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May 14

HYDRA: Unifying Multi-modal Generation and Understanding via Representation-Harmonized Tokenization

Unified Multimodal Models struggle to bridge the fundamental gap between the abstract representations needed for visual understanding and the detailed primitives required for generation. Existing approaches typically compromise by employing decoupled encoders, stacking representation encoder atop VAEs, or utilizing discrete quantization. However, these methods often disrupt information coherence and lead to optimization conflicts. To this end, we introduce HYDRA-TOK, a representation-harmonized pure ViT in the insight that visual modeling should evolve from generation to understanding. HYDRA-TOK reformulates the standard backbone into a progressive learner that transitions from a Gen-ViT, which captures structure-preserving primitives, to a Sem-ViT for semantic encoding. Crucially, this transition is mediated by a Generation-Semantic Bottleneck (GSB), which compresses features into a low-dimensional space to filter noise for robust synthesis, then restores dimensionality to empower complex semantic comprehension. Built upon this foundation, we present HYDRA, a native unified framework integrating perception and generation within a single parameter space. Extensive experiments establish HYDRA as a new state-of-the-art. It sets a benchmark in visual reconstruction (rFID 0.08) and achieves top-tier generation performance on GenEval (0.86), DPG-Bench (86.4), and WISE (0.53), while simultaneously outperforming previous native UMMs by an average of 10.0 points across eight challenging understanding benchmarks.

  • 12 authors
·
Mar 16

Calibrated Multimodal Representation Learning with Missing Modalities

Multimodal representation learning harmonizes distinct modalities by aligning them into a unified latent space. Recent research generalizes traditional cross-modal alignment to produce enhanced multimodal synergy but requires all modalities to be present for a common instance, making it challenging to utilize prevalent datasets with missing modalities. We provide theoretical insights into this issue from an anchor shift perspective. Observed modalities are aligned with a local anchor that deviates from the optimal one when all modalities are present, resulting in an inevitable shift. To address this, we propose CalMRL for multimodal representation learning to calibrate incomplete alignments caused by missing modalities. Specifically, CalMRL leverages the priors and the inherent connections among modalities to model the imputation for the missing ones at the representation level. To resolve the optimization dilemma, we employ a bi-step learning method with the closed-form solution of the posterior distribution of shared latents. We validate its mitigation of anchor shift and convergence with theoretical guidance. By equipping the calibrated alignment with the existing advanced method, we offer new flexibility to absorb data with missing modalities, which is originally unattainable. Extensive experiments and comprehensive analyses demonstrate the superiority of CalMRL. Our code, model checkpoints, and evaluation raw data will be publicly available.

  • 7 authors
·
Nov 14, 2025

Harmonizing Multi-Objective LLM Unlearning via Unified Domain Representation and Bidirectional Logit Distillation

Large Language Models (LLMs) unlearning is crucial for removing hazardous or privacy-leaking information from the model. Practical LLM unlearning demands satisfying multiple challenging objectives simultaneously: removing undesirable knowledge, preserving general utility, avoiding over-refusal of neighboring concepts, and, crucially, ensuring robustness against adversarial probing attacks. However, existing unlearning methods primarily focus on a limited subset of these goals, typically unlearning efficacy and utility preservation while overlooking robustness and boundary behaviors. Naively extending these methods to multi-objective settings may lead to unlearning task interference. We propose a novel multi-objective unlearning framework that harmonizes multiple unlearning objectives through a data and optimization co-design: We standardize training corpora into a unified data representation to reduce the domain gap, and then introduce a bidirectional distillation method that simultaneously elicits desired behavior from a context-instructed teacher while suppressing undesirable behavior in the student model. Theoretical and empirical analyses show that our method aligns domain distributions and converts seemingly irrelevant unlearning tasks into cooperative optimization. Evaluation demonstrates state-of-the-art performance, which enables balanced and reliable unlearning across diverse, challenging requirements.

  • 3 authors
·
Apr 15

LUCAS-MEGA: A Large-Scale Multimodal Dataset for Representation Learning in Soil-Environment Systems

Understanding soil is fundamental to agriculture, carbon cycling, and environmental sustainability, yet progress is limited by fragmented and heterogeneous datasets that constrain modeling to small-scale predictive settings rather than high-dimensional representation learning. We introduce LUCAS-MEGA, a large-scale multimodal dataset constructed through systematic data fusion of European soil-environment observations, with the LUCAS survey as its backbone. The fused dataset comprises over 70,000 samples and more than 1,000 features spanning physical, chemical, environmental, biological, and visual attributes, aggregated from 68 source datasets. To enable integration at scale, we develop SoilFuser, a multi-agent, human-in-the-loop data fusion pipeline that standardizes heterogeneous data formats and measurement protocols, resolves inconsistencies and invalid entries (e.g., unit inconsistencies, codebook mismatches, and erroneous values), incorporates natural language annotations, and harmonizes multimodal attributes and metadata into a unified, machine learning-ready feature space. The resulting dataset captures key characteristics of real-world soil observations, including multimodality, uneven feature coverage, and heterogeneous uncertainty. To demonstrate the usability of LUCAS-MEGA for data-driven modeling, we pretrain a multimodal tabular transformer (SoilFormer) using a self-supervised objective based on feature masking, achieving stable training, strong predictive performance, and representations that support uncertainty-aware prediction. We further show that the learned representations recover relationships consistent with established soil processes. LUCAS-MEGA is released with open access and is accompanied by composable, agent-friendly APIs that support structured querying and data-driven workflows.

  • 4 authors
·
May 4

MSTAR: Box-free Multi-query Scene Text Retrieval with Attention Recycling

Scene text retrieval has made significant progress with the assistance of accurate text localization. However, existing approaches typically require costly bounding box annotations for training. Besides, they mostly adopt a customized retrieval strategy but struggle to unify various types of queries to meet diverse retrieval needs. To address these issues, we introduce Muti-query Scene Text retrieval with Attention Recycling (MSTAR), a box-free approach for scene text retrieval. It incorporates progressive vision embedding to dynamically capture the multi-grained representation of texts and harmonizes free-style text queries with style-aware instructions. Additionally, a multi-instance matching module is integrated to enhance vision-language alignment. Furthermore, we build the Multi-Query Text Retrieval (MQTR) dataset, the first benchmark designed to evaluate the multi-query scene text retrieval capability of models, comprising four query types and 16k images. Extensive experiments demonstrate the superiority of our method across seven public datasets and the MQTR dataset. Notably, MSTAR marginally surpasses the previous state-of-the-art model by 6.4% in MAP on Total-Text while eliminating box annotation costs. Moreover, on the MQTR benchmark, MSTAR significantly outperforms the previous models by an average of 8.5%. The code and datasets are available at https://github.com/yingift/MSTAR.

  • 5 authors
·
Dec 21, 2025

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation:Application in De Novo Peptide Sequencing

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

  • 8 authors
·
Oct 9, 2025

Harmonizing Visual Representations for Unified Multimodal Understanding and Generation

Unifying visual understanding and generation within a single multimodal framework remains a significant challenge, as the two inherently heterogeneous tasks require representations at different levels of granularity. Current approaches that utilize vector quantization (VQ) or variational autoencoders (VAE) for unified visual representation prioritize intrinsic imagery features over semantics, compromising understanding performance. In this work, we take inspiration from masked image modelling (MIM) that learns rich semantics via a mask-and-reconstruct pre-training and its successful extension to masked autoregressive (MAR) image generation. A preliminary study on the MAR encoder's representation reveals exceptional linear probing accuracy and precise feature response to visual concepts, which indicates MAR's potential for visual understanding tasks beyond its original generation role. Based on these insights, we present Harmon, a unified autoregressive framework that harmonizes understanding and generation tasks with a shared MAR encoder. Through a three-stage training procedure that progressively optimizes understanding and generation capabilities, Harmon achieves state-of-the-art image generation results on the GenEval, MJHQ30K and WISE benchmarks while matching the performance of methods with dedicated semantic encoders (e.g., Janus) on image understanding benchmarks. Our code and models will be available at https://github.com/wusize/Harmon.

  • 9 authors
·
Mar 27, 2025

Relightful Harmonization: Lighting-aware Portrait Background Replacement

Portrait harmonization aims to composite a subject into a new background, adjusting its lighting and color to ensure harmony with the background scene. Existing harmonization techniques often only focus on adjusting the global color and brightness of the foreground and ignore crucial illumination cues from the background such as apparent lighting direction, leading to unrealistic compositions. We introduce Relightful Harmonization, a lighting-aware diffusion model designed to seamlessly harmonize sophisticated lighting effect for the foreground portrait using any background image. Our approach unfolds in three stages. First, we introduce a lighting representation module that allows our diffusion model to encode lighting information from target image background. Second, we introduce an alignment network that aligns lighting features learned from image background with lighting features learned from panorama environment maps, which is a complete representation for scene illumination. Last, to further boost the photorealism of the proposed method, we introduce a novel data simulation pipeline that generates synthetic training pairs from a diverse range of natural images, which are used to refine the model. Our method outperforms existing benchmarks in visual fidelity and lighting coherence, showing superior generalization in real-world testing scenarios, highlighting its versatility and practicality.

  • 8 authors
·
Dec 11, 2023

OptimusKG: Unifying biomedical knowledge in a modern multimodal graph

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constrains, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,531 nodes across 10 entity types, 21,813,816 edges across 26 relation types, and 67,249,863 property instances encoding 110,276,843 values across 150 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance across molecular, anatomical, clinical, and environmental domains. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

  • 8 authors
·
Apr 28

MM-Lego: Modular Biomedical Multimodal Models with Minimal Fine-Tuning

Learning holistic computational representations in physical, chemical or biological systems requires the ability to process information from different distributions and modalities within the same model. Thus, the demand for multimodal machine learning models has sharply risen for modalities that go beyond vision and language, such as sequences, graphs, time series, or tabular data. While there are many available multimodal fusion and alignment approaches, most of them require end-to-end training, scale quadratically with the number of modalities, cannot handle cases of high modality imbalance in the training set, or are highly topology-specific, making them too restrictive for many biomedical learning tasks. This paper presents Multimodal Lego (MM-Lego), a modular and general-purpose fusion and model merging framework to turn any set of encoders into a competitive multimodal model with no or minimal fine-tuning. We achieve this by introducing a wrapper for unimodal encoders that enforces lightweight dimensionality assumptions between modalities and harmonises their representations by learning features in the frequency domain to enable model merging with little signal interference. We show that MM-Lego 1) can be used as a model merging method which achieves competitive performance with end-to-end fusion models without any fine-tuning, 2) can operate on any unimodal encoder, and 3) is a model fusion method that, with minimal fine-tuning, achieves state-of-the-art results on six benchmarked multimodal biomedical tasks.

  • 3 authors
·
May 30, 2024

Harmonizing Generalization and Personalization in Federated Prompt Learning

Federated Prompt Learning (FPL) incorporates large pre-trained Vision-Language models (VLM) into federated learning through prompt tuning. The transferable representations and remarkable generalization capacity of VLM make them highly compatible with the integration of federated learning. Addressing data heterogeneity in federated learning requires personalization, but excessive focus on it across clients could compromise the model's ability to generalize effectively. To preserve the impressive generalization capability of VLM, it is crucial to strike a balance between personalization and generalization in FPL. To tackle this challenge, we proposed Federated Prompt Learning with CLIP Generalization and low-rank Personalization (FedPGP), which employs pre-trained CLIP to provide knowledge-guidance on the global prompt for improved generalization and incorporates a low-rank adaptation term to personalize the global prompt. Further, FedPGP integrates a prompt-wise contrastive loss to achieve knowledge guidance and personalized adaptation simultaneously, enabling a harmonious balance between personalization and generalization in FPL. We conduct extensive experiments on various datasets to explore base-to-novel generalization in both category-level and domain-level scenarios with heterogeneous data, showing the superiority of FedPGP in balancing generalization and personalization.

  • 4 authors
·
May 15, 2024

The Best of the Two Worlds: Harmonizing Semantic and Hash IDs for Sequential Recommendation

Conventional Sequential Recommender Systems (SRS) typically assign unique Hash IDs (HID) to construct item embeddings. These HID embeddings effectively learn collaborative information from historical user-item interactions, making them vulnerable to situations where most items are rarely consumed (the long-tail problem). Recent methods that incorporate auxiliary information often suffer from noisy collaborative sharing caused by co-occurrence signals or semantic homogeneity caused by flat dense embeddings. Semantic IDs (SIDs), with their capability of code sharing and multi-granular semantic modeling, provide a promising alternative. However, the collaborative overwhelming phenomenon hinders the further development of SID-based methods. The quantization mechanisms commonly compromise the uniqueness of identifiers required for modeling head items, creating a performance seesaw between head and tail items. To address this dilemma, we propose \name, a novel framework that harmonizes the SID and HID. Specifically, we devise a dual-branch modeling architecture that enables the model to capture both the multi-granular semantics within SID while preserving the unique collaborative identity of HID. Furthermore, we introduce a dual-level alignment strategy that bridges the two representations, facilitating knowledge transfer and supporting robust preference modeling. Extensive experiments on three real-world datasets show that \name~ effectively balances recommendation quality for both head and tail items while surpassing the existing baselines. The implementation code can be found onlinehttps://github.com/ziwliu8/H2Rec.

  • 7 authors
·
Dec 11, 2025

EVA: Towards a universal model of the immune system

The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell resolution and are evaluated on technical metrics often disconnected from actual drug development tasks and challenges. Here, we introduce EVA, the first cross-species, multimodal foundation model of immunology and inflammation, a therapeutic area where shared pathogenic mechanisms create unique opportunities for transfer learning. EVA harmonizes transcriptomics data across species, platforms, and resolutions, and integrates histology data to produce rich, unified patient representations. We establish clear scaling laws, demonstrating that increasing model size and compute translates to improvements in both pretraining and downstream tasks performance. We introduce a comprehensive evaluation suite of 39 tasks spanning the drug development pipeline: zero-shot target efficacy and gene function prediction for discovery, cross-species or cross-diseases molecular perturbations for preclinical development, and patient stratification with treatment response prediction or disease activity prediction for clinical trials applications. We benchmark EVA against several state-of-the-art biological foundation models and baselines on these tasks, and demonstrate state-of-the-art results on each task category. Using mechanistic interpretability, we further identify biological meaningful features, revealing intertwined representations across species and technologies. We release an open version of EVA for transcriptomics to accelerate research on immune-mediated diseases.

  • 11 authors
·
Feb 10