Jan Niehues

Sophia J. Wagner, Daniel Reisenbüchler, Nicholas P. West et al.

Background: Deep learning (DL) can extract predictive and prognostic biomarkers from routine pathology slides in colorectal cancer. For example, a DL test for the diagnosis of microsatellite instability (MSI) in CRC has been approved in 2022. Current approaches rely on convolutional neural networks (CNNs). Transformer networks are outperforming CNNs and are replacing them in many applications, but have not been used for biomarker prediction in cancer at a large scale. In addition, most DL approaches have been trained on small patient cohorts, which limits their clinical utility. Methods: In this study, we developed a new fully transformer-based pipeline for end-to-end biomarker prediction from pathology slides. We combine a pre-trained transformer encoder and a transformer network for patch aggregation, capable of yielding single and multi-target prediction at patient level. We train our pipeline on over 9,000 patients from 10 colorectal cancer cohorts. Results: A fully transformer-based approach massively improves the performance, generalizability, data efficiency, and interpretability as compared with current state-of-the-art algorithms. After training on a large multicenter cohort, we achieve a sensitivity of 0.97 with a negative predictive value of 0.99 for MSI prediction on surgical resection specimens. We demonstrate for the first time that resection specimen-only training reaches clinical-grade performance on endoscopic biopsy tissue, solving a long-standing diagnostic problem. Interpretation: A fully transformer-based end-to-end pipeline trained on thousands of pathology slides yields clinical-grade performance for biomarker prediction on surgical resections and biopsies. Our new methods are freely available under an open source license.

Gustav Müller-Franzes, Jan Moritz Niehues, Firas Khader et al.

The success of Deep Learning applications critically depends on the quality and scale of the underlying training data. Generative adversarial networks (GANs) can generate arbitrary large datasets, but diversity and fidelity are limited, which has recently been addressed by denoising diffusion probabilistic models (DDPMs) whose superiority has been demonstrated on natural images. In this study, we propose Medfusion, a conditional latent DDPM for medical images. We compare our DDPM-based model against GAN-based models, which constitute the current state-of-the-art in the medical domain. Medfusion was trained and compared with (i) StyleGan-3 on n=101,442 images from the AIROGS challenge dataset to generate fundoscopies with and without glaucoma, (ii) ProGAN on n=191,027 from the CheXpert dataset to generate radiographs with and without cardiomegaly and (iii) wGAN on n=19,557 images from the CRCMS dataset to generate histopathological images with and without microsatellite stability. In the AIROGS, CRMCS, and CheXpert datasets, Medfusion achieved lower (=better) FID than the GANs (11.63 versus 20.43, 30.03 versus 49.26, and 17.28 versus 84.31). Also, fidelity (precision) and diversity (recall) were higher (=better) for Medfusion in all three datasets. Our study shows that DDPM are a superior alternative to GANs for image synthesis in the medical domain.

Danni Liu, Jan Niehues

While large language models demonstrate remarkable capabilities at task-specific applications through fine-tuning, extending these benefits across diverse languages is essential for broad accessibility. However, effective cross-lingual transfer is hindered by LLM performance gaps across languages and the scarcity of fine-tuning data in many languages. Through analysis of LLM internal representations from over 1,000+ language pairs, we discover that middle layers exhibit the strongest potential for cross-lingual alignment. Building on this finding, we propose a middle-layer alignment objective integrated into task-specific training. Our experiments on slot filling, machine translation, and structured text generation show consistent improvements in cross-lingual transfer, especially to lower-resource languages. The method is robust to the choice of alignment languages and generalizes to languages unseen during alignment. Furthermore, we show that separately trained alignment modules can be merged with existing task-specific modules, improving cross-lingual capabilities without full re-training. Our code is publicly available (https://github.com/dannigt/mid-align).

Maike Züfle, Ondrej Klejch, Nicholas Sanders et al.

Spoken conversational systems require more than accurate speech generation to have human-like conversations: to feel natural and engaging, they must produce conversational behaviour that adapts dynamically to the context. Current spoken conversational systems, however, rarely allow such customization, limiting their naturalness and usability. In this work, we present the first open, instruction-following full-duplex conversational speech model that can be trained efficiently under typical academic resource constraints. By keeping the audio encoder frozen and finetuning only the language model, our model requires just 2,000 hours of data, without relying on large-scale pretraining or multi-stage optimization. The model can follow explicit instructions to control speaker voice, conversation topic, conversational behaviour (e.g., backchanneling and interruptions), and dialogue initiation. We propose a single-stage training protocol and systematically analyze design choices. Both the model and training code will be released to enable reproducible research on controllable full-duplex speech systems.

Zhaolin Li, Jan Niehues

Automatic speech recognition (ASR) still covers only a small fraction of the world's languages, mainly due to supervised data scarcity. In-context learning (ICL) with large language models (LLMs) addresses this problem, but prior work largely focuses on high-resource languages covered during training and text-only settings. This paper investigates whether speech LLMs can learn unseen languages with multimodal ICL (MICL), and how this learning can be used to improve ASR. We conduct experiments with two speech LLMs, Phi-4 and Qwen3-Omni, on three diverse endangered languages. Firstly, we find that MICL is effective for unseen languages, leveraging both speech and text modalities. We further show that cross-lingual transfer learning improves MICL efficiency on target languages without training on them. Moreover, we analyze attention patterns to interpret MICL mechanisms, and we observe layer-dependent preferences between audio and text context, with an overall bias towards text. Finally, we show that prompt-based ASR with speech LLMs performs poorly on unseen languages, motivating a simple ASR system that combines a stronger acoustic model with a speech LLM via MICL-based selection of acoustic hypotheses. Results show that MICL consistently improves ASR performance, and that cross-lingual transfer learning matches or outperforms corpus-trained language models without using target-language data. Our code is publicly available.

Sai Koneru, Matthias Huck, Jan Niehues

There has been significant progress in open-source text-only translation large language models (LLMs) with better language coverage and quality. However, these models can be only used in cascaded pipelines for speech translation (ST), performing automatic speech recognition first followed by translation. This introduces additional latency, which is particularly critical in simultaneous ST (SimulST), and prevents the model from exploiting multimodal context, such as images, which can aid disambiguation. Pretrained multimodal foundation models (MMFMs) already possess strong perception and reasoning capabilities across multiple modalities, but generally lack the multilingual coverage and specialized translation performance of dedicated translation LLMs. To build an effective multimodal translation system, we propose an end-to-end approach that fuses MMFMs with translation LLMs. We introduce a novel fusion strategy that connects hidden states from multiple layers of a pretrained MMFM to a translation LLM, enabling joint end-to-end training. The resulting model, OmniFusion, built on Omni 2.5-7B as the MMFM and SeedX PPO-7B as the translation LLM, can perform speech-to-text, speech-and-image-to-text, and text-and-image-to-text translation. Experiments demonstrate that OmniFusion effectively leverages both audio and visual inputs, achieves a 1-second latency reduction in SimulST compared to cascaded pipelines and also improves the overall translation quality\footnote{Code is available at https://github.com/saikoneru/OmniFusion}.

Fabian Retkowski, Maike Züfle, Thai Binh Nguyen et al.

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.

Hyunji Lee, Danni Liu, Supriti Sinhamahapatra et al.

Multimodal foundation models aim to create a unified representation space that abstracts away from surface features like language syntax or modality differences. To investigate this, we study the internal representations of three recent models, analyzing the model activations from semantically equivalent sentences across languages in the text and speech modalities. Our findings reveal that: 1) Cross-modal representations converge over model layers, except in the initial layers specialized at text and speech processing. 2) Length adaptation is crucial for reducing the cross-modal gap between text and speech, although current approaches' effectiveness is primarily limited to high-resource languages. 3) Speech exhibits larger cross-lingual differences than text. 4) For models not explicitly trained for modality-agnostic representations, the modality gap is more prominent than the language gap.

Maike Züfle, Jan Niehues

Large language models (LLMs) excel in natural language processing but adapting these LLMs to speech processing tasks efficiently is not straightforward. Direct task-specific fine-tuning is limited by overfitting risks, data requirements, and computational costs. To address these challenges, we propose a scalable, two-stage training approach: (1) A task-independent speech pretraining stage using contrastive learning to align text and speech representations over all layers, followed by (2) a task-specific fine-tuning stage requiring minimal data. This approach outperforms traditional ASR pretraining and enables the model to surpass models specialized on speech translation and question answering while being trained on only 10% of the task-specific data.

Sara Papi, Maike Züfle, Marco Gaido et al.

Recent advances in large language models have catalyzed the development of multimodal LLMs (MLLMs) that integrate text, speech, and vision within unified frameworks. As MLLMs evolve from narrow, monolingual, task-specific systems to general-purpose instruction-following models, a key frontier lies in evaluating their multilingual and multimodal capabilities over both long and short contexts. However, existing benchmarks fall short in evaluating these dimensions jointly: they are often limited to English, mostly focus on one single modality at a time, rely on short-form contexts, or lack human annotations -- hindering comprehensive assessment of model performance across languages, modalities, and task complexity. To address these gaps, we introduce MCIF (Multimodal Crosslingual Instruction Following), the first multilingual human-annotated benchmark based on scientific talks that is designed to evaluate instruction-following in crosslingual, multimodal settings over both short- and long-form inputs. MCIF spans three core modalities -- speech, vision, and text -- and four diverse languages (English, German, Italian, and Chinese), enabling a comprehensive evaluation of MLLMs' abilities to interpret instructions across languages and combine them with multimodal contextual information. MCIF is released under a CC-BY 4.0 license to encourage open research and progress in MLLMs development.