual units, and estimating timestamps that govern their on-screen duration. Past attempts to automate this process rely, to varying degrees, on automatic transcripts, employed diversely for the three subtasks. In response to the acknowledged limitations associated with this reliance on transcripts, recent research has shifted towards transcription-free solutions for translation and segmentation, leaving the direct generation of timestamps as uncharted territory. To fill this gap, we introduce the first direct model capable of producing automatic subtitles, entirely eliminating any dependence on intermediate transcripts also for timestamp prediction. Experimental results, backed by manual evaluation, showcase our solution's new state-of-the-art performance across multiple language pairs and diverse conditions.

Lecture transcript translation helps learners understand online courses, however, building a high-quality lecture machine translation system lacks publicly available parallel corpora. To address this, we examine a framework for parallel corpus mining, which provides a quick and effective way to mine a parallel corpus from publicly available lectures on Coursera. To create the parallel corpora, we propose a dynamic programming based sentence alignment algorithm which leverages the cosine similarity of machine-translated sentences. The sentence alignment F1 score reaches 96%, which is higher than using the BERTScore, LASER, or sentBERT methods. For both English--Japanese and English--Chinese lecture translations, we extracted parallel corpora of approximately 50,000 lines and created development and test sets through manual filtering for benchmarking translation performance. Through machine translation experiments, we show that the mined corpora enhance the quality of lecture transcript translation when used in conjunction with out-of-domain parallel corpora via multistage fine-tuning. Furthermore, this study also suggests guidelines for gathering and cleaning corpora, mining parallel sentences, cleaning noise in the mined data, and creating high-quality evaluation splits. For the sake of reproducibility, we have released the corpora as well as the code to create them. The dataset is available at https://github.com/shyyhs/CourseraParallelCorpusMining.

Audio chaptering, the task of automatically segmenting long-form audio into coherent sections, is increasingly important for navigating podcasts, lectures, and videos. Despite its relevance, research remains limited and text-based, leaving key questions unresolved about leveraging audio information, handling ASR errors, and transcript-free evaluation. We address these gaps through three contributions: (1) a systematic comparison between text-based models with acoustic features, a novel audio-only architecture (AudioSeg) operating on learned audio representations, and multimodal LLMs; (2) empirical analysis of factors affecting performance, including transcript quality, acoustic features, duration, and speaker composition; and (3) formalized evaluation protocols contrasting transcript-dependent text-space protocols with transcript-invariant time-space protocols. Our experiments on YTSeg reveal that AudioSeg substantially outperforms text-based approaches, pauses provide the largest acoustic gains, and MLLMs remain limited by context length and weak instruction following, yet MLLMs are promising on shorter audio.

TTS systems with autoregressive semantic modeling have demonstrated strong zero-shot voice cloning performance and rich expressive variation, but their sequential decoding incurs substantial latency. Non-autoregressive alternatives offer much faster generation, yet often rely on more restrictive reference conditioning, such as requiring transcripts of the reference speech during inference. We present Tacit-TTS, an efficient transcript-free zero-shot voice cloning system distilled from IndexTTS2. Our model replaces autoregressive text-to-semantic decoding with masked non-autoregressive generation, introduces training-free acoustic length estimation, and accelerates the flow-matching renderer through ReFlow distillation. Across two English and two Mandarin datasets, Tacit-TTS achieves competitive zero-shot quality while generating speech over 10x faster than IndexTTS2 for utterances longer than 5 seconds. Its transcript-free conditioning further supports cross-lingual and non-lexical references. We validate this capability using references from eight other languages, infant babble, and synthetic gibberish, where transcript-dependent systems often degrade or fail due to unreliable ASR transcripts.

In a spoken dialogue system, an NLU model is preceded by a speech recognition system that can deteriorate the performance of natural language understanding. This paper proposes a method for investigating the impact of speech recognition errors on the performance of natural language understanding models. The proposed method combines the back transcription procedure with a fine-grained technique for categorizing the errors that affect the performance of NLU models. The method relies on the usage of synthesized speech for NLU evaluation. We show that the use of synthesized speech in place of audio recording does not change the outcomes of the presented technique in a significant way.

Parliamentary transcripts provide a valuable resource to understand the reality and know about the most important facts that occur over time in our societies. Furthermore, the political debates captured in these transcripts facilitate research on political discourse from a computational social science perspective. In this paper we release the first version of a newly compiled corpus from Basque parliamentary transcripts. The corpus is characterized by heavy Basque-Spanish code-switching, and represents an interesting resource to study political discourse in contrasting languages such as Basque and Spanish. We enrich the corpus with metadata related to relevant attributes of the speakers and speeches (language, gender, party...) and process the text to obtain named entities and lemmas. The obtained metadata is then used to perform a detailed corpus analysis which provides interesting insights about the language use of the Basque political representatives across time, parties and gender.

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

Writing down lyrics for human consumption involves not only accurately capturing word sequences, but also incorporating punctuation and formatting for clarity and to convey contextual information. This includes song structure, emotional emphasis, and contrast between lead and background vocals. While automatic lyrics transcription (ALT) systems have advanced beyond producing unstructured strings of words and are able to draw on wider context, ALT benchmarks have not kept pace and continue to focus exclusively on words. To address this gap, we introduce Jam-ALT, a comprehensive lyrics transcription benchmark. The benchmark features a complete revision of the JamendoLyrics dataset, in adherence to industry standards for lyrics transcription and formatting, along with evaluation metrics designed to capture and assess the lyric-specific nuances, laying the foundation for improving the readability of lyrics. We apply the benchmark to recent transcription systems and present additional error analysis, as well as an experimental comparison with a classical music dataset.

We propose Cotatron, a transcription-guided speech encoder for speaker-independent linguistic representation. Cotatron is based on the multispeaker TTS architecture and can be trained with conventional TTS datasets. We train a voice conversion system to reconstruct speech with Cotatron features, which is similar to the previous methods based on Phonetic Posteriorgram (PPG). By training and evaluating our system with 108 speakers from the VCTK dataset, we outperform the previous method in terms of both naturalness and speaker similarity. Our system can also convert speech from speakers that are unseen during training, and utilize ASR to automate the transcription with minimal reduction of the performance. Audio samples are available at https://mindslab-ai.github.io/cotatron, and the code with a pre-trained model will be made available soon.

We describe a system that generates speaker-annotated transcripts of meetings by using a virtual microphone array, a set of spatially distributed asynchronous recording devices such as laptops and mobile phones. The system is composed of continuous audio stream alignment, blind beamforming, speech recognition, speaker diarization using prior speaker information, and system combination. When utilizing seven input audio streams, our system achieves a word error rate (WER) of 22.3% and comes within 3% of the close-talking microphone WER on the non-overlapping speech segments. The speaker-attributed WER (SAWER) is 26.7%. The relative gains in SAWER over the single-device system are 14.8%, 20.3%, and 22.4% for three, five, and seven microphones, respectively. The presented system achieves a 13.6% diarization error rate when 10% of the speech duration contains more than one speaker. The contribution of each component to the overall performance is also investigated, and we validate the system with experiments on the NIST RT-07 conference meeting test set.

Background: Two strains of the endoparasitoid Cotesia typhae present a differential parasitism success on the host, Sesamia nonagrioides. One is virulent on both permissive and resistant host populations, and the other only on the permissive host. This interaction provides a very interesting frame for studying virulence factors. Here, we used a combination of comparative transcriptomic and proteomic analyses to unravel the molecular basis underlying virulence differences between the strains.Results: First, we report that virulence genes are mostly expressed during the nymphal stage of the parasitoid. Especially, proviral genes are broadly up-regulated at this stage, while their expression is only expected in the host. Parasitoid gene expression in the host increases with time, indicating the production of more virulence factors. Secondly, comparison between strains reveals differences in venom composition, with 12 proteins showing differential abundance. Proviral expression in the host displays a strong temporal variability, along with differential patterns between strains. Notably, a subset of proviral genes including protein-tyrosine phosphatases is specifically over-expressed in the resistant host parasitized by the less virulent strain, 24 hours after parasitism. This result particularly hints at host modulation of proviral expression.Conclusions: This study sheds light on the temporal expression of virulence factors of Cotesia typhae, both in the host and in the parasitoid. It also identifies potential molecular candidates driving differences in parasitism success between two strains. Together, those findings provide a path for further exploration of virulence mechanisms in parasitoid wasps, and offer insights into host-parasitoid coevolution.

Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for evaluating multimodal learning methods that leverage both histology images and gene expression data. Here, we present HESCAPE, a large-scale benchmark for cross-modal contrastive pretraining in spatial transcriptomics, built on a curated pan-organ dataset spanning 6 different gene panels and 54 donors. We systematically evaluated state-of-the-art image and gene expression encoders across multiple pretraining strategies and assessed their effectiveness on two downstream tasks: gene mutation classification and gene expression prediction. Our benchmark demonstrates that gene expression encoders are the primary determinant of strong representational alignment, and that gene models pretrained on spatial transcriptomics data outperform both those trained without spatial data and simple baseline approaches. However, downstream task evaluation reveals a striking contradiction: while contrastive pretraining consistently improves gene mutation classification performance, it degrades direct gene expression prediction compared to baseline encoders trained without cross-modal objectives. We identify batch effects as a key factor that interferes with effective cross-modal alignment. Our findings highlight the critical need for batch-robust multimodal learning approaches in spatial transcriptomics. To accelerate progress in this direction, we release HESCAPE, providing standardized datasets, evaluation protocols, and benchmarking tools for the community

Interpretability methods have recently gained significant attention, particularly in the context of large language models, enabling insights into linguistic representations, error detection, and model behaviors such as hallucinations and repetitions. However, these techniques remain underexplored in automatic speech recognition (ASR), despite their potential to advance both the performance and interpretability of ASR systems. In this work, we adapt and systematically apply established interpretability methods such as logit lens, linear probing, and activation patching, to examine how acoustic and semantic information evolves across layers in ASR systems. Our experiments reveal previously unknown internal dynamics, including specific encoder-decoder interactions responsible for repetition hallucinations and semantic biases encoded deep within acoustic representations. These insights demonstrate the benefits of extending and applying interpretability techniques to speech recognition, opening promising directions for future research on improving model transparency and robustness.

Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST can significantly enhance the analysis of vast and complex data sources, unlocking new perspectives on the intricacies of biological tissues. However, modeling ST data is inherently challenging due to the need to extract multi-scale information from tissue slices containing vast numbers of cells. This process requires integrating macro-scale tissue morphology, micro-scale cellular microenvironment, and gene-scale gene expression profile. To address this challenge, we propose SToFM, a multi-scale Spatial Transcriptomics Foundation Model. SToFM first performs multi-scale information extraction on each ST slice, to construct a set of ST sub-slices that aggregate macro-, micro- and gene-scale information. Then an SE(2) Transformer is used to obtain high-quality cell representations from the sub-slices. Additionally, we construct SToCorpus-88M, the largest high-resolution spatial transcriptomics corpus for pretraining. SToFM achieves outstanding performance on a variety of downstream tasks, such as tissue region semantic segmentation and cell type annotation, demonstrating its comprehensive understanding of ST data through capturing and integrating multi-scale information.

Music transcription plays a pivotal role in Music Information Retrieval (MIR), particularly for stringed instruments like the guitar, where symbolic music notations such as MIDI lack crucial playability information. This contribution introduces the Fretting-Transformer, an encoderdecoder model that utilizes a T5 transformer architecture to automate the transcription of MIDI sequences into guitar tablature. By framing the task as a symbolic translation problem, the model addresses key challenges, including string-fret ambiguity and physical playability. The proposed system leverages diverse datasets, including DadaGP, GuitarToday, and Leduc, with novel data pre-processing and tokenization strategies. We have developed metrics for tablature accuracy and playability to quantitatively evaluate the performance. The experimental results demonstrate that the Fretting-Transformer surpasses baseline methods like A* and commercial applications like Guitar Pro. The integration of context-sensitive processing and tuning/capo conditioning further enhances the model's performance, laying a robust foundation for future developments in automated guitar transcription.

The International Phonetic Alphabet (IPA) serves to systematize phonemes in language, enabling precise textual representation of pronunciation. In Bengali phonology and phonetics, ongoing scholarly deliberations persist concerning the IPA standard and core Bengali phonemes. This work examines prior research, identifies current and potential issues, and suggests a framework for a Bengali IPA standard, facilitating linguistic analysis and NLP resource creation and downstream technology development. In this work, we present a comprehensive study of Bengali IPA transcription and introduce a novel IPA transcription framework incorporating a novel dataset with DL-based benchmarks.

Spatial transcriptomics (ST) provides spatially resolved measurements of gene expression, enabling characterization of the molecular landscape of human tissue beyond histological assessment as well as localized readouts that can be aligned with morphology. Concurrently, the success of multimodal foundation models that integrate vision with complementary modalities suggests that morphomolecular coupling between local expression and morphology can be systematically used to improve histological representations themselves. We introduce Spatial Expression-Aligned Learning (SEAL), a vision-omics self-supervised learning framework that infuses localized molecular information into pathology vision encoders. Rather than training new encoders from scratch, SEAL is designed as a parameter-efficient vision-omics finetuning method that can be flexibly applied to widely used pathology foundation models. We instantiate SEAL by training on over 700,000 paired gene expression spot-tissue region examples spanning tumor and normal samples from 14 organs. Tested across 38 slide-level and 15 patch-level downstream tasks, SEAL provides a drop-in replacement for pathology foundation models that consistently improves performance over widely used vision-only and ST prediction baselines on slide-level molecular status, pathway activity, and treatment response prediction, as well as patch-level gene expression prediction tasks. Additionally, SEAL encoders exhibit robust domain generalization on out-of-distribution evaluations and enable new cross-modal capabilities such as gene-to-image retrieval. Our work proposes a general framework for ST-guided finetuning of pathology foundation models, showing that augmenting existing models with localized molecular supervision is an effective and practical step for improving visual representations and expanding their cross-modal utility.

Spatial transcriptomics (ST) provides high-resolution pathological images and whole-transcriptomic expression profiles at individual spots across whole-slide scales. This setting makes it an ideal data source to develop multimodal foundation models. Although recent studies attempted to fine-tune visual encoders with trainable gene encoders based on spot-level, the absence of a wider slide perspective and spatial intrinsic relationships limits their ability to capture ST-specific insights effectively. Here, we introduce ST-Align, the first foundation model designed for ST that deeply aligns image-gene pairs by incorporating spatial context, effectively bridging pathological imaging with genomic features. We design a novel pretraining framework with a three-target alignment strategy for ST-Align, enabling (1) multi-scale alignment across image-gene pairs, capturing both spot- and niche-level contexts for a comprehensive perspective, and (2) cross-level alignment of multimodal insights, connecting localized cellular characteristics and broader tissue architecture. Additionally, ST-Align employs specialized encoders tailored to distinct ST contexts, followed by an Attention-Based Fusion Network (ABFN) for enhanced multimodal fusion, effectively merging domain-shared knowledge with ST-specific insights from both pathological and genomic data. We pre-trained ST-Align on 1.3 million spot-niche pairs and evaluated its performance through two downstream tasks across six datasets, demonstrating superior zero-shot and few-shot capabilities. ST-Align highlights the potential for reducing the cost of ST and providing valuable insights into the distinction of critical compositions within human tissue.

Recent Audio Large Language Models (AudioLLMs) exhibit a striking performance inversion: while excelling at complex reasoning tasks, they consistently underperform on fine-grained acoustic perception. We attribute this gap to a fundamental limitation of ASR-centric training, which provides precise linguistic targets but implicitly teaches models to suppress paralinguistic cues and acoustic events as noise. To address this, we propose Unified Audio Schema (UAS), a holistic and structured supervision framework that organizes audio information into three explicit components -- Transcription, Paralinguistics, and Non-linguistic Events -- within a unified JSON format. This design achieves comprehensive acoustic coverage without sacrificing the tight audio-text alignment that enables reasoning. We validate the effectiveness of this supervision strategy by applying it to both discrete and continuous AudioLLM architectures. Extensive experiments on MMSU, MMAR, and MMAU demonstrate that UAS-Audio yields consistent improvements, boosting fine-grained perception by 10.9% on MMSU over the same-size state-of-the-art models while preserving robust reasoning capabilities. Our code and model are publicly available at https://github.com/Tencent/Unified_Audio_Schema.

Despite the central role that melody plays in music perception, it remains an open challenge in music information retrieval to reliably detect the notes of the melody present in an arbitrary music recording. A key challenge in melody transcription is building methods which can handle broad audio containing any number of instrument ensembles and musical styles - existing strategies work well for some melody instruments or styles but not all. To confront this challenge, we leverage representations from Jukebox (Dhariwal et al. 2020), a generative model of broad music audio, thereby improving performance on melody transcription by 20% relative to conventional spectrogram features. Another obstacle in melody transcription is a lack of training data - we derive a new dataset containing 50 hours of melody transcriptions from crowdsourced annotations of broad music. The combination of generative pre-training and a new dataset for this task results in 77% stronger performance on melody transcription relative to the strongest available baseline. By pairing our new melody transcription approach with solutions for beat detection, key estimation, and chord recognition, we build Sheet Sage, a system capable of transcribing human-readable lead sheets directly from music audio. Audio examples can be found at https://chrisdonahue.com/sheetsage and code at https://github.com/chrisdonahue/sheetsage .

We introduce HK-LegiCoST, a new three-way parallel corpus of Cantonese-English translations, containing 600+ hours of Cantonese audio, its standard traditional Chinese transcript, and English translation, segmented and aligned at the sentence level. We describe the notable challenges in corpus preparation: segmentation, alignment of long audio recordings, and sentence-level alignment with non-verbatim transcripts. Such transcripts make the corpus suitable for speech translation research when there are significant differences between the spoken and written forms of the source language. Due to its large size, we are able to demonstrate competitive speech translation baselines on HK-LegiCoST and extend them to promising cross-corpus results on the FLEURS Cantonese subset. These results deliver insights into speech recognition and translation research in languages for which non-verbatim or ``noisy'' transcription is common due to various factors, including vernacular and dialectal speech.

Automatic Text Recognition (ATR) now supplies digital humanities with large volumes of unstructured, heterogeneous, and often noisy text in ancient languages. Downstream semantic analysestext reuse identification, alignment, and semantic search-rely on sentence embeddings, yet existing methods transfer poorly to ancient languages: generic multilingual encoders underperform, specialized language models yield anisotropic representation spaces, and labeled similarity data is unavailable. We study two fully unsupervised strategies - TSDAE and contrastive sentence embedding (CSE) - that adapt a specialized token-level language model into a corpus-specific sentence encoder using only raw sentences. On the philologically central case of biblical reuse in patristic literature (2,935 expert-verified parallels in Latin and Ancient Greek, from Augustine, Jerome, and Athanasius), we decompose reuse identification into two separately evaluated tasks-binary detection and correspondence retrieval-and benchmark the adapted encoders against multilingual, specialized, distilled, and supervised fine-tuned baselines, as well as on artificially noised data simulating HTR artifacts and scribal abbreviations. The adapted encoders outperform all baselines on both tasks, with complementary profiles: TSDAE leads detection given a large in-domain corpus, while CSE leads retrieval, reaches its optimum with as few as 4-8k raw in-domain sentences-a few tens of seconds of training on a laptop GPU-and transfers across works and authors, including to noisy post-ATR text when retrained directly on it. UMAP atlases relate the geometric effect of each strategy to the measured gains, and the full pipeline-segmentation, fine-tuning, cross-corpus semantic search-is made available to non-specialists through the online tool Paraphrasis.

Spatial transcriptomics (ST) provides unprecedented insights into tumor heterogeneity by capturing spatially resolved gene expression, yet its high experimental cost hinders large-scale adoption. Consequently, computational approaches that predict spatial gene expression directly from hematoxylin and eosin slides, termed virtual ST, have rapidly emerged. Despite this progress, assessing advances in the field remains difficult due to insufficient benchmarking: prior studies rely on small, heterogeneous datasets, inconsistent training and inference pipelines, and limited evaluation of biological interpretability and model robustness. To address these gaps, we present STP-BENCH, a standardized benchmark for virtual ST models. STP-BENCH comprises six cancer types spanning two ST platforms (Visium and Xenium), with each training dataset containing more than 30,000 spots and at least 15 slides to ensure statistical reliability. We evaluate 21 predictive approaches, re-implemented with a unified pathology foundation model as the morphological encoder when architecturally applicable. Beyond conventional benchmarks that report average predictive accuracy on highly variable genes, we systematically examine which genes and gene sets are recoverable from histomorphology. We further evaluate the downstream biological utility of predicted profiles through cell-type deconvolution and spatial domain identification, and assess model reliability under domain shifts and data scaling. Notably, unified morphological encoding substantially re-orders model rankings established in prior studies, indicating that architectural innovations and image encoding have been conflated in previous evaluations. We publicly release STP-BENCH to support reproducibility and serve as a community benchmark at https://github.com/NEXGEM/STP-Bench.

Competitive music transcription models require large amounts of paired audio-score data, which is scarce due to collection costs, alignment difficulty, and copyright restrictions. Meanwhile, vast quantities of unpaired audio recordings and symbolic scores are freely available but have gone unused. We adopt a cycle-consistent translation framework in which a small amount of paired data acts as a minimal anchor, unlocking the full potential of the unpaired pool. We find that: unpaired data yields surprisingly large gains, especially under limited supervision; unpaired audio contributes more than unpaired scores; incorporating unlabeled audio from a new instrument during training improves transcription for that instrument without any paired supervision. Together, these results suggest that scaling unpaired data offers a practical path toward high-quality transcription for instruments where labeled data remains scarce.

Predicting transcriptional responses to genetic perturbations is central to understanding gene function. Existing predictors primarily rely on transcriptomic measurements, although chromatin accessibility provides complementary information about the cellular context in which perturbations act. Using this information requires linking chromatin context to specific perturbations and accounting for baseline differences between independently sampled control and perturbed populations. We propose ChromaPert, a chromatin-informed framework for predicting state-dependent perturbation responses. ChromaPert combines molecular and DNA-informed locus priors with paired control RNA--ATAC features to jointly represent target identity and measured cellular context. Its Chromatin-Guided Response Router (CGRR) builds a source bank of control-derived expression offsets and retrieves relevant sources using perturbation/locus or control-ATAC similarity. These offsets account for baseline differences, while conditional transport flow learns the remaining response. Across three unseen-target and held-out-state settings on K562 CAT-ATAC and Perturb-Multiome, ChromaPert achieves the highest all-gene response correlation among evaluated methods. When transferring known perturbations to held-out states, it improves correlation by 23.2% across all genes and 46.2% for the twenty most responsive genes over the strongest respective baselines. Correct RNA--ATAC pairing improves recovery of chromatin-associated response slopes over shuffled pairing, while cross-state predictions retain state-specific responses to the same perturbation.

Predicting transcriptional responses to genetic perturbations could reduce the experimental burden of functional genomics, but extrapolation to genes that were never perturbed during training remains difficult. We present Stable-Shift, a structured method for estimating unseen-gene responses. Stable-Shift aggregates single-cell measurements into perturbation-level expression shifts, fits a low-rank response basis using training perturbations only, and predicts an unseen gene's coordinates in that basis from biological context. The context combines STRING interactions, network structure, control-cell expression statistics, and Gene Ontology annotations; the evaluated implementation uses graph convolution to integrate these inputs. On the supplied K562 Perturb-seq benchmark, Stable-Shift obtained 0.592 cosine similarity, compared with 0.569 for GEARS, together with higher Spearman correlation and top-gene precision among the evaluated methods. Its mean cosine similarity over five unseen-gene splits was 0.589 +/- 0.008. The same ordering was observed in the supplied graph-aware, residualized, gene-space, and Norman-dataset comparisons. These results support further study of biologically structured latent-response prediction, while the lower gene-space accuracy and sensitivity to sparse graph neighborhoods limit the scope of the present conclusions.

Spatial transcriptomics (ST) provides spatially resolved gene expression profiling but remains expensive, motivating the prediction of ST from histology images. Generative models have emerged as a mainstream paradigm for ST prediction due to their ability to model the conditional distribution of gene expression and capture its inherent stochasticity. However, these methods typically treat genes as independent prediction targets and overlook the intrinsic gene-gene interactions in biological systems, which limits their ability to preserve biologically meaningful co-expression patterns. We argue that gene-gene interactions, which reflect shared pathways and regulatory mechanisms, are essential for generating numerically accurate and biologically coherent ST profiles. In this paper, we propose CorrFlow, a correlation-guided flow matching framework for histology-to-ST prediction that explicitly models gene-gene dependencies through two complementary mechanisms. First, we introduce an annealed masked flow matching strategy, where subsets of genes are progressively masked following a timestep-dependent annealing schedule, encouraging the model to infer masked genes conditioned on the remaining genes and promoting joint conditional modeling beyond per-gene marginal estimation. Second, we devise a gene graph-regularized optimization scheme that integrates prior knowledge from the STRING database and data-driven co-expression estimated by WGCNA to construct a gene affinity graph, which enforces both local consistency and global smoothness in the predicted expression. Extensive experiments across 12 datasets show that CorrFlow achieves the best average PCC and HPCC among evaluated methods, leading to more biologically coherent ST predictions.

With the explosive growth of livestream broadcasting, there is an urgent need for new summarization technology that enables us to create a preview of streamed content and tap into this wealth of knowledge. However, the problem is nontrivial due to the informal nature of spoken language. Further, there has been a shortage of annotated datasets that are necessary for transcript summarization. In this paper, we present StreamHover, a framework for annotating and summarizing livestream transcripts. With a total of over 500 hours of videos annotated with both extractive and abstractive summaries, our benchmark dataset is significantly larger than currently existing annotated corpora. We explore a neural extractive summarization model that leverages vector-quantized variational autoencoder to learn latent vector representations of spoken utterances and identify salient utterances from the transcripts to form summaries. We show that our model generalizes better and improves performance over strong baselines. The results of this study provide an avenue for future research to improve summarization solutions for efficient browsing of livestreams.

Aspect-based meeting transcript summarization aims to produce multiple summaries, each focusing on one aspect of content in a meeting transcript. It is challenging as sentences related to different aspects can mingle together, and those relevant to a specific aspect can be scattered throughout the long transcript of a meeting. The traditional summarization methods produce one summary mixing information of all aspects, which cannot deal with the above challenges of aspect-based meeting transcript summarization. In this paper, we propose a two-stage method for aspect-based meeting transcript summarization. To select the input content related to specific aspects, we train a sentence classifier on a dataset constructed from the AMI corpus with pseudo-labeling. Then we merge the sentences selected for a specific aspect as the input for the summarizer to produce the aspect-based summary. Experimental results on the AMI corpus outperform many strong baselines, which verifies the effectiveness of our proposed method.

Phone call transcript labeling is prohibitively expensive (approximately 2 USD per minute) due to privacy regulations, consent requirements, and manual annotation costs requiring 3 hours of expert time per hour of audio. Existing extraction methods fail on conversational speech containing disfluencies, interruptions, and speaker overlap. We introduce LingVarBench, a synthetic data generation pipeline that addresses these constraints through automated validation. First, we prompt an LLM to generate realistic structured field values across multiple use cases. Second, we recursively prompt the model to transform these values into thousands of natural conversational utterances containing typical phone call characteristics. Third, we validate each synthetic utterance by testing whether a separate LLM-based extractor can recover the original structured information. We employ DSPy's SIMBA optimizer to automatically synthesize extraction prompts from validated synthetic transcripts, eliminating manual prompt engineering. Our optimized prompts achieve up to 95 percent accuracy for numeric fields (vs. 88-89 percent zero-shot), 90 percent for names (vs. 47-79 percent), and over 80 percent for dates (vs. 72-77 percent) on real customer transcripts, demonstrating substantial gains over zero-shot prompting. The synthetic-to-real transfer demonstrates that conversational patterns learned from generated data generalize effectively to authentic phone calls containing background noise and domain-specific terminology. LingVarBench provides the first systematic benchmark for structured extraction from synthetic conversational data, demonstrating that automated prompt optimization overcomes cost and privacy barriers preventing large-scale phone call analysis in commercial settings.

Recent advances in zero-shot text-to-speech (TTS) have substantially improved speech quality and voice cloning fidelity. However, many zero-shot TTS systems still depend on audio prompt transcripts at inference time. This dependency limits cross-lingual voice cloning, since in-the-wild reference audio is often untranscribed. In this technical report, we present Confucius4-TTS, a multilingual zero-shot TTS system that supports 14 languages and performs both intra-lingual and cross-lingual reference cloning without requiring transcripts of audio prompts. Confucius4-TTS follows a two-stage architecture, consisting of text-to-semantic (T2S) and semantic-to-acoustic (S2A) modules. The LLM-based T2S module uses a learnable speaker encoder to extract timbre features from self-supervised speech representations, and the conditional flow-matching S2A module converts the predicted semantic tokens into mel-spectrograms. The same model also supports continuation cloning when a reference transcript is available. Confucius4-TTS is trained on large-scale multilingual speech data. It achieves high intelligibility and speaker similarity on public benchmarks. On the CV3-Eval cross-lingual benchmark, Confucius4-TTS obtains an average WER of 3.73% across six directions. On our internal cross-lingual set, it achieves the best average overall rank in human evaluation among recent open-source and commercial systems. We release code, model checkpoints, and demos at https://github.com/netease-youdao/Confucius4-TTS.

Cross-cultural understanding has become increasingly important in today's highly connected, cross-national world. The success of LLM-based technologies is now driving the development of automated tools to aid understanding for nonnative people trying to succeed in cross-cultural environments. Building such automated tools is often done by leveraging in-thewild text, audio, and video data. This paper presents techniques for improving speech recognition-based transcript creation in multiple languages from videos to better train these automated tools. The focus is on processes and speech tools that can easily be used by cross-cultural tool builders without requiring deep speech processing expertise. Using publicly available videos from YouTube and Whisper-based tools, average transcription error rate across seven languages (Spanish, Japanese, Korean, Mandarin, Turkish, Russian, and Hebrew) of 30% are observed. With a modest amount of fine-tuning data, the average error rate can be reduced to 20% making such output much more usable for downstream processing. Speech and metadata associated with these videos that can be used by the community to further refine these experiments are released as well.

Multitrack music transcription aims to transcribe a music audio input into the musical notes of multiple instruments simultaneously. It is a very challenging task that typically requires a more complex model to achieve satisfactory result. In addition, prior works mostly focus on transcriptions of regular instruments, however, neglecting vocals, which are usually the most important signal source if present in a piece of music. In this paper, we propose a novel deep neural network architecture, Perceiver TF, to model the time-frequency representation of audio input for multitrack transcription. Perceiver TF augments the Perceiver architecture by introducing a hierarchical expansion with an additional Transformer layer to model temporal coherence. Accordingly, our model inherits the benefits of Perceiver that posses better scalability, allowing it to well handle transcriptions of many instruments in a single model. In experiments, we train a Perceiver TF to model 12 instrument classes as well as vocal in a multi-task learning manner. Our result demonstrates that the proposed system outperforms the state-of-the-art counterparts (e.g., MT3 and SpecTNT) on various public datasets.

Large-scale, weakly-supervised speech recognition models, such as Whisper, have demonstrated impressive results on speech recognition across domains and languages. However, their application to long audio transcription via buffered or sliding window approaches is prone to drifting, hallucination & repetition; and prohibits batched transcription due to their sequential nature. Further, timestamps corresponding each utterance are prone to inaccuracies and word-level timestamps are not available out-of-the-box. To overcome these challenges, we present WhisperX, a time-accurate speech recognition system with word-level timestamps utilising voice activity detection and forced phoneme alignment. In doing so, we demonstrate state-of-the-art performance on long-form transcription and word segmentation benchmarks. Additionally, we show that pre-segmenting audio with our proposed VAD Cut & Merge strategy improves transcription quality and enables a twelve-fold transcription speedup via batched inference.

Automatic Music Transcription (AMT) has been recognized as a key enabling technology with a wide range of applications. Given the task's complexity, best results have typically been reported for systems focusing on specific settings, e.g. instrument-specific systems tend to yield improved results over instrument-agnostic methods. Similarly, higher accuracy can be obtained when only estimating frame-wise f_0 values and neglecting the harder note event detection. Despite their high accuracy, such specialized systems often cannot be deployed in the real-world. Storage and network constraints prohibit the use of multiple specialized models, while memory and run-time constraints limit their complexity. In this paper, we propose a lightweight neural network for musical instrument transcription, which supports polyphonic outputs and generalizes to a wide variety of instruments (including vocals). Our model is trained to jointly predict frame-wise onsets, multipitch and note activations, and we experimentally show that this multi-output structure improves the resulting frame-level note accuracy. Despite its simplicity, benchmark results show our system's note estimation to be substantially better than a comparable baseline, and its frame-level accuracy to be only marginally below those of specialized state-of-the-art AMT systems. With this work we hope to encourage the community to further investigate low-resource, instrument-agnostic AMT systems.

Automatic Music Transcription (AMT), inferring musical notes from raw audio, is a challenging task at the core of music understanding. Unlike Automatic Speech Recognition (ASR), which typically focuses on the words of a single speaker, AMT often requires transcribing multiple instruments simultaneously, all while preserving fine-scale pitch and timing information. Further, many AMT datasets are "low-resource", as even expert musicians find music transcription difficult and time-consuming. Thus, prior work has focused on task-specific architectures, tailored to the individual instruments of each task. In this work, motivated by the promising results of sequence-to-sequence transfer learning for low-resource Natural Language Processing (NLP), we demonstrate that a general-purpose Transformer model can perform multi-task AMT, jointly transcribing arbitrary combinations of musical instruments across several transcription datasets. We show this unified training framework achieves high-quality transcription results across a range of datasets, dramatically improving performance for low-resource instruments (such as guitar), while preserving strong performance for abundant instruments (such as piano). Finally, by expanding the scope of AMT, we expose the need for more consistent evaluation metrics and better dataset alignment, and provide a strong baseline for this new direction of multi-task AMT.

Current automatic lyrics transcription (ALT) benchmarks focus exclusively on word content and ignore the finer nuances of written lyrics including formatting and punctuation, which leads to a potential misalignment with the creative products of musicians and songwriters as well as listeners' experiences. For example, line breaks are important in conveying information about rhythm, emotional emphasis, rhyme, and high-level structure. To address this issue, we introduce Jam-ALT, a new lyrics transcription benchmark based on the JamendoLyrics dataset. Our contribution is twofold. Firstly, a complete revision of the transcripts, geared specifically towards ALT evaluation by following a newly created annotation guide that unifies the music industry's guidelines, covering aspects such as punctuation, line breaks, spelling, background vocals, and non-word sounds. Secondly, a suite of evaluation metrics designed, unlike the traditional word error rate, to capture such phenomena. We hope that the proposed benchmark contributes to the ALT task, enabling more precise and reliable assessments of transcription systems and enhancing the user experience in lyrics applications such as subtitle renderings for live captioning or karaoke.

In the past few decades, Japanese comics, commonly referred to as Manga, have transcended both cultural and linguistic boundaries to become a true worldwide sensation. Yet, the inherent reliance on visual cues and illustration within manga renders it largely inaccessible to individuals with visual impairments. In this work, we seek to address this substantial barrier, with the aim of ensuring that manga can be appreciated and actively engaged by everyone. Specifically, we tackle the problem of diarisation i.e. generating a transcription of who said what and when, in a fully automatic way. To this end, we make the following contributions: (1) we present a unified model, Magi, that is able to (a) detect panels, text boxes and character boxes, (b) cluster characters by identity (without knowing the number of clusters apriori), and (c) associate dialogues to their speakers; (2) we propose a novel approach that is able to sort the detected text boxes in their reading order and generate a dialogue transcript; (3) we annotate an evaluation benchmark for this task using publicly available [English] manga pages. The code, evaluation datasets and the pre-trained model can be found at: https://github.com/ragavsachdeva/magi.

Automatic music transcription (AMT) is the task of transcribing audio recordings into symbolic representations. Recently, neural network-based methods have been applied to AMT, and have achieved state-of-the-art results. However, many previous systems only detect the onset and offset of notes frame-wise, so the transcription resolution is limited to the frame hop size. There is a lack of research on using different strategies to encode onset and offset targets for training. In addition, previous AMT systems are sensitive to the misaligned onset and offset labels of audio recordings. Furthermore, there are limited researches on sustain pedal transcription on large-scale datasets. In this article, we propose a high-resolution AMT system trained by regressing precise onset and offset times of piano notes. At inference, we propose an algorithm to analytically calculate the precise onset and offset times of piano notes and pedal events. We show that our AMT system is robust to the misaligned onset and offset labels compared to previous systems. Our proposed system achieves an onset F1 of 96.72% on the MAESTRO dataset, outperforming previous onsets and frames system of 94.80%. Our system achieves a pedal onset F1 score of 91.86\%, which is the first benchmark result on the MAESTRO dataset. We have released the source code and checkpoints of our work at https://github.com/bytedance/piano_transcription.

We introduce an approach to identifying speaker names in dialogue transcripts, a crucial task for enhancing content accessibility and searchability in digital media archives. Despite the advancements in speech recognition, the task of text-based speaker identification (SpeakerID) has received limited attention, lacking large-scale, diverse datasets for effective model training. Addressing these gaps, we present a novel, large-scale dataset derived from the MediaSum corpus, encompassing transcripts from a wide range of media sources. We propose novel transformer-based models tailored for SpeakerID, leveraging contextual cues within dialogues to accurately attribute speaker names. Through extensive experiments, our best model achieves a great precision of 80.3\%, setting a new benchmark for SpeakerID. The data and code are publicly available here: https://github.com/adobe-research/speaker-identification

Multi-instrument music transcription aims to convert polyphonic music recordings into musical scores assigned to each instrument. This task is challenging for modeling as it requires simultaneously identifying multiple instruments and transcribing their pitch and precise timing, and the lack of fully annotated data adds to the training difficulties. This paper introduces YourMT3+, a suite of models for enhanced multi-instrument music transcription based on the recent language token decoding approach of MT3. We enhance its encoder by adopting a hierarchical attention transformer in the time-frequency domain and integrating a mixture of experts. To address data limitations, we introduce a new multi-channel decoding method for training with incomplete annotations and propose intra- and cross-stem augmentation for dataset mixing. Our experiments demonstrate direct vocal transcription capabilities, eliminating the need for voice separation pre-processors. Benchmarks across ten public datasets show our models' competitiveness with, or superiority to, existing transcription models. Further testing on pop music recordings highlights the limitations of current models. Fully reproducible code and datasets are available with demos at https://github.com/mimbres/YourMT3.

This paper introduces PublicHearingBR, a Brazilian Portuguese dataset designed for summarizing long documents. The dataset consists of transcripts of public hearings held by the Brazilian Chamber of Deputies, paired with news articles and structured summaries containing the individuals participating in the hearing and their statements or opinions. The dataset supports the development and evaluation of long document summarization systems in Portuguese. Our contributions include the dataset, a hybrid summarization system to establish a baseline for future studies, and a discussion on evaluation metrics for summarization involving large language models, addressing the challenge of hallucination in the generated summaries. As a result of this discussion, the dataset also provides annotated data that can be used in Natural Language Inference tasks in Portuguese.

The recent advancement of speech recognition technology has been driven by large-scale datasets and attention-based architectures, but many challenges still remain, especially for low-resource languages and dialects. This paper explores the integration of weakly supervised transcripts from TV subtitles into automatic speech recognition (ASR) systems, aiming to improve both verbatim transcriptions and automatically generated subtitles. To this end, verbatim data and subtitles are regarded as different domains or languages, due to their distinct characteristics. We propose and compare several end-to-end architectures that are designed to jointly model both modalities with separate or shared encoders and decoders. The proposed methods are able to jointly generate a verbatim transcription and a subtitle. Evaluation on Flemish (Belgian Dutch) demonstrates that a model with cascaded encoders and separate decoders allows to represent the differences between the two data types most efficiently while improving on both domains. Despite differences in domain and linguistic variations, combining verbatim transcripts with subtitle data leads to notable ASR improvements without the need for extensive preprocessing. Additionally, experiments with a large-scale subtitle dataset show the scalability of the proposed approach. The methods not only improve ASR accuracy but also generate subtitles that closely match standard written text, offering several potential applications.

Note-level Automatic Singing Voice Transcription (AST) converts singing recordings into note sequences, facilitating the automatic annotation of singing datasets for Singing Voice Synthesis (SVS) applications. Current AST methods, however, struggle with accuracy and robustness when used for practical annotation. This paper presents ROSVOT, the first robust AST model that serves SVS, incorporating a multi-scale framework that effectively captures coarse-grained note information and ensures fine-grained frame-level segmentation, coupled with an attention-based pitch decoder for reliable pitch prediction. We also established a comprehensive annotation-and-training pipeline for SVS to test the model in real-world settings. Experimental findings reveal that ROSVOT achieves state-of-the-art transcription accuracy with either clean or noisy inputs. Moreover, when trained on enlarged, automatically annotated datasets, the SVS model outperforms its baseline, affirming the capability for practical application. Audio samples are available at https://rosvot.github.io.

Spoken language conveys meaning not only through words but also through intonation, emotion, and emphasis. Sentence stress, the emphasis placed on specific words within a sentence, is crucial for conveying speaker intent and has been extensively studied in linguistics. In this work, we introduce WHISTRESS, an alignment-free approach for enhancing transcription systems with sentence stress detection. To support this task, we propose TINYSTRESS-15K, a scalable, synthetic training data for the task of sentence stress detection which resulted from a fully automated dataset creation process. We train WHISTRESS on TINYSTRESS-15K and evaluate it against several competitive baselines. Our results show that WHISTRESS outperforms existing methods while requiring no additional input priors during training or inference. Notably, despite being trained on synthetic data, WHISTRESS demonstrates strong zero-shot generalization across diverse benchmarks. Project page: https://pages.cs.huji.ac.il/adiyoss-lab/whistress.

In this paper, we introduce Jointist, an instrument-aware multi-instrument framework that is capable of transcribing, recognizing, and separating multiple musical instruments from an audio clip. Jointist consists of the instrument recognition module that conditions the other modules: the transcription module that outputs instrument-specific piano rolls, and the source separation module that utilizes instrument information and transcription results. The instrument conditioning is designed for an explicit multi-instrument functionality while the connection between the transcription and source separation modules is for better transcription performance. Our challenging problem formulation makes the model highly useful in the real world given that modern popular music typically consists of multiple instruments. However, its novelty necessitates a new perspective on how to evaluate such a model. During the experiment, we assess the model from various aspects, providing a new evaluation perspective for multi-instrument transcription. We also argue that transcription models can be utilized as a preprocessing module for other music analysis tasks. In the experiment on several downstream tasks, the symbolic representation provided by our transcription model turned out to be helpful to spectrograms in solving downbeat detection, chord recognition, and key estimation.

Automatic lyrics transcription (ALT) remains a challenging task in the field of music information retrieval, despite great advances in automatic speech recognition (ASR) brought about by transformer-based architectures in recent years. One of the major challenges in ALT is the high amplitude of interfering audio signals relative to conventional ASR due to musical accompaniment. Recent advances in music source separation have enabled automatic extraction of high-quality separated vocals, which could potentially improve ALT performance. However, the effect of source separation has not been systematically investigated in order to establish best practices for its use. This work examines the impact of source separation on ALT using Whisper, a state-of-the-art open source ASR model. We evaluate Whisper's performance on original audio, separated vocals, and vocal stems across short-form and long-form transcription tasks. For short-form, we suggest a concatenation method that results in a consistent reduction in Word Error Rate (WER). For long-form, we propose an algorithm using source separation as a vocal activity detector to derive segment boundaries, which results in a consistent reduction in WER relative to Whisper's native long-form algorithm. Our approach achieves state-of-the-art results for an open source system on the Jam-ALT long-form ALT benchmark, without any training or fine-tuning. We also publish MUSDB-ALT, the first dataset of long-form lyric transcripts following the Jam-ALT guidelines for which vocal stems are publicly available.

The Charlie Parker Omnibook is a cornerstone of jazz music education, described by pianist Ethan Iverson as "the most important jazz education text ever published". In this work we propose a new transcription pipeline and explore the extent to which state of the art music technology is able to reconstruct these scores directly from the audio without human intervention. Our pipeline includes: a newly trained source separation model for saxophone, a new MIDI transcription model for solo saxophone and an adaptation of an existing MIDI-to-score method for monophonic instruments. To assess this pipeline we also provide an enhanced dataset of Charlie Parker transcriptions as score-audio pairs with accurate MIDI alignments and downbeat annotations. This represents a challenging new benchmark for automatic audio-to-score transcription that we hope will advance research into areas beyond transcribing audio-to-MIDI alone. Together, these form another step towards producing scores that musicians can use directly, without the need for onerous corrections or revisions. To facilitate future research, all model checkpoints and data are made available to download along with code for the transcription pipeline. Improvements in our modular pipeline could one day make the automatic transcription of complex jazz solos a routine possibility, thereby enriching the resources available for music education and preservation.

Automatic music transcription (AMT) has achieved high accuracy for piano due to the availability of large, high-quality datasets such as MAESTRO and MAPS, but comparable datasets are not yet available for other instruments. In recent work, however, it has been demonstrated that aligning scores to transcription model activations can produce high quality AMT training data for instruments other than piano. Focusing on the guitar, we refine this approach to training on score data using a dataset of commercially available score-audio pairs. We propose the use of a high-resolution piano transcription model to train a new guitar transcription model. The resulting model obtains state-of-the-art transcription results on GuitarSet in a zero-shot context, improving on previously published methods.

Automatic speech recognition (ASR) systems often struggle with domain-specific terminology, especially in specialized settings such as academic lectures. To address this, we define the SlideASR task, which leverages the rich visual information from presentation slides to improve transcription accuracy. Existing pipeline methods for this task tend to be complex and underperform. Although omni-modal large language models (OLLMs) provide a promising end-to-end framework, they frequently fail in practice by degenerating into simple optical character recognition (OCR) systems. To overcome this, we propose Visually-Anchored Policy Optimization (VAPO), a novel post-training method designed to control the model's reasoning process. Drawing on the Chain-of-Thought reasoning paradigm, VAPO enforces a structured "Look before Transcription" procedure using a <think><answer> format. Specifically, the model first performs OCR on the slide content within the think step, then generates the transcription by referencing this recognized visual information in the answer step. This reasoning process is optimized via reinforcement learning with four distinct rewards targeting format compliance, OCR accuracy, ASR quality, and visual anchoring consistency. To support further research, we construct SlideASR-Bench, a new entity-rich benchmark consisting of a synthetic dataset for training and testing, and a challenging real-world set for evaluation. Extensive experiments demonstrate that VAPO significantly improves recognition of domain-specific terms, establishing an effective end-to-end paradigm for SlideASR.

Automatic Speech Recognition (ASR) transcripts, especially in low-resource languages like Bangla, contain a critical ambiguity: word-word repetitions can be either Repetition Disfluency (unintentional ASR error/hesitation) or Morphological Reduplication (a deliberate grammatical construct). Standard disfluency correction fails by erroneously deleting valid linguistic information. To solve this, we introduce the first publicly available, 20,000-row Bangla corpus, manually annotated to explicitly distinguish between these two phenomena in noisy ASR transcripts. We benchmark this novel resource using two paradigms: state-of-the-art multilingual Large Language Models (LLMs) and task-specific fine-tuning of encoder models. LLMs achieve competitive performance (up to 82.68\% accuracy) with few-shot prompting. However, fine-tuning proves superior, with the language-specific BanglaBERT model achieving the highest accuracy of 84.78\% and an F1 score of 0.677. This establishes a strong, linguistically-informed baseline and provides essential data for developing sophisticated, semantic-preserving text normalization systems for Bangla.

Automatic drum transcription (ADT) is traditionally formulated as a discriminative task to predict drum events from audio spectrograms. In this work, we redefine ADT as a conditional generative task and introduce Noise-to-Notes (N2N), a framework leveraging diffusion modeling to transform audio-conditioned Gaussian noise into drum events with associated velocities. This generative diffusion approach offers distinct advantages, including a flexible speed-accuracy trade-off and strong inpainting capabilities. However, the generation of binary onset and continuous velocity values presents a challenge for diffusion models, and to overcome this, we introduce an Annealed Pseudo-Huber loss to facilitate effective joint optimization. Finally, to augment low-level spectrogram features, we propose incorporating features extracted from music foundation models (MFMs), which capture high-level semantic information and enhance robustness to out-of-domain drum audio. Experimental results demonstrate that including MFM features significantly improves robustness and N2N establishes a new state-of-the-art performance across multiple ADT benchmarks.

Automatic Music Transcription (AMT) converts audio recordings into symbolic musical representations. Training deep neural networks (DNNs) for AMT typically requires strongly aligned training pairs with precise frame-level annotations. Since creating such datasets is costly and impractical for many musical contexts, weakly aligned approaches using segment-level annotations have gained traction. However, existing methods often rely on Dynamic Time Warping (DTW) or soft alignment loss functions, both of which still require local semantic correspondences, making them error-prone and computationally expensive. In this article, we introduce CountEM, a novel AMT framework that eliminates the need for explicit local alignment by leveraging note event histograms as supervision, enabling lighter computations and greater flexibility. Using an Expectation-Maximization (EM) approach, CountEM iteratively refines predictions based solely on note occurrence counts, significantly reducing annotation efforts while maintaining high transcription accuracy. Experiments on piano, guitar, and multi-instrument datasets demonstrate that CountEM matches or surpasses existing weakly supervised methods, improving AMT's robustness, scalability, and efficiency. Our project page is available at https://yoni-yaffe.github.io/count-the-notes.

Speaker-Attributed, Time-Stamped Transcription (SATS) aims to transcribe what is said and to precisely determine the timing of each speaker, which is particularly valuable for meeting transcription. Existing SATS systems rarely adopt an end-to-end formulation and are further constrained by limited context windows, weak long-range speaker memory, and the inability to output timestamps. To address these limitations, we present MOSS Transcribe Diarize, a unified multimodal large language model that jointly performs Speaker-Attributed, Time-Stamped Transcription in an end-to-end paradigm. Trained on extensive real wild data and equipped with a 128k context window for up to 90-minute inputs, MOSS Transcribe Diarize scales well and generalizes robustly. Across comprehensive evaluations, it outperforms state-of-the-art commercial systems on multiple public and in-house benchmarks.

Automatic Lyrics Transcription (ALT) for Vietnamese music presents unique challenges due to its tonal complexity and dialectal variations, but remains largely unexplored due to the lack of a dedicated dataset. Therefore, we curated the first large-scale Vietnamese ALT dataset (VietLyrics), comprising 647 hours of songs with line-level aligned lyrics and metadata to address these issues. Our evaluation of current ASRbased approaches reveal significant limitations, including frequent transcription errors and hallucinations in non-vocal segments. To improve performance, we fine-tuned Whisper models on the VietLyrics dataset, achieving superior results compared to existing multilingual ALT systems, including LyricWhiz. We publicly release VietLyrics and our models, aiming to advance Vietnamese music computing research while demonstrating the potential of this approach for ALT in low-resource language and music.

Source separation is the process of isolating individual sounds in an auditory mixture of multiple sounds [1], and has a variety of applications ranging from speech enhancement and lyric transcription [2] to digital audio production for music. Furthermore, Automatic Music Transcription (AMT) is the process of converting raw music audio into sheet music that musicians can read [3]. Historically, these tasks have faced challenges such as significant audio noise, long training times, and lack of free-use data due to copyright restrictions. However, recent developments in deep learning have brought new promising approaches to building low-distortion stems and generating sheet music from audio signals [4]. Using spectrogram masking, deep neural networks, and the MuseScore API, we attempt to create an end-to-end pipeline that allows for an initial music audio mixture (e.g...wav file) to be separated into instrument stems, converted into MIDI files, and transcribed into sheet music for each component instrument.

With recent advances in modeling and the increasing amount of supervised training data, automatic speech recognition (ASR) systems have achieved remarkable performance on general speech. However, the word error rate (WER) of state-of-the-art ASR remains high for named entities. Since named entities are often the most critical keywords, misrecognizing them can affect all downstream applications, especially when the ASR system functions as the front end of a complex system. In this paper, we introduce a large language model (LLM) revision mechanism to revise incorrect named entities in ASR predictions by leveraging the LLM's reasoning ability as well as local context (e.g., lecture notes) containing a set of correct named entities. Finally, we introduce the NER-MIT-OpenCourseWare dataset, containing 45 hours of data from MIT courses for development and testing. On this dataset, our proposed technique achieves up to 30\% relative WER reduction for named entities.

Predicting high-dimensional transcriptional responses to genetic perturbations is challenging due to severe experimental noise and sparse gene-level effects. Existing methods often suffer from mean collapse, where high correlation is achieved by predicting global average expression rather than perturbation-specific responses, leading to many false positives and limited biological interpretability. Recent approaches incorporate biological knowledge graphs into perturbation models, but these graphs are typically treated as dense and static, which can propagate noise and obscure true perturbation signals. We propose AdaPert, a perturbation-conditioned framework that addresses mean collapse by explicitly modeling sparsity and biological structure. AdaPert learns perturbation-specific subgraphs from biological knowledge graphs and applies adaptive learning to separate true signals from noise. Across multiple genetic perturbation benchmarks, AdaPert consistently outperforms existing baselines and achieves substantial improvements on DEG-aware evaluation metrics, indicating more accurate recovery of perturbation-specific transcriptional changes.

Simultaneous machine translation (SiMT) has traditionally relied on offline machine translation models coupled with human-engineered heuristics or learned policies. We propose Hikari, a policy-free, fully end-to-end model that performs simultaneous speech-to-text translation and streaming transcription by encoding READ/WRITE decisions into a probabilistic WAIT token mechanism. We also introduce Decoder Time Dilation, a mechanism that reduces autoregressive overhead and ensures a balanced training distribution. Additionally, we present a supervised fine-tuning strategy that trains the model to recover from delays, significantly improving the quality-latency trade-off. Evaluated on English-to-Japanese, German, and Russian, Hikari achieves new state-of-the-art BLEU scores in both low- and high-latency regimes, outperforming recent baselines.

Recent advances in Automatic Speech Recognition (ASR) and Large Language Models (LLMs) have significantly improved speech understanding capabilities. However, multi-speaker speech transcription remains challenging task, constrained by highly similar speaker voices, rapid turn-taking transitions, overlapping utterances and inaccurate speaker boundary segmentation. These challenges become particularly pronounced in real-world conversational audio, where speaker dynamics and acoustic conditions are highly variable. This technical report presents SoulX-Transcriber, a unified multi-speaker transcription system that jointly models speaker diarization (SD) and ASR within an LLM-based framework. SoulX-Transcriber adopts a two-stage training strategy to improve both speaker discrimination and transcription robustness. In the first stage, speaker-aware multi-task continuous pre-training enhances speaker representation learning and boundary perception. In the second stage, supervised fine-tuning further optimizes the model for accurate end-to-end speaker-attributed transcription under complex multi-speaker conditions. SoulX-Transcriber delivers strong performance and robustness across multiple public benchmarks, including AliMeeting, AISHELL-4, and AMI, while maintaining high adaptability to multi-domain scenarios.

We present MulTTiPop, a dataset of pop music segments and their associated multitrack MIDI recordings for the evaluation of automatic music transcription models. MulTTiPop contains 572 segments of popular music totaling 3.5 hours of audio, and contains songs from diverse genres and decades from the 1930s to 2000s. To collect this dataset, we perform metadata-based matching on song segments from the Lakh MIDI and TheoryTab datasets, manually identify an anchor beat between the audio and MIDI, then use beat tracking on the audio and warp the MIDI to match its tempo and timing. We evaluate state-of-the-art automatic music transcription models on MulTTiPop and find substantial room for improvement, with the best model achieving 38% Onset F1. More details and sound examples of MulTTiPop are available at https://gclef-cmu.org/multtipop.

Visual piano transcription (VPT) is the task of obtaining a symbolic representation of a piano performance from visual information alone (e.g., from a top-down video of the piano keyboard). In this work we propose a VPT system based on the vision transformer (ViT), which surpasses previous methods based on convolutional neural networks (CNNs). Our system is trained on the newly introduced R3 dataset, consisting of ca.~31 hours of synchronized video and MIDI recordings of piano performances. We additionally introduce an approach to predict note offsets, which has not been previously explored in this context. We show that our system outperforms the state-of-the-art on the PianoYT dataset for onset prediction and on the R3 dataset for both onsets and offsets.

Audio-based piano transcription performs well on onset, pitch, and velocity, but the sustain pedal lets sound persist long after key release, so audio systems predict pedal-extended offsets rather than physical key release. Yet existing Visual Piano Transcription (VPT) systems focus on onset detection from short video windows, offset accuracy lags onset by a wide margin, and note-level velocity has not been reported. To address these gaps, we present V2N (Video to Notes), the first complete VPT system: a shared temporal backbone feeds task-specific heads for onset, offset, key hold, and velocity, jointly trained with per-frame supervision rather than only at the window center. Ablations show that multi-task supervision enables offset and velocity prediction while improving onset accuracy; longer temporal context yields further improvements. V2N sets new state-of-the-art results on PianoVAM and R3.

Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. Existing approaches often rely on auxiliary cell-state encoders, hierarchical variational autoencoders, dedicated Transformer encoder-decoder modules, or gene-interaction priors to compress high-dimensional expression profiles into latent representations. While effective, these designs increase architectural complexity and may limit scalability and generalizability. This paper introduces OCOO-T, a minimalist flow-matching-based AIVC model for transcriptional perturbation response prediction. OCOO-T utilizes a vanilla Transformer stack that operates directly on continuous gene expression profiles and formulates perturbation response prediction as a continuous-time denoising process. Perturbation embeddings, dosage information, and cell-line/cell-type specificity are integrated through adaptive layer normalization and in-context tokens. Comprehensive evaluations on Tahoe100M, Replogle, and PBMC benchmarks demonstrate that OCOO-T achieves state-of-the-art performance across diverse perturbations and cell types while effectively scaling to long transcriptional profiles through patching and depatching of cellular contexts. By leveraging the simplicity of Transformer-based denoising for single-cell omics, OCOO-T provides an effective and scalable framework for in-silico cellular simulation.

Whisper is a widely used foundation model for automatic speech recognition (ASR), but its generative decoder can produce fluent hallucinated transcripts for inputs containing little or no speech. We propose a training-free, inference-time method to reduce these hallucinations using low-rank projection of decoder activations. A compact hallucination-associated subspace is estimated from non-speech calibration data, and decoder hidden states are projected away from this subspace during inference. We evaluate two variants: always-on, which applies projection to all inputs, and gated, which applies it only when Whisper predicts that an input is likely non-speech. Across non-speech benchmarks, always-on projection reduces average hallucination rate (HR) from 31.31% to 2.44%, a 92.21% relative reduction, while gated projection reduces HR to 3.74%, an 88.05% relative reduction, with lower false rejection of genuine speech. On LibriSpeech, gated projection increases absolute word error rate (WER) by 0.33-4.39 percentage points and yields false-rejection rates (FRR) of 0.41--9.97% across model and split settings. These results show that low-rank activation projection can substantially suppress Whisper hallucinations without retraining, while providing a controllable trade-off between hallucination suppression and speech recognition performance.

This paper shows that latent-space predictive pretraining can provide a scalable route to foundation models for spatial transcriptomics. Existing spatial transcriptomics foundation models primarily reconstruct masked gene identities or expression values, potentially encouraging the reproduction of assay-specific technical variation and limiting representation transferability. To avoid directly reconstructing such variation, we shift the prediction target from observed gene measurements to latent cell representations and introduce CellWorld, which predicts the latent representations of masked cells from visible spatial context and a limited partial-expression hint. We pretrain four CellWorld variants, spanning 5.74M to 94.56M trainable parameters, on a corpus of 46 million human cells. Our controlled scaling experiments show that performance improves with model capacity, particularly on spatial tasks, while spatial transfer depends more on sufficient optimization and broad biological source diversity than on cell count alone. Across four held-out datasets, even CellWorld-Small, with 5.74M trainable parameters, outperforms every baseline on all 11 linear-probe benchmarks and all seven fine-tuned spatial benchmarks. Most notably, a frozen CellWorld-Large pretrained on only 5\% of the corpus with broad biological source coverage outperforms every fully fine-tuned baseline across all seven spatial benchmarks. Code is available at https://github.com/UoM-HealthAI/CellWorld.

Speech-to-IPA transcription is useful when the desired output is pronunciation rather than orthographic text, but competitive multilingual systems are often large and evaluation is sensitive to normalization choices. This paper presents BranchShine, a 33M-parameter raw-audio CTC recognizer with a lightweight convolutional front end and a 19-block RoPE E-Branchformer encoder. We find that BranchShine provides a compact and competitive operating point for IPA transcription under matched normalization and scoring. On a 16,660-utterance multilingual test set covering 41 language labels, BranchShine obtains 9.19% whitespace-insensitive IPA character error rate, compared with 9.78% for the 575.00M-parameter PhoneticXEUS baseline. A secondary child speech reading analysis shows a complementary operating profile: BranchShine is more conservative on incorrect readings, while Whisper-Medium is stronger on exact acceptance of correct readings. Overall, the results indicate that a compact raw-audio-to-IPA model can approach much larger baselines on character-level IPA transcription.

Transcribing music into a human-readable score requires a coherent understanding of rhythm, harmony, melody, and form. Two obstacles limit this goal: annotated recordings are scarce, and accurate local predictions can still produce inconsistent musical sequences. We present SheetSage2, a unified music transcription framework that combines synthetic data, task-specific structured decoding, and autoregressive distillation. Automatically annotated MIDI, rendered into audio, provides scalable supervision across music understanding tasks. Task-specific structured decoders integrate complementary musical cues and their temporal dependencies to produce musically coherent scores. Autoregressive distillation further retains transcription accuracy without task-specific dynamic programming at inference. Across eight benchmark collections, a single SheetSage2-AR model exceeds the listed prior systems on 12 of 15 benchmark--metric pairs in our evaluation, substantially improving over SheetSage1 and surpassing task-specific models on several benchmarks. Model weights and inference code are publicly available.

Existing audio-to-score (A2S) systems primarily focus on classical music, and the application to popular music remains underexplored. This paper first presents the new SheetSage-A2S Dataset, which includes 61 hours of audio with **kern score encodings for 9,468 clips originating from 6,066 unique songs, the first of its kind to facilitate A2S research for popular music. Additionally, we improve on existing A2S approaches by using data augmentation and MuQ, a pretrained feature-extraction model for music audio, to enhance generalisation abilities and extract meaningful audio features. Results show that the proposed A2S model achieves 4.98% symbol error rate (SER) on the Quartets collection for classical music, which significantly outperforms the 15.3% SER from the existing state-of-the-art (Alfaro-Contreras et al. 2024). Additionally, our model achieves 20.92% SER on the SheetSage-A2S dataset for popular music, serving as a strong benchmark for future research. The dataset, model, and code are made publicly available at: https://github.com/Multimodal-Music-Research-Lab/SheetSage2Kern_model.

Automatic Music Transcription (AMT) for guitar remains limited by three challenges: existing systems often fail to capture expressive techniques such as slides, bends, and percussive hits; they often assign notes to incorrect string-fret combinations; and they are typically trained on clean recordings, limiting their generalization to noisy real-world audio. To address these challenges, we propose TART, a modular four-stage audio-to-tablature pipeline consisting of (1) an audio-to-MIDI transcription model, (2) an expressive technique classifier, (3) an audio-conditioned T5 encoder-decoder for string-fret assignment, and (4) an automated tablature generator. We evaluate TART in a zero-shot setting on GuitarSet, EGDB, and two augmented benchmarks, Noisy GuitarSet and Noisy EGDB. Averaged across these four benchmarks, TART achieves 81.35% audio-to-MIDI F50 (+6.67 points over the best prior baseline), 71.8% string-fret Tab F1 (+8.5 points over the best prior baseline), and 54.08% end-to-end Tab F1. To our knowledge, TART is the first framework to generate guitar tablature with both fingering and expressive technique annotations directly from guitar audio.

Time accurate speech transcription is essential in critical appli- cations, such as medical conversation transcription, reading as- sessment, and atypical speech recognition. Encoder-decoder auto- matic speech recognition models, such as Whisper, do not produce word-level timestamps out-of-the-box for all languages. Existing approaches to word-level time stamp estimation either use an exter- nal CTC model capable of frame level phoneme/character prediction which is computationally expensive, or use the cross attention scores internal to the model which gives coarse time stamps. We consider timestamped speech transcription for Hindi in this paper. We pro- pose a CTC-based approach, in which we train a low-complexity character level CTC head directly on the Whisper encoder output, to address the complexity and granularity limitations of existing works. We evaluate the system using manually-annotated word-level times- tamps. Experiments show that the proposed internal-CTC based approach performs similar to using an external CTC model and better than the cross attention score-based approaches. Further, we study the usage of CTC-head output to detect and mitigate hallu- cinations in conversational speech. Our results show that a simple token length criterion derived from the CTC output can improve the transcription quality for short segments where hallucinations are more probable.

To understand the function of cortical circuits it is necessary to classify their underlying cellular diversity. Traditional attempts based on comparing anatomical or physiological features of neurons and glia, while productive, have not resulted in a unified taxonomy of neural cell types. The recent development of single-cell transcriptomics has enabled, for the first time, systematic high-throughput profiling of large numbers of cortical cells and the generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data have revealed the existence of clear clusters, many of which correspond to cell types defined by traditional criteria, and which are conserved across cortical areas and species. To capitalize on these innovations and advance the field, we, the Copenhagen Convention Group, propose the community adopts a transcriptome-based taxonomy of the cell types in the adult mammalian neocortex. This core classification should be ontological, hierarchical and use a standardized nomenclature. It should be configured to flexibly incorporate new data from multiple approaches, developmental stages and a growing number of species, enabling improvement and revision of the classification. This community-based strategy could serve as a common foundation for future detailed analysis and reverse engineering of cortical circuits and serve as an example for cell type classification in other parts of the nervous system and other organs.

Gene expression is widely measured in biomedicine, yet clinical outcome prediction remains challenging due to high dimensionality, strong feature correlations, and limited labeled data. Large self-supervised transcriptomic foundation models often fail to outperform simple supervised baselines. Tabular foundation models offer an alternative through in-context learning, but are typically pretrained on generic synthetic data rather than transcriptomic structure. We ask whether transcriptomics-aware pretraining, rather than scale, is the missing ingredient. Towards this end, we introduce GeneICL, a 4.2M-parameter tabular foundation model combining a semi-synthetic pretraining prior built from measured bulk expression profiles with a parameter-efficient recurrent architecture. We further enable right-censored survival prediction via a training-free reduction to regression using Cox partial-likelihood residuals. We evaluate GeneICL on 80 clinical outcome-prediction tasks spanning classification, regression, and survival. Tabular foundation models consistently outperform self-supervised transcriptomic models, while GeneICL achieves the best overall rank among evaluated foundation models and tuned baselines. GeneICL does so with up to 387times fewer parameters, no gradient updates at inference, and predictions within seconds on a laptop CPU.

Single-instrument automatic music transcription (AMT) has advanced substantially, yet choral applications require soprano, alto, tenor, and bass (SATB) to be transcribed as separate parts. Recent note-level choral AMT instead produces a single merged note track, limiting rehearsal, education, and score reconstruction. To address this limitation, we introduce Part-aware Choral Transcription (PawCT), to our knowledge the first end-to-end neural framework that identifies active SATB parts from choral audio and transcribes each into a separate note-level track. PawCT combines part-specific onset, offset, and frame prediction with part-presence estimation, union-level supervision, and structured training targets using a range prior (RP) based on SATB pitch ranges and its ordered-continuity (OC) extension, which adds within-part melodic continuity and cross-part pitch ordering. On YouChorale, PawCT-RP-OC achieves a macro part-aware note F1 of 0.225 at a 50-ms onset tolerance, outperforming an adapted choral baseline (0.165) by 36.4% relative and a two-stage post-hoc assignment pipeline (0.175). Its part-agnostic variant, PagCT, achieves a 50-ms onset F1 of 0.382, compared with 0.237 for the previous state-of-the-art choral AMT model. Cross-dataset evaluations on CSD and Cantoria further assess performance under dataset shift. These results demonstrate the benefit of jointly modeling note transcription and vocal-part assignment. Code and demos are available at https://hanyu-meng.github.io/Paw_Choral_AMT_Demo/.

Enabling engagement of manga by visually impaired individuals presents a significant challenge due to its inherently visual nature. With the goal of fostering accessibility, this paper aims to generate a dialogue transcript of a complete manga chapter, entirely automatically, with a particular emphasis on ensuring narrative consistency. This entails identifying (i) what is being said, i.e., detecting the texts on each page and classifying them into essential vs non-essential, and (ii) who is saying it, i.e., attributing each dialogue to its speaker, while ensuring the same characters are named consistently throughout the chapter. To this end, we introduce: (i) Magiv2, a model that is capable of generating high-quality chapter-wide manga transcripts with named characters and significantly higher precision in speaker diarisation over prior works; (ii) an extension of the PopManga evaluation dataset, which now includes annotations for speech-bubble tail boxes, associations of text to corresponding tails, classifications of text as essential or non-essential, and the identity for each character box; and (iii) a new character bank dataset, which comprises over 11K characters from 76 manga series, featuring 11.5K exemplar character images in total, as well as a list of chapters in which they appear. The code, trained model, and both datasets can be found at: https://github.com/ragavsachdeva/magi

We introduce CallCenterEN, a large-scale (91,706 conversations, corresponding to 10448 audio hours), real-world English call center transcript dataset designed to support research and development in customer support and sales AI systems. This is the largest release to-date of open source call center transcript data of this kind. The dataset includes inbound and outbound calls between agents and customers, with accents from India, the Philippines and the United States. The dataset includes high-quality, PII-redacted human-readable transcriptions. All personally identifiable information (PII) has been rigorously removed to ensure compliance with global data protection laws. The audio is not included in the public release due to biometric privacy concerns. Given the scarcity of publicly available real-world call center datasets, CallCenterEN fills a critical gap in the landscape of available ASR corpora, and is released under a CC BY-NC 4.0 license for non-commercial research use.

While autoregressive (AR) LLM-based ASR systems achieve strong accuracy, their sequential decoding limits parallelism and incurs high latency. We propose NLE, a non-autoregressive (NAR) approach that formulates speech recognition as conditional transcript editing, enabling fully parallel prediction. NLE extracts acoustic embeddings and an initial hypothesis from a pretrained speech encoder, then refines the hypothesis using a bidirectional LLM editor trained with a latent alignment objective. An interleaved padding strategy exploits the identity mapping bias of Transformers, allowing the model to focus on corrections rather than full reconstruction. On the Open ASR leaderboard, NLE++ achieves 5.67% average WER with an RTFx (inverse real-time factor) of 1630. In single-utterance scenarios, NLE achieves 27x speedup over the AR baseline, making it suitable for real-time applications.

In many Vietnamese schools, grades are still being inputted into the database manually, which is not only inefficient but also prone to human error. Thus, the automation of this process is highly necessary, which can only be achieved if we can extract information from academic transcripts. In this paper, we test our improved CRNN model in extracting information from 126 transcripts, with 1008 vertical lines, 3859 horizontal lines, and 2139 handwritten test scores. Then, this model is compared to the Baseline model. The results show that our model significantly outperforms the Baseline model with an accuracy of 99.6% in recognizing vertical lines, 100% in recognizing horizontal lines, and 96.11% in recognizing handwritten test scores.

We introduce LyricWhiz, a robust, multilingual, and zero-shot automatic lyrics transcription method achieving state-of-the-art performance on various lyrics transcription datasets, even in challenging genres such as rock and metal. Our novel, training-free approach utilizes Whisper, a weakly supervised robust speech recognition model, and GPT-4, today's most performant chat-based large language model. In the proposed method, Whisper functions as the "ear" by transcribing the audio, while GPT-4 serves as the "brain," acting as an annotator with a strong performance for contextualized output selection and correction. Our experiments show that LyricWhiz significantly reduces Word Error Rate compared to existing methods in English and can effectively transcribe lyrics across multiple languages. Furthermore, we use LyricWhiz to create the first publicly available, large-scale, multilingual lyrics transcription dataset with a CC-BY-NC-SA copyright license, based on MTG-Jamendo, and offer a human-annotated subset for noise level estimation and evaluation. We anticipate that our proposed method and dataset will advance the development of multilingual lyrics transcription, a challenging and emerging task.

Prosody plays an important role in characterizing the style of a speaker or an emotion, but most non-parallel voice or emotion style transfer algorithms do not convert any prosody information. Two major components of prosody are pitch and rhythm. Disentangling the prosody information, particularly the rhythm component, from the speech is challenging because it involves breaking the synchrony between the input speech and the disentangled speech representation. As a result, most existing prosody style transfer algorithms would need to rely on some form of text transcriptions to identify the content information, which confines their application to high-resource languages only. Recently, SpeechSplit has made sizeable progress towards unsupervised prosody style transfer, but it is unable to extract high-level global prosody style in an unsupervised manner. In this paper, we propose AutoPST, which can disentangle global prosody style from speech without relying on any text transcriptions. AutoPST is an Autoencoder-based Prosody Style Transfer framework with a thorough rhythm removal module guided by the self-expressive representation learning. Experiments on different style transfer tasks show that AutoPST can effectively convert prosody that correctly reflects the styles of the target domains.

We demonstrate that carefully adjusting the tokenizer of the Whisper speech recognition model significantly improves the precision of word-level timestamps when applying dynamic time warping to the decoder's cross-attention scores. We fine-tune the model to produce more verbatim speech transcriptions and employ several techniques to increase robustness against multiple speakers and background noise. These adjustments achieve state-of-the-art performance on benchmarks for verbatim speech transcription, word segmentation, and the timed detection of filler events, and can further mitigate transcription hallucinations. The code is available open https://github.com/nyrahealth/CrisperWhisper.

This paper introduces Moonshine, a family of speech recognition models optimized for live transcription and voice command processing. Moonshine is based on an encoder-decoder transformer architecture and employs Rotary Position Embedding (RoPE) instead of traditional absolute position embeddings. The model is trained on speech segments of various lengths, but without using zero-padding, leading to greater efficiency for the encoder during inference time. When benchmarked against OpenAI's Whisper tiny.en, Moonshine Tiny demonstrates a 5x reduction in compute requirements for transcribing a 10-second speech segment while incurring no increase in word error rates across standard evaluation datasets. These results highlight Moonshine's potential for real-time and resource-constrained applications.

Fact-checking is extensively studied in the context of misinformation and disinformation, addressing objective inaccuracies. However, a softer form of misinformation involves responses that are factually correct but lack certain features such as clarity and relevance. This challenge is prevalent in formal Question-Answer (QA) settings such as press conferences in finance, politics, sports, and other domains, where subjective answers can obscure transparency. Despite this, there is a lack of manually annotated datasets for subjective features across multiple dimensions. To address this gap, we introduce SubjECTive-QA, a human annotated dataset on Earnings Call Transcripts' (ECTs) QA sessions as the answers given by company representatives are often open to subjective interpretations and scrutiny. The dataset includes 49,446 annotations for long-form QA pairs across six features: Assertive, Cautious, Optimistic, Specific, Clear, and Relevant. These features are carefully selected to encompass the key attributes that reflect the tone of the answers provided during QA sessions across different domain. Our findings are that the best-performing Pre-trained Language Model (PLM), RoBERTa-base, has similar weighted F1 scores to Llama-3-70b-Chat on features with lower subjectivity, such as Relevant and Clear, with a mean difference of 2.17% in their weighted F1 scores. The models perform significantly better on features with higher subjectivity, such as Specific and Assertive, with a mean difference of 10.01% in their weighted F1 scores. Furthermore, testing SubjECTive-QA's generalizability using QAs from White House Press Briefings and Gaggles yields an average weighted F1 score of 65.97% using our best models for each feature, demonstrating broader applicability beyond the financial domain. SubjECTive-QA is publicly available under the CC BY 4.0 license

Text data is commonly utilized as a primary input to enhance Speech Emotion Recognition (SER) performance and reliability. However, the reliance on human-transcribed text in most studies impedes the development of practical SER systems, creating a gap between in-lab research and real-world scenarios where Automatic Speech Recognition (ASR) serves as the text source. Hence, this study benchmarks SER performance using ASR transcripts with varying Word Error Rates (WERs) from eleven models on three well-known corpora: IEMOCAP, CMU-MOSI, and MSP-Podcast. Our evaluation includes both text-only and bimodal SER with six fusion techniques, aiming for a comprehensive analysis that uncovers novel findings and challenges faced by current SER research. Additionally, we propose a unified ASR error-robust framework integrating ASR error correction and modality-gated fusion, achieving lower WER and higher SER results compared to the best-performing ASR transcript. These findings provide insights into SER with ASR assistance, especially for real-world applications.

With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and properties of the target disease. Here, we introduce the first generative model capable of tailoring anticancer compounds for a specific biomolecular profile. Using a RL framework, the transcriptomic profiles of cancer cells are used as a context for the generation of candidate molecules. Our molecule generator combines two separately pretrained variational autoencoders (VAEs) - the first VAE encodes transcriptomic profiles into a smooth, latent space which in turn is used to condition a second VAE to generate novel molecular structures on the given transcriptomic profile. The generative process is optimized through PaccMann, a previously developed drug sensitivity prediction model to obtain effective anticancer compounds for the given context (i.e., transcriptomic profile). We demonstrate how the molecule generation can be biased towards compounds with high predicted inhibitory effect against individual cell lines or specific cancer sites. We verify our approach by investigating candidate drugs generated against specific cancer types and find the highest structural similarity to existing compounds with known efficacy against these cancer types. We envision our approach to transform in silico anticancer drug design by leveraging the biomolecular characteristics of the disease in order to increase success rates in lead compound discovery.

Recent video large language models (Video LLMs) often depend on costly human annotations or proprietary model APIs (e.g., GPT-4o) to produce training data, which limits their training at scale. In this paper, we explore large-scale training for Video LLM with cheap automatic speech recognition (ASR) transcripts. Specifically, we propose a novel streaming training approach that densely interleaves the ASR words and video frames according to their timestamps. Compared to previous studies in vision-language representation with ASR, our method naturally fits the streaming characteristics of ASR, thus enabling the model to learn temporally-aligned, fine-grained vision-language modeling. To support the training algorithm, we introduce a data production pipeline to process YouTube videos and their closed captions (CC, same as ASR), resulting in Live-CC-5M dataset for pre-training and Live-WhisperX-526K dataset for high-quality supervised fine-tuning (SFT). Remarkably, even without SFT, the ASR-only pre-trained LiveCC-7B-Base model demonstrates competitive general video QA performance and exhibits a new capability in real-time video commentary. To evaluate this, we carefully design a new LiveSports-3K benchmark, using LLM-as-a-judge to measure the free-form commentary. Experiments show our final LiveCC-7B-Instruct model can surpass advanced 72B models (Qwen2.5-VL-72B-Instruct, LLaVA-Video-72B) in commentary quality even working in a real-time mode. Meanwhile, it achieves state-of-the-art results at the 7B/8B scale on popular video QA benchmarks such as VideoMME and OVOBench, demonstrating the broad generalizability of our approach. All resources of this paper have been released at https://showlab.github.io/livecc.

This work explores the problem of generating task graphs of real-world activities. Different from prior formulations, we consider a setting where text transcripts of instructional videos performing a real-world activity (e.g., making coffee) are provided and the goal is to identify the key steps relevant to the task as well as the dependency relationship between these key steps. We propose a novel task graph generation approach that combines the reasoning capabilities of instruction-tuned language models along with clustering and ranking components to generate accurate task graphs in a completely unsupervised manner. We show that the proposed approach generates more accurate task graphs compared to a supervised learning approach on tasks from the ProceL and CrossTask datasets.

In this paper we propose a novel generative approach, DiffRoll, to tackle automatic music transcription (AMT). Instead of treating AMT as a discriminative task in which the model is trained to convert spectrograms into piano rolls, we think of it as a conditional generative task where we train our model to generate realistic looking piano rolls from pure Gaussian noise conditioned on spectrograms. This new AMT formulation enables DiffRoll to transcribe, generate and even inpaint music. Due to the classifier-free nature, DiffRoll is also able to be trained on unpaired datasets where only piano rolls are available. Our experiments show that DiffRoll outperforms its discriminative counterpart by 19 percentage points (ppt.) and our ablation studies also indicate that it outperforms similar existing methods by 4.8 ppt. Source code and demonstration are available https://sony.github.io/DiffRoll/.

Most of the current supervised automatic music transcription (AMT) models lack the ability to generalize. This means that they have trouble transcribing real-world music recordings from diverse musical genres that are not presented in the labelled training data. In this paper, we propose a semi-supervised framework, ReconVAT, which solves this issue by leveraging the huge amount of available unlabelled music recordings. The proposed ReconVAT uses reconstruction loss and virtual adversarial training. When combined with existing U-net models for AMT, ReconVAT achieves competitive results on common benchmark datasets such as MAPS and MusicNet. For example, in the few-shot setting for the string part version of MusicNet, ReconVAT achieves F1-scores of 61.0% and 41.6% for the note-wise and note-with-offset-wise metrics respectively, which translates into an improvement of 22.2% and 62.5% compared to the supervised baseline model. Our proposed framework also demonstrates the potential of continual learning on new data, which could be useful in real-world applications whereby new data is constantly available.

Background: Clinical documentation represents a significant burden for healthcare providers, with physicians spending up to 2 hours daily on administrative tasks. Recent advances in large language models (LLMs) offer promising solutions, but privacy concerns and computational requirements limit their adoption in healthcare settings. Objective: To develop and evaluate a privacy-preserving, on-device medical transcription system using a fine-tuned Llama 3.2 1B model capable of generating structured medical notes from medical transcriptions while maintaining complete data sovereignty entirely in the browser. Methods: We fine-tuned a Llama 3.2 1B model using Parameter-Efficient Fine-Tuning (PEFT) with LoRA on 1,500 synthetic medical transcription-to-structured note pairs. The model was evaluated against the base Llama 3.2 1B on two datasets: 100 endocrinology transcripts and 140 modified ACI benchmark cases. Evaluation employed both statistical metrics (ROUGE, BERTScore, BLEURT) and LLM-as-judge assessments across multiple clinical quality dimensions. Results: The fine-tuned OnDevice model demonstrated substantial improvements over the base model. On the ACI benchmark, ROUGE-1 scores increased from 0.346 to 0.496, while BERTScore F1 improved from 0.832 to 0.866. Clinical quality assessments showed marked reduction in major hallucinations (from 85 to 35 cases) and enhanced factual correctness (2.81 to 3.54 on 5-point scale). Similar improvements were observed on the internal evaluation dataset, with composite scores increasing from 3.13 to 4.43 (+41.5%). Conclusions: Fine-tuning compact LLMs for medical transcription yields clinically meaningful improvements while enabling complete on-device browser deployment. This approach addresses key barriers to AI adoption in healthcare: privacy preservation, cost reduction, and accessibility for resource-constrained environments.

Recent breakthroughs in singing voice synthesis (SVS) have heightened the demand for high-quality annotated datasets, yet manual annotation remains prohibitively labor-intensive and resource-intensive. Existing automatic singing annotation (ASA) methods, however, primarily tackle isolated aspects of the annotation pipeline. To address this fundamental challenge, we present STARS, which is, to our knowledge, the first unified framework that simultaneously addresses singing transcription, alignment, and refined style annotation. Our framework delivers comprehensive multi-level annotations encompassing: (1) precise phoneme-audio alignment, (2) robust note transcription and temporal localization, (3) expressive vocal technique identification, and (4) global stylistic characterization including emotion and pace. The proposed architecture employs hierarchical acoustic feature processing across frame, word, phoneme, note, and sentence levels. The novel non-autoregressive local acoustic encoders enable structured hierarchical representation learning. Experimental validation confirms the framework's superior performance across multiple evaluation dimensions compared to existing annotation approaches. Furthermore, applications in SVS training demonstrate that models utilizing STARS-annotated data achieve significantly enhanced perceptual naturalness and precise style control. This work not only overcomes critical scalability challenges in the creation of singing datasets but also pioneers new methodologies for controllable singing voice synthesis. Audio samples are available at https://gwx314.github.io/stars-demo/.

TRPM4 is overexpressed in prostate cancer (PCa) associated with metastasis or recurrence. There is paucity of information pertaining to TRPM4 characterization and functions at single-cell level in PCa. In this study, generalized additive model (GAM) was utilized to model the relationship between TRPM4 and genes shortlisted using Spearman-Kendall dual-filter in aggressive PCa and benign prostate (BP) control cells derived from scRNA-seq dataset. Seven ribosomal genes (RPL10, RPL27, RPL28, RPS2, RPS8, RPS12, and RPS26; averaged into Ribo as the gene set), passed the dual-filter specifically in PCa cells. GAM modeling of TRPM4-Ribo significantly outperformed TRPM4 modeling with alternative cancer gene sets (GSK-3B, mTOR, NF-KB, PI3K/AKT, and Wnt). Cell explanatory power (CEP) classification was devised and verified by cross-validation to identify individual PCa cells most well-predicted by the model. CEP classification binarized PCa cells into top-ranked explanatory power (TREP; more well-predicted by the model) and non-TREP cells. In TRPM4-Ribo GAM plots, distribution pattern of TREP cells shifted at an inflection point (IP) i.e., the specific TRPM4 expression value that further binarized the plot into pre-IP (TRPM4 values below IP) and post-IP (TRPM4 values above IP) regions, producing a quadrant of TREP versus non-TREP cells for each PCa patient. Gene Ontology (GO) enrichment analysis showed that pre-IP TREP cells enriched for immune-related GOs, while post-IP TREP cells enriched for ribosomal, translation, and cell adhesion GOs. In conclusion, the CEP-IP framework based on pairwise genes produces quadrants of cancer cell subpopulations, enabling the identification of distinctive biology with potential therapeutic implications.

The digitization of vocal music scores presents unique challenges that go beyond traditional Optical Music Recognition (OMR) and Optical Character Recognition (OCR), as it necessitates preserving the critical alignment between music notation and lyrics. This alignment is essential for proper interpretation and processing in practical applications. This paper introduces and formalizes, for the first time, the Aligned Music Notation and Lyrics Transcription (AMNLT) challenge, which addresses the complete transcription of vocal scores by jointly considering music symbols, lyrics, and their synchronization. We analyze different approaches to address this challenge, ranging from traditional divide-and-conquer methods that handle music and lyrics separately, to novel end-to-end solutions including direct transcription, unfolding mechanisms, and language modeling. To evaluate these methods, we introduce four datasets of Gregorian chants, comprising both real and synthetic sources, along with custom metrics specifically designed to assess both transcription and alignment accuracy. Our experimental results demonstrate that end-to-end approaches generally outperform heuristic methods in the alignment challenge, with language models showing particular promise in scenarios where sufficient training data is available. This work establishes the first comprehensive framework for AMNLT, providing both theoretical foundations and practical solutions for preserving and digitizing vocal music heritage.

This work introduces audio2chart, a framework for the automatic generation of Guitar Hero style charts directly from raw audio. The task is formalized as a sequence prediction problem, where models are trained to generate discrete chart tokens aligned with the audio on discrete time steps. An unconditional baseline demonstrates strong predictive performance, while the addition of audio conditioning yields consistent improvements across accuracy based metrics. This work demonstrates that incorporating audio conditioning is both feasible and effective for improving note prediction in automatic chart generation. The complete codebase for training and inference is publicly available on GitHub supporting reproducible research on neural chart generation. A family of pretrained models is released on Hugging Face.

Despite its widespread use, Bengali lacks a robust automated International Phonetic Alphabet (IPA) transcription system that effectively supports both standard language and regional dialectal texts. Existing approaches struggle to handle regional variations, numerical expressions, and generalize poorly to previously unseen words. To address these limitations, we propose BanglaIPA, a novel IPA generation system that integrates a character-based vocabulary with word-level alignment. The proposed system accurately handles Bengali numerals and demonstrates strong performance across regional dialects. BanglaIPA improves inference efficiency by leveraging a precomputed word-to-IPA mapping dictionary for previously observed words. The system is evaluated on the standard Bengali and six regional variations of the DUAL-IPA dataset. Experimental results show that BanglaIPA outperforms baseline IPA transcription models by 58.4-78.7% and achieves an overall mean word error rate of 11.4%, highlighting its robustness in phonetic transcription generation for the Bengali language.