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Sep 28

De novo peptide sequencing rescoring and FDR estimation with Winnow

Machine learning has markedly advanced de novo peptide sequencing (DNS) for mass spectrometry-based proteomics. DNS tools offer a reliable way to identify peptides without relying on reference databases, extending proteomic analysis and unlocking applications into less-charted regions of the proteome. However, they still face a key limitation. DNS tools lack principled methods for estimating false discovery rates (FDR) and instead rely on model-specific confidence scores that are often miscalibrated. This limits trust in results, hinders cross-model comparisons and reduces validation success. Here we present Winnow, a model-agnostic framework for estimating FDR from calibrated DNS outputs. Winnow maps raw model scores to calibrated confidences using a neural network trained on peptide-spectrum match (PSM)-derived features. From these calibrated scores, Winnow computes PSM-specific error metrics and an experiment-wide FDR estimate using a novel decoy-free FDR estimator. It supports both zero-shot and dataset-specific calibration, enabling flexible application via direct inference, fine-tuning, or training a custom model. We demonstrate that, when applied to InstaNovo predictions, Winnow's calibrator improves recall at fixed FDR thresholds, and its FDR estimator tracks true error rates when benchmarked against reference proteomes and database search. Winnow ensures accurate FDR control across datasets, helping unlock the full potential of DNS.

InstaDeepAI InstaDeep Ltd
·
Sep 29, 2025

DataFlex-RL: An Evaluation Platform for RLVR Data Policies

Data policies for reinforcement learning with verifiable rewards (RLVR) determine which rollouts are used, how strongly they are weighted, and which domains contribute to subsequent training batches. We introduce DataFlex-RL, an evaluation platform for comparing these choices under a common GRPO recipe. Our primary experiment evaluates 13 configurations across 12 matched seeds using Qwen2.5-7B-Base and 12 mathematics, logic, and science benchmarks. Uniform GRPO improves the domain-balanced average accuracy by 7.76 percentage points over the untrained checkpoint. None of the eight rollout-selection or reweighting methods achieves a paired 95% confidence interval that excludes zero relative to uniform sampling, and none of the three adaptive mixtures outperforms a fixed equal mixture at the same level of precision. A corrected 12-seed extension on Llama-3.1-8B-Base places the additional methods on the same score scale as the original controls, but does not reveal a consistent winner in terms of observed mean performance. We also quantify evaluation sensitivity by rescoring nine Qwen2.5-7B-Instruct runs using a math-heavy six-benchmark summary, consisting of five mathematics benchmarks and GPQA-Diamond but no logic benchmark, and comparing it with the domain-balanced 12-benchmark summary. The resulting rankings are negatively correlated, with a correlation coefficient of -0.33, whereas summaries that retain all 12 benchmarks largely agree. Across the controlled settings studied here, changing the data policy measurably changes the training process but does not produce a reproducible improvement over uniform training.

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

StepOPSD: Step-Aware Online Preference Distillation for Agent Reinforcement Learning

Reinforcement learning for multi-turn agents suffers from a credit-assignment mismatch: rewards are sparse and trajectory-level, while success often hinges on a few local decisions. Existing online policy distillation (OPD) provides denser token-level supervision, but typically treats heterogeneous agent trajectories as monolithic strings rather than causal interaction units. We present StepOPSD, a post-rollout preference self-distillation framework that takes the agent step as the unit of credit redistribution. StepOPSD decomposes trajectories into action-centered step segments, rescoring them under hindsight-enriched teacher contexts and converting token-level log-probability gaps into sign-preserving advantage shaping with a normalized per-step credit budget before the GRPO update. Across ALFWorld and Search-QA with Qwen3-1.7B and Qwen2.5-3B-Instruct, StepOPSD attains best or second-best results on subsets most sensitive to local causal errors, including first-place performance on ALFWorld Heat (79.1%), PickTwo (95.0%), Search-QA TriviaQA (61.6%), and tied-best performance on HotpotQA (40.4%). The results further reveal a consistent two-knob law: smaller α_clip acts as a broadly stabilizing local trust region, whereas the optimal global mixing strength λ_mix remains task-dependent. These findings suggest that step-aware distillation is most useful when trajectory-level rewards are weakly aligned with the local action that determines downstream success.

  • 3 authors
·
May 25

Masked Audio Generation using a Single Non-Autoregressive Transformer

We introduce MAGNeT, a masked generative sequence modeling method that operates directly over several streams of audio tokens. Unlike prior work, MAGNeT is comprised of a single-stage, non-autoregressive transformer. During training, we predict spans of masked tokens obtained from a masking scheduler, while during inference we gradually construct the output sequence using several decoding steps. To further enhance the quality of the generated audio, we introduce a novel rescoring method in which, we leverage an external pre-trained model to rescore and rank predictions from MAGNeT, which will be then used for later decoding steps. Lastly, we explore a hybrid version of MAGNeT, in which we fuse between autoregressive and non-autoregressive models to generate the first few seconds in an autoregressive manner while the rest of the sequence is being decoded in parallel. We demonstrate the efficiency of MAGNeT for the task of text-to-music and text-to-audio generation and conduct an extensive empirical evaluation, considering both objective metrics and human studies. The proposed approach is comparable to the evaluated baselines, while being significantly faster (x7 faster than the autoregressive baseline). Through ablation studies and analysis, we shed light on the importance of each of the components comprising MAGNeT, together with pointing to the trade-offs between autoregressive and non-autoregressive modeling, considering latency, throughput, and generation quality. Samples are available on our demo page https://pages.cs.huji.ac.il/adiyoss-lab/MAGNeT.

  • 9 authors
·
Jan 9, 2024 14

SLAM-AAC: Enhancing Audio Captioning with Paraphrasing Augmentation and CLAP-Refine through LLMs

Automated Audio Captioning (AAC) aims to generate natural textual descriptions for input audio signals. Recent progress in audio pre-trained models and large language models (LLMs) has significantly enhanced audio understanding and textual reasoning capabilities, making improvements in AAC possible. In this paper, we propose SLAM-AAC to further enhance AAC with paraphrasing augmentation and CLAP-Refine through LLMs. Our approach uses the self-supervised EAT model to extract fine-grained audio representations, which are then aligned with textual embeddings via lightweight linear layers. The caption generation LLM is efficiently fine-tuned using the LoRA adapter. Drawing inspiration from the back-translation method in machine translation, we implement paraphrasing augmentation to expand the Clotho dataset during pre-training. This strategy helps alleviate the limitation of scarce audio-text pairs and generates more diverse captions from a small set of audio clips. During inference, we introduce the plug-and-play CLAP-Refine strategy to fully exploit multiple decoding outputs, akin to the n-best rescoring strategy in speech recognition. Using the CLAP model for audio-text similarity calculation, we could select the textual descriptions generated by multiple searching beams that best match the input audio. Experimental results show that SLAM-AAC achieves state-of-the-art performance on Clotho V2 and AudioCaps, surpassing previous mainstream models.

  • 8 authors
·
Oct 12, 2024

Denoising LM: Pushing the Limits of Error Correction Models for Speech Recognition

Language models (LMs) have long been used to improve results of automatic speech recognition (ASR) systems, but they are unaware of the errors that ASR systems make. Error correction models are designed to fix ASR errors, however, they showed little improvement over traditional LMs mainly due to the lack of supervised training data. In this paper, we present Denoising LM (DLM), which is a scaled error correction model trained with vast amounts of synthetic data, significantly exceeding prior attempts meanwhile achieving new state-of-the-art ASR performance. We use text-to-speech (TTS) systems to synthesize audio, which is fed into an ASR system to produce noisy hypotheses, which are then paired with the original texts to train the DLM. DLM has several key ingredients: (i) up-scaled model and data; (ii) usage of multi-speaker TTS systems; (iii) combination of multiple noise augmentation strategies; and (iv) new decoding techniques. With a Transformer-CTC ASR, DLM achieves 1.5% word error rate (WER) on test-clean and 3.3% WER on test-other on Librispeech, which to our knowledge are the best reported numbers in the setting where no external audio data are used and even match self-supervised methods which use external audio data. Furthermore, a single DLM is applicable to different ASRs, and greatly surpassing the performance of conventional LM based beam-search rescoring. These results indicate that properly investigated error correction models have the potential to replace conventional LMs, holding the key to a new level of accuracy in ASR systems.

  • 6 authors
·
May 24, 2024

Generative Late-Interaction Embeddings For Visual Document Retrieval

Late-interaction retrieval is the state-of-the-art for visual document search, but it pays for its accuracy in storage. Existing compression methods retain a subset or local average of the N~1,000 vectors per page. Under aggressive storage budgets, however, these methods degrade sharply, and alternatives require retraining the encoder. Investigating this degradation across three encoders, we found two consistent properties: the vectors lie exactly on the unit sphere and concentrate near a manifold of intrinsic dimension five to six. This geometry yields two insights. First, standard k-means centroids fall inside the sphere, causing systematic underestimation of MaxSim scores. Normalizing them to the surface is a free correction worth up to +0.093 nDCG@5 over raw centroids. Second, because the page manifold has few degrees of freedom, the full set of vectors can be regenerated from only a few. To this end, we introduce Generative Late-Interaction Embeddings (GLIE): k << N vectors per page learned from the normalized centroids to serve as both a lightweight index and a basis for regenerating the page's full embedding set. At query time, search runs exclusively on these k vectors, and a decoder expands only the top candidates back to all N vectors for exact rescoring. At four vectors per page on ViDoRe v1, GLIE retains nearly 80% of the uncompressed system's nDCG@5, against 70% for the best prior post-hoc method. These results use a 415K-parameter network fitted in under three GPU-minutes on just a thousand training pages. At a matched training budget, fine-tuning the encoder does not reach even the training-free stage of GLIE, and the full system beats it at every budget. These patterns hold across a second encoder and ViDoRe v2. By reconstructing evidence on demand rather than sampling it, GLIE opens a new axis for storage-efficient retrieval, with the decoder as its main design surface.