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Dec 12

Reconstructing the Charlie Parker Omnibook using an audio-to-score automatic transcription pipeline

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.

  • 2 authors
·
May 26, 2024

Dynamics of Toxicity in Political Podcasts

Toxicity in digital media poses significant challenges, yet little attention has been given to its dynamics within the rapidly growing medium of podcasts. This paper addresses this gap by analyzing political podcast data to study the emergence and propagation of toxicity, focusing on conversation chains-structured reply patterns within podcast transcripts. Leveraging state-of-the-art transcription models and advanced conversational analysis techniques, we systematically examine toxic discourse in over 30 popular political podcasts in the United States. Our key contributions include: (1) creating a comprehensive dataset of transcribed and diarized political podcasts, identifying thousands of toxic instances using Google's Perspective API, (2) uncovering concerning trends where a majority of episodes contain at least one toxic instance, (3) introducing toxic conversation chains and analyzing their structural and linguistic properties, revealing characteristics such as longer durations, repetitive patterns, figurative language, and emotional cues tied to anger and annoyance, (4) identifying demand-related words like 'want', 'like', and 'know' as precursors to toxicity, and (5) developing predictive models to anticipate toxicity shifts based on annotated change points. Our findings provide critical insights into podcast toxicity and establish a foundation for future research on real-time monitoring and intervention mechanisms to foster healthier discourse in this influential medium.

  • 6 authors
·
Jan 21

The Effect of Spectrogram Reconstruction on Automatic Music Transcription: An Alternative Approach to Improve Transcription Accuracy

Most of the state-of-the-art automatic music transcription (AMT) models break down the main transcription task into sub-tasks such as onset prediction and offset prediction and train them with onset and offset labels. These predictions are then concatenated together and used as the input to train another model with the pitch labels to obtain the final transcription. We attempt to use only the pitch labels (together with spectrogram reconstruction loss) and explore how far this model can go without introducing supervised sub-tasks. In this paper, we do not aim at achieving state-of-the-art transcription accuracy, instead, we explore the effect that spectrogram reconstruction has on our AMT model. Our proposed model consists of two U-nets: the first U-net transcribes the spectrogram into a posteriorgram, and a second U-net transforms the posteriorgram back into a spectrogram. A reconstruction loss is applied between the original spectrogram and the reconstructed spectrogram to constrain the second U-net to focus only on reconstruction. We train our model on three different datasets: MAPS, MAESTRO, and MusicNet. Our experiments show that adding the reconstruction loss can generally improve the note-level transcription accuracy when compared to the same model without the reconstruction part. Moreover, it can also boost the frame-level precision to be higher than the state-of-the-art models. The feature maps learned by our U-net contain gridlike structures (not present in the baseline model) which implies that with the presence of the reconstruction loss, the model is probably trying to count along both the time and frequency axis, resulting in a higher note-level transcription accuracy.

  • 4 authors
·
Oct 19, 2020

An End-to-End Trainable Neural Network for Image-based Sequence Recognition and Its Application to Scene Text Recognition

Image-based sequence recognition has been a long-standing research topic in computer vision. In this paper, we investigate the problem of scene text recognition, which is among the most important and challenging tasks in image-based sequence recognition. A novel neural network architecture, which integrates feature extraction, sequence modeling and transcription into a unified framework, is proposed. Compared with previous systems for scene text recognition, the proposed architecture possesses four distinctive properties: (1) It is end-to-end trainable, in contrast to most of the existing algorithms whose components are separately trained and tuned. (2) It naturally handles sequences in arbitrary lengths, involving no character segmentation or horizontal scale normalization. (3) It is not confined to any predefined lexicon and achieves remarkable performances in both lexicon-free and lexicon-based scene text recognition tasks. (4) It generates an effective yet much smaller model, which is more practical for real-world application scenarios. The experiments on standard benchmarks, including the IIIT-5K, Street View Text and ICDAR datasets, demonstrate the superiority of the proposed algorithm over the prior arts. Moreover, the proposed algorithm performs well in the task of image-based music score recognition, which evidently verifies the generality of it.

  • 3 authors
·
Jul 21, 2015

A Lightweight Instrument-Agnostic Model for Polyphonic Note Transcription and Multipitch Estimation

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.

  • 5 authors
·
Mar 18, 2022

Preserving Privacy, Increasing Accessibility, and Reducing Cost: An On-Device Artificial Intelligence Model for Medical Transcription and Note Generation

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.

  • 6 authors
·
Jul 2 1

SongPrep: A Preprocessing Framework and End-to-end Model for Full-song Structure Parsing and Lyrics Transcription

Artificial Intelligence Generated Content (AIGC) is currently a popular research area. Among its various branches, song generation has attracted growing interest. Despite the abundance of available songs, effective data preparation remains a significant challenge. Converting these songs into training-ready datasets typically requires extensive manual labeling, which is both time consuming and costly. To address this issue, we propose SongPrep, an automated preprocessing pipeline designed specifically for song data. This framework streamlines key processes such as source separation, structure analysis, and lyric recognition, producing structured data that can be directly used to train song generation models. Furthermore, we introduce SongPrepE2E, an end-to-end structured lyrics recognition model based on pretrained language models. Without the need for additional source separation, SongPrepE2E is able to analyze the structure and lyrics of entire songs and provide precise timestamps. By leveraging context from the whole song alongside pretrained semantic knowledge, SongPrepE2E achieves low Diarization Error Rate (DER) and Word Error Rate (WER) on the proposed SSLD-200 dataset. Downstream tasks demonstrate that training song generation models with the data output by SongPrepE2E enables the generated songs to closely resemble those produced by humans.

  • 9 authors
·
Sep 22

Look before Transcription: End-to-End SlideASR with Visually-Anchored Policy Optimization

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.

  • 5 authors
·
Oct 8

LiveCC: Learning Video LLM with Streaming Speech Transcription at Scale

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.

  • 6 authors
·
Apr 22 2

Mel-RoFormer for Vocal Separation and Vocal Melody Transcription

Developing a versatile deep neural network to model music audio is crucial in MIR. This task is challenging due to the intricate spectral variations inherent in music signals, which convey melody, harmonics, and timbres of diverse instruments. In this paper, we introduce Mel-RoFormer, a spectrogram-based model featuring two key designs: a novel Mel-band Projection module at the front-end to enhance the model's capability to capture informative features across multiple frequency bands, and interleaved RoPE Transformers to explicitly model the frequency and time dimensions as two separate sequences. We apply Mel-RoFormer to tackle two essential MIR tasks: vocal separation and vocal melody transcription, aimed at isolating singing voices from audio mixtures and transcribing their lead melodies, respectively. Despite their shared focus on singing signals, these tasks possess distinct optimization objectives. Instead of training a unified model, we adopt a two-step approach. Initially, we train a vocal separation model, which subsequently serves as a foundation model for fine-tuning for vocal melody transcription. Through extensive experiments conducted on benchmark datasets, we showcase that our models achieve state-of-the-art performance in both vocal separation and melody transcription tasks, underscoring the efficacy and versatility of Mel-RoFormer in modeling complex music audio signals.

  • 3 authors
·
Sep 6, 2024

Large Language Models are Efficient Learners of Noise-Robust Speech Recognition

Recent advances in large language models (LLMs) have promoted generative error correction (GER) for automatic speech recognition (ASR), which leverages the rich linguistic knowledge and powerful reasoning ability of LLMs to improve recognition results. The latest work proposes a GER benchmark with HyPoradise dataset to learn the mapping from ASR N-best hypotheses to ground-truth transcription by efficient LLM finetuning, which shows great effectiveness but lacks specificity on noise-robust ASR. In this work, we extend the benchmark to noisy conditions and investigate if we can teach LLMs to perform denoising for GER just like what robust ASR do}, where one solution is introducing noise information as a conditioner into LLM. However, directly incorporating noise embeddings from audio encoder could harm the LLM tuning due to cross-modality gap. To this end, we propose to extract a language-space noise embedding from the N-best list to represent the noise conditions of source speech, which can promote the denoising process in GER. Furthermore, in order to enhance its representation ability of audio noise, we design a knowledge distillation (KD) approach via mutual information estimation to distill the real noise information in audio embeddings to our language embedding. Experiments on various latest LLMs demonstrate our approach achieves a new breakthrough with up to 53.9% correction improvement in terms of word error rate while with limited training data. Analysis shows that our language-space noise embedding can well represent the noise conditions of source speech, under which off-the-shelf LLMs show strong ability of language-space denoising.

  • 7 authors
·
Jan 18, 2024

Style-Talker: Finetuning Audio Language Model and Style-Based Text-to-Speech Model for Fast Spoken Dialogue Generation

The rapid advancement of large language models (LLMs) has significantly propelled the development of text-based chatbots, demonstrating their capability to engage in coherent and contextually relevant dialogues. However, extending these advancements to enable end-to-end speech-to-speech conversation bots remains a formidable challenge, primarily due to the extensive dataset and computational resources required. The conventional approach of cascading automatic speech recognition (ASR), LLM, and text-to-speech (TTS) models in a pipeline, while effective, suffers from unnatural prosody because it lacks direct interactions between the input audio and its transcribed text and the output audio. These systems are also limited by their inherent latency from the ASR process for real-time applications. This paper introduces Style-Talker, an innovative framework that fine-tunes an audio LLM alongside a style-based TTS model for fast spoken dialog generation. Style-Talker takes user input audio and uses transcribed chat history and speech styles to generate both the speaking style and text for the response. Subsequently, the TTS model synthesizes the speech, which is then played back to the user. While the response speech is being played, the input speech undergoes ASR processing to extract the transcription and speaking style, serving as the context for the ensuing dialogue turn. This novel pipeline accelerates the traditional cascade ASR-LLM-TTS systems while integrating rich paralinguistic information from input speech. Our experimental results show that Style-Talker significantly outperforms the conventional cascade and speech-to-speech baselines in terms of both dialogue naturalness and coherence while being more than 50% faster.

  • 5 authors
·
Aug 13, 2024

Speech-to-LaTeX: New Models and Datasets for Converting Spoken Equations and Sentences

Conversion of spoken mathematical expressions is a challenging task that involves transcribing speech into a strictly structured symbolic representation while addressing the ambiguity inherent in the pronunciation of equations. Although significant progress has been achieved in automatic speech recognition (ASR) and language models (LM), the problem of converting spoken mathematics into LaTeX remains underexplored. This task directly applies to educational and research domains, such as lecture transcription or note creation. Based on ASR post-correction, prior work requires 2 transcriptions, focuses only on isolated equations, has a limited test set, and provides neither training data nor multilingual coverage. To address these issues, we present the first fully open-source large-scale dataset, comprising over 66,000 human-annotated audio samples of mathematical equations and sentences in both English and Russian, drawn from diverse scientific domains. In addition to the ASR post-correction models and few-shot prompting, we apply audio language models, demonstrating comparable character error rate (CER) results on the MathSpeech benchmark (28% vs. 30%) for the equations conversion. In contrast, on the proposed S2L-equations benchmark, our models outperform the MathSpeech model by a substantial margin of more than 40 percentage points, even after accounting for LaTeX formatting artifacts (27% vs. 64%). We establish the first benchmark for mathematical sentence recognition (S2L-sentences) and achieve an equation CER of 40%. This work lays the groundwork for future advances in multimodal AI, with a particular focus on mathematical content recognition.

  • 9 authors
·
Aug 5 2

GigaSpeech 2: An Evolving, Large-Scale and Multi-domain ASR Corpus for Low-Resource Languages with Automated Crawling, Transcription and Refinement

The evolution of speech technology has been spurred by the rapid increase in dataset sizes. Traditional speech models generally depend on a large amount of labeled training data, which is scarce for low-resource languages. This paper presents GigaSpeech 2, a large-scale, multi-domain, multilingual speech recognition corpus. It is designed for low-resource languages and does not rely on paired speech and text data. GigaSpeech 2 comprises about 30,000 hours of automatically transcribed speech, including Thai, Indonesian, and Vietnamese, gathered from unlabeled YouTube videos. We also introduce an automated pipeline for data crawling, transcription, and label refinement. Specifically, this pipeline uses Whisper for initial transcription and TorchAudio for forced alignment, combined with multi-dimensional filtering for data quality assurance. A modified Noisy Student Training is developed to further refine flawed pseudo labels iteratively, thus enhancing model performance. Experimental results on our manually transcribed evaluation set and two public test sets from Common Voice and FLEURS confirm our corpus's high quality and broad applicability. Notably, ASR models trained on GigaSpeech 2 can reduce the word error rate for Thai, Indonesian, and Vietnamese on our challenging and realistic YouTube test set by 25% to 40% compared to the Whisper large-v3 model, with merely 10% model parameters. Furthermore, our ASR models trained on Gigaspeech 2 yield superior performance compared to commercial services. We believe that our newly introduced corpus and pipeline will open a new avenue for low-resource speech recognition and significantly facilitate research in this area.

  • 16 authors
·
Jun 17, 2024

STARS: A Unified Framework for Singing Transcription, Alignment, and Refined Style Annotation

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/.

  • 9 authors
·
Jul 9

CarelessWhisper: Turning Whisper into a Causal Streaming Model

Automatic Speech Recognition (ASR) has seen remarkable progress, with models like OpenAI Whisper and NVIDIA Canary achieving state-of-the-art (SOTA) performance in offline transcription. However, these models are not designed for streaming (online or real-time) transcription, due to limitations in their architecture and training methodology. We propose a method to turn the transformer encoder-decoder model into a low-latency streaming model that is careless about future context. We present an analysis explaining why it is not straightforward to convert an encoder-decoder transformer to a low-latency streaming model. Our proposed method modifies the existing (non-causal) encoder to a causal encoder by fine-tuning both the encoder and decoder using Low-Rank Adaptation (LoRA) and a weakly aligned dataset. We then propose an updated inference mechanism that utilizes the fine-tune causal encoder and decoder to yield greedy and beam-search decoding, and is shown to be locally optimal. Experiments on low-latency chunk sizes (less than 300 msec) show that our fine-tuned model outperforms existing non-fine-tuned streaming approaches in most cases, while using a lower complexity. Additionally, we observe that our training process yields better alignment, enabling a simple method for extracting word-level timestamps. We release our training and inference code, along with the fine-tuned models, to support further research and development in streaming ASR.

  • 3 authors
·
Aug 17

Adapting Multilingual Speech Representation Model for a New, Underresourced Language through Multilingual Fine-tuning and Continued Pretraining

In recent years, neural models learned through self-supervised pretraining on large scale multilingual text or speech data have exhibited promising results for underresourced languages, especially when a relatively large amount of data from related language(s) is available. While the technology has a potential for facilitating tasks carried out in language documentation projects, such as speech transcription, pretraining a multilingual model from scratch for every new language would be highly impractical. We investigate the possibility for adapting an existing multilingual wav2vec 2.0 model for a new language, focusing on actual fieldwork data from a critically endangered tongue: Ainu. Specifically, we (i) examine the feasibility of leveraging data from similar languages also in fine-tuning; (ii) verify whether the model's performance can be improved by further pretraining on target language data. Our results show that continued pretraining is the most effective method to adapt a wav2vec 2.0 model for a new language and leads to considerable reduction in error rates. Furthermore, we find that if a model pretrained on a related speech variety or an unrelated language with similar phonological characteristics is available, multilingual fine-tuning using additional data from that language can have positive impact on speech recognition performance when there is very little labeled data in the target language.

  • 4 authors
·
Jan 17, 2023

Leveraging Large Language Models for Exploiting ASR Uncertainty

While large language models excel in a variety of natural language processing (NLP) tasks, to perform well on spoken language understanding (SLU) tasks, they must either rely on off-the-shelf automatic speech recognition (ASR) systems for transcription, or be equipped with an in-built speech modality. This work focuses on the former scenario, where LLM's accuracy on SLU tasks is constrained by the accuracy of a fixed ASR system on the spoken input. Specifically, we tackle speech-intent classification task, where a high word-error-rate can limit the LLM's ability to understand the spoken intent. Instead of chasing a high accuracy by designing complex or specialized architectures regardless of deployment costs, we seek to answer how far we can go without substantially changing the underlying ASR and LLM, which can potentially be shared by multiple unrelated tasks. To this end, we propose prompting the LLM with an n-best list of ASR hypotheses instead of only the error-prone 1-best hypothesis. We explore prompt-engineering to explain the concept of n-best lists to the LLM; followed by the finetuning of Low-Rank Adapters on the downstream tasks. Our approach using n-best lists proves to be effective on a device-directed speech detection task as well as on a keyword spotting task, where systems using n-best list prompts outperform those using 1-best ASR hypothesis; thus paving the way for an efficient method to exploit ASR uncertainty via LLMs for speech-based applications.

  • 7 authors
·
Sep 9, 2023

Exploiting Music Source Separation for Automatic Lyrics Transcription with Whisper

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.

  • 4 authors
·
Jun 18

Aligned Music Notation and Lyrics Transcription

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.

TASTE: Text-Aligned Speech Tokenization and Embedding for Spoken Language Modeling

Large Language Models (LLMs) excel in text-based natural language processing tasks but remain constrained by their reliance on textual inputs and outputs. To enable more natural human-LLM interaction, recent progress have focused on deriving a spoken language model (SLM) that can not only listen but also generate speech. To achieve this, a promising direction is to conduct speech-text joint modeling. However, recent SLM still lag behind text LLM due to the modality mismatch. One significant mismatch can be the sequence lengths between speech and text tokens. To address this, we introduce Text-Aligned Speech Tokenization and Embedding (TASTE), a method that directly addresses the modality gap by aligning speech token with the corresponding text transcription during the tokenization stage. We propose a method that can achieve this through the special aggregation mechanism and with speech reconstruction as the training objective. We conduct extensive experiments and show that TASTE can preserve essential paralinguistic information while dramatically reducing the token sequence length. Furthermore, by leveraging TASTE, we can adapt text-based LLMs into effective SLMs with parameter-efficient fine-tuning techniques such as Low-Rank Adaptation (LoRA). Experimental results on benchmark tasks, including SALMON and StoryCloze, demonstrate that TASTE-based SLMs perform similarly to previous full-finetuning methods. To our knowledge, TASTE is the first end-to-end approach that utilizes a reconstruction objective to automatically learn a text-aligned speech tokenization and embedding suitable for spoken language modeling. Our demo, code, and models are publicly available at https://github.com/mtkresearch/TASTE-SpokenLM.

  • 5 authors
·
Apr 9

Edge-ASR: Towards Low-Bit Quantization of Automatic Speech Recognition Models

Recent advances in Automatic Speech Recognition (ASR) have demonstrated remarkable accuracy and robustness in diverse audio applications, such as live transcription and voice command processing. However, deploying these models on resource constrained edge devices (e.g., IoT device, wearables) still presents substantial challenges due to strict limits on memory, compute and power. Quantization, particularly Post-Training Quantization (PTQ), offers an effective way to reduce model size and inference cost without retraining. Despite its importance, the performance implications of various advanced quantization methods and bit-width configurations on ASR models remain unclear. In this work, we present a comprehensive benchmark of eight state-of-the-art (SOTA) PTQ methods applied to two leading edge-ASR model families, Whisper and Moonshine. We systematically evaluate model performances (i.e., accuracy, memory I/O and bit operations) across seven diverse datasets from the open ASR leaderboard, analyzing the impact of quantization and various configurations on both weights and activations. Built on an extension of the LLM compression toolkit, our framework integrates edge-ASR models, diverse advanced quantization algorithms, a unified calibration and evaluation data pipeline, and detailed analysis tools. Our results characterize the trade-offs between efficiency and accuracy, demonstrating that even 3-bit quantization can succeed on high capacity models when using advanced PTQ techniques. These findings provide valuable insights for optimizing ASR models on low-power, always-on edge devices.

  • 7 authors
·
Jul 10

HyPoradise: An Open Baseline for Generative Speech Recognition with Large Language Models

Advancements in deep neural networks have allowed automatic speech recognition (ASR) systems to attain human parity on several publicly available clean speech datasets. However, even state-of-the-art ASR systems experience performance degradation when confronted with adverse conditions, as a well-trained acoustic model is sensitive to variations in the speech domain, e.g., background noise. Intuitively, humans address this issue by relying on their linguistic knowledge: the meaning of ambiguous spoken terms is usually inferred from contextual cues thereby reducing the dependency on the auditory system. Inspired by this observation, we introduce the first open-source benchmark to utilize external large language models (LLMs) for ASR error correction, where N-best decoding hypotheses provide informative elements for true transcription prediction. This approach is a paradigm shift from the traditional language model rescoring strategy that can only select one candidate hypothesis as the output transcription. The proposed benchmark contains a novel dataset, HyPoradise (HP), encompassing more than 334,000 pairs of N-best hypotheses and corresponding accurate transcriptions across prevalent speech domains. Given this dataset, we examine three types of error correction techniques based on LLMs with varying amounts of labeled hypotheses-transcription pairs, which gains a significant word error rate (WER) reduction. Experimental evidence demonstrates the proposed technique achieves a breakthrough by surpassing the upper bound of traditional re-ranking based methods. More surprisingly, LLM with reasonable prompt and its generative capability can even correct those tokens that are missing in N-best list. We make our results publicly accessible for reproducible pipelines with released pre-trained models, thus providing a new evaluation paradigm for ASR error correction with LLMs.

  • 6 authors
·
Sep 27, 2023

It's Never Too Late: Fusing Acoustic Information into Large Language Models for Automatic Speech Recognition

Recent studies have successfully shown that large language models (LLMs) can be successfully used for generative error correction (GER) on top of the automatic speech recognition (ASR) output. Specifically, an LLM is utilized to carry out a direct mapping from the N-best hypotheses list generated by an ASR system to the predicted output transcription. However, despite its effectiveness, GER introduces extra data uncertainty since the LLM is trained without taking into account acoustic information available in the speech signal. In this work, we aim to overcome such a limitation by infusing acoustic information before generating the predicted transcription through a novel late fusion solution termed Uncertainty-Aware Dynamic Fusion (UADF). UADF is a multimodal fusion approach implemented into an auto-regressive decoding process and works in two stages: (i) It first analyzes and calibrates the token-level LLM decision, and (ii) it then dynamically assimilates the information from the acoustic modality. Experimental evidence collected from various ASR tasks shows that UADF surpasses existing fusion mechanisms in several ways. It yields significant improvements in word error rate (WER) while mitigating data uncertainty issues in LLM and addressing the poor generalization relied with sole modality during fusion. We also demonstrate that UADF seamlessly adapts to audio-visual speech recognition.

  • 7 authors
·
Feb 8, 2024

A Survey on Non-Intrusive ASR Refinement: From Output-Level Correction to Full-Model Distillation

Automatic Speech Recognition (ASR) has become an integral component of modern technology, powering applications such as voice-activated assistants, transcription services, and accessibility tools. Yet ASR systems continue to struggle with the inherent variability of human speech, such as accents, dialects, and speaking styles, as well as environmental interference, including background noise. Moreover, domain-specific conversations often employ specialized terminology, which can exacerbate transcription errors. These shortcomings not only degrade raw ASR accuracy but also propagate mistakes through subsequent natural language processing pipelines. Because redesigning an ASR model is costly and time-consuming, non-intrusive refinement techniques that leave the model's architecture unchanged have become increasingly popular. In this survey, we systematically review current non-intrusive refinement approaches and group them into five classes: fusion, re-scoring, correction, distillation, and training adjustment. For each class, we outline the main methods, advantages, drawbacks, and ideal application scenarios. Beyond method classification, this work surveys adaptation techniques aimed at refining ASR in domain-specific contexts, reviews commonly used evaluation datasets along with their construction processes, and proposes a standardized set of metrics to facilitate fair comparisons. Finally, we identify open research gaps and suggest promising directions for future work. By providing this structured overview, we aim to equip researchers and practitioners with a clear foundation for developing more robust, accurate ASR refinement pipelines.

  • 6 authors
·
Aug 10

SpeakerLM: End-to-End Versatile Speaker Diarization and Recognition with Multimodal Large Language Models

The Speaker Diarization and Recognition (SDR) task aims to predict "who spoke when and what" within an audio clip, which is a crucial task in various real-world multi-speaker scenarios such as meeting transcription and dialogue systems. Existing SDR systems typically adopt a cascaded framework, combining multiple modules such as speaker diarization (SD) and automatic speech recognition (ASR). The cascaded systems suffer from several limitations, such as error propagation, difficulty in handling overlapping speech, and lack of joint optimization for exploring the synergy between SD and ASR tasks. To address these limitations, we introduce SpeakerLM, a unified multimodal large language model for SDR that jointly performs SD and ASR in an end-to-end manner. Moreover, to facilitate diverse real-world scenarios, we incorporate a flexible speaker registration mechanism into SpeakerLM, enabling SDR under different speaker registration settings. SpeakerLM is progressively developed with a multi-stage training strategy on large-scale real data. Extensive experiments show that SpeakerLM demonstrates strong data scaling capability and generalizability, outperforming state-of-the-art cascaded baselines on both in-domain and out-of-domain public SDR benchmarks. Furthermore, experimental results show that the proposed speaker registration mechanism effectively ensures robust SDR performance of SpeakerLM across diverse speaker registration conditions and varying numbers of registered speakers.

  • 9 authors
·
Aug 8

GENERator: A Long-Context Generative Genomic Foundation Model

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

  • 8 authors
·
Feb 11

StressTest: Can YOUR Speech LM Handle the Stress?

Sentence stress refers to emphasis, placed on specific words within a spoken utterance to highlight or contrast an idea, or to introduce new information. It is often used to imply an underlying intention that is not explicitly stated. Recent advances in speech-aware language models (SLMs) have enabled direct processing of audio, allowing models to bypass transcription and access the full richness of the speech signal and perform audio reasoning tasks such as spoken question answering. Despite the crucial role of sentence stress in shaping meaning and speaker intent, it remains largely overlooked in evaluation and development of such models. In this work, we address this gap by introducing StressTest, a benchmark specifically designed to evaluate a model's ability to distinguish between interpretations of spoken sentences based on the stress pattern. We assess the performance of several leading SLMs and find that, despite their overall capabilities, they perform poorly on such tasks. To overcome this limitation, we propose a novel synthetic data generation pipeline, and create Stress17k, a training set that simulates change of meaning implied by stress variation. Then, we empirically show that optimizing models with this synthetic dataset aligns well with real-world recordings and enables effective finetuning of SLMs. Results suggest, that our finetuned model, StresSLM, significantly outperforms existing models on both sentence stress reasoning and detection tasks. Code, models, data, and audio samples - pages.cs.huji.ac.il/adiyoss-lab/stresstest.

  • 3 authors
·
May 28 2

Fleurs-SLU: A Massively Multilingual Benchmark for Spoken Language Understanding

While recent multilingual automatic speech recognition models claim to support thousands of languages, ASR for low-resource languages remains highly unreliable due to limited bimodal speech and text training data. Better multilingual spoken language understanding (SLU) can strengthen massively the robustness of multilingual ASR by levering language semantics to compensate for scarce training data, such as disambiguating utterances via context or exploiting semantic similarities across languages. Even more so, SLU is indispensable for inclusive speech technology in roughly half of all living languages that lack a formal writing system. However, the evaluation of multilingual SLU remains limited to shallower tasks such as intent classification or language identification. To address this, we present Fleurs-SLU, a multilingual SLU benchmark that encompasses topical speech classification in 102 languages and multiple-choice question answering through listening comprehension in 92 languages. We extensively evaluate both end-to-end speech classification models and cascaded systems that combine speech-to-text transcription with subsequent classification by large language models on Fleurs-SLU. Our results show that cascaded systems exhibit greater robustness in multilingual SLU tasks, though speech encoders can achieve competitive performance in topical speech classification when appropriately pre-trained. We further find a strong correlation between robust multilingual ASR, effective speech-to-text translation, and strong multilingual SLU, highlighting the mutual benefits between acoustic and semantic speech representations.

  • 4 authors
·
Jan 10

SpeechTaxi: On Multilingual Semantic Speech Classification

Recent advancements in multilingual speech encoding as well as transcription raise the question of the most effective approach to semantic speech classification. Concretely, can (1) end-to-end (E2E) classifiers obtained by fine-tuning state-of-the-art multilingual speech encoders (MSEs) match or surpass the performance of (2) cascading (CA), where speech is first transcribed into text and classification is delegated to a text-based classifier. To answer this, we first construct SpeechTaxi, an 80-hour multilingual dataset for semantic speech classification of Bible verses, covering 28 diverse languages. We then leverage SpeechTaxi to conduct a wide range of experiments comparing E2E and CA in monolingual semantic speech classification as well as in cross-lingual transfer. We find that E2E based on MSEs outperforms CA in monolingual setups, i.e., when trained on in-language data. However, MSEs seem to have poor cross-lingual transfer abilities, with E2E substantially lagging CA both in (1) zero-shot transfer to languages unseen in training and (2) multilingual training, i.e., joint training on multiple languages. Finally, we devise a novel CA approach based on transcription to Romanized text as a language-agnostic intermediate representation and show that it represents a robust solution for languages without native ASR support. Our SpeechTaxi dataset is publicly available at: https://huggingface.co/ datasets/LennartKeller/SpeechTaxi/.

  • 2 authors
·
Sep 10, 2024

MiniMax-Speech: Intrinsic Zero-Shot Text-to-Speech with a Learnable Speaker Encoder

We introduce MiniMax-Speech, an autoregressive Transformer-based Text-to-Speech (TTS) model that generates high-quality speech. A key innovation is our learnable speaker encoder, which extracts timbre features from a reference audio without requiring its transcription. This enables MiniMax-Speech to produce highly expressive speech with timbre consistent with the reference in a zero-shot manner, while also supporting one-shot voice cloning with exceptionally high similarity to the reference voice. In addition, the overall quality of the synthesized audio is enhanced through the proposed Flow-VAE. Our model supports 32 languages and demonstrates excellent performance across multiple objective and subjective evaluations metrics. Notably, it achieves state-of-the-art (SOTA) results on objective voice cloning metrics (Word Error Rate and Speaker Similarity) and has secured the top position on the public TTS Arena leaderboard. Another key strength of MiniMax-Speech, granted by the robust and disentangled representations from the speaker encoder, is its extensibility without modifying the base model, enabling various applications such as: arbitrary voice emotion control via LoRA; text to voice (T2V) by synthesizing timbre features directly from text description; and professional voice cloning (PVC) by fine-tuning timbre features with additional data. We encourage readers to visit https://minimax-ai.github.io/tts_tech_report for more examples.

  • 20 authors
·
May 12 4

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

  • 13 authors
·
Jun 14, 2024

Affective social anthropomorphic intelligent system

Human conversational styles are measured by the sense of humor, personality, and tone of voice. These characteristics have become essential for conversational intelligent virtual assistants. However, most of the state-of-the-art intelligent virtual assistants (IVAs) are failed to interpret the affective semantics of human voices. This research proposes an anthropomorphic intelligent system that can hold a proper human-like conversation with emotion and personality. A voice style transfer method is also proposed to map the attributes of a specific emotion. Initially, the frequency domain data (Mel-Spectrogram) is created by converting the temporal audio wave data, which comprises discrete patterns for audio features such as notes, pitch, rhythm, and melody. A collateral CNN-Transformer-Encoder is used to predict seven different affective states from voice. The voice is also fed parallelly to the deep-speech, an RNN model that generates the text transcription from the spectrogram. Then the transcripted text is transferred to the multi-domain conversation agent using blended skill talk, transformer-based retrieve-and-generate generation strategy, and beam-search decoding, and an appropriate textual response is generated. The system learns an invertible mapping of data to a latent space that can be manipulated and generates a Mel-spectrogram frame based on previous Mel-spectrogram frames to voice synthesize and style transfer. Finally, the waveform is generated using WaveGlow from the spectrogram. The outcomes of the studies we conducted on individual models were auspicious. Furthermore, users who interacted with the system provided positive feedback, demonstrating the system's effectiveness.

  • 5 authors
·
Apr 19, 2023

Automatic Pronunciation Error Detection and Correction of the Holy Quran's Learners Using Deep Learning

Assessing spoken language is challenging, and quantifying pronunciation metrics for machine learning models is even harder. However, for the Holy Quran, this task is simplified by the rigorous recitation rules (tajweed) established by Muslim scholars, enabling highly effective assessment. Despite this advantage, the scarcity of high-quality annotated data remains a significant barrier. In this work, we bridge these gaps by introducing: (1) A 98% automated pipeline to produce high-quality Quranic datasets -- encompassing: Collection of recitations from expert reciters, Segmentation at pause points (waqf) using our fine-tuned wav2vec2-BERT model, Transcription of segments, Transcript verification via our novel Tasmeea algorithm; (2) 850+ hours of audio (~300K annotated utterances); (3) A novel ASR-based approach for pronunciation error detection, utilizing our custom Quran Phonetic Script (QPS) to encode Tajweed rules (unlike the IPA standard for Modern Standard Arabic). QPS uses a two-level script: (Phoneme level): Encodes Arabic letters with short/long vowels. (Sifa level): Encodes articulation characteristics of every phoneme. We further include comprehensive modeling with our novel multi-level CTC Model which achieved 0.16% average Phoneme Error Rate (PER) on the testset. We release all code, data, and models as open-source: https://obadx.github.io/prepare-quran-dataset/

  • 3 authors
·
Aug 27

Whistle: Data-Efficient Multilingual and Crosslingual Speech Recognition via Weakly Phonetic Supervision

There exist three approaches for multilingual and crosslingual automatic speech recognition (MCL-ASR) - supervised pretraining with phonetic or graphemic transcription, and self-supervised pretraining. We find that pretraining with phonetic supervision has been underappreciated so far for MCL-ASR, while conceptually it is more advantageous for information sharing between different languages. This paper explores the approach of pretraining with weakly phonetic supervision towards data-efficient MCL-ASR, which is called Whistle. We relax the requirement of gold-standard human-validated phonetic transcripts, and obtain International Phonetic Alphabet (IPA) based transcription by leveraging the LanguageNet grapheme-to-phoneme (G2P) models. We construct a common experimental setup based on the CommonVoice dataset, called CV-Lang10, with 10 seen languages and 2 unseen languages. A set of experiments are conducted on CV-Lang10 to compare, as fair as possible, the three approaches under the common setup for MCL-ASR. Experiments demonstrate the advantages of phoneme-based models (Whistle) for MCL-ASR, in terms of speech recognition for seen languages, crosslingual performance for unseen languages with different amounts of few-shot data, overcoming catastrophic forgetting, and training efficiency. It is found that when training data is more limited, phoneme supervision can achieve better results compared to subword supervision and self-supervision, thereby providing higher data-efficiency. To support reproducibility and promote future research along this direction, we release the code, models and data for the entire pipeline of Whistle at https://github.com/thu-spmi/CAT/tree/master/egs/cv-lang10.

  • 5 authors
·
Jun 4, 2024

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

ibm-research IBM Research
·
Jun 26

Find Central Dogma Again

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

  • 1 authors
·
Feb 10

BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models

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.

ibm-research IBM Research
·
Jun 17