LatentVerse: A Framework for Understanding Shared and Modality-Specific Information in Multimodal Latent Representations

Reasoning-driven universal multimodal embedding has advanced rapidly by introducing Chain-of-Thought (CoT) reasoning into the embedding pipeline. Despite the strong performance across both general and complex tasks, this paradigm suffers from two core limitations: (i) autoregressive CoT reasoning incurs high computational cost, making it impractical for low-latency retrieval; and (ii) embedding performance is heavily coupled with CoT annotation quality, making large-scale training unreliable. These raise fundamental questions: Is textual CoT the optimal form of reasoning for embedding, and can effective embedding reasoning be accomplished in latent space? To this end, we propose LaME (Latent Reasoning Multimodal Embedding), which formulates embedding-oriented latent reasoning as a weakly supervised information bottleneck. LaME employs K learnable reason tokens as a fixed-capacity bottleneck, completing all reasoning within a single forward pass. The two weak supervision signals structurally decouple contrastive from autoregressive objectives and eliminate dependence on CoT annotations, while a two-stage training pipeline ensures stable convergence. Experiments on MMEB-v2 and MRMR show that LaME achieves competitive performance, surpassing some explicit CoT-based models, while delivering 60x faster inference than explicit CoT methods and 2x faster than latent baselines with throughput comparable to discriminative embedding models. Code is available at https://github.com/PeppaWu/LaME.

We study multimodal learning under missing modalities, with particular motivation from bioscience applications in which heterogeneous modalities are often only partially available when decisions need to be made. We propose Latent World Recovery (LWR), a framework built on two key ideas: (i) modality-specific embeddings from different modalities are aligned in a shared latent space, and (ii) a unified representation is constructed by fusing only the embeddings of the modalities that are actually available at both training and inference time. Rather than imputing missing modalities or requiring a fixed modality set, LWR treats each modality as a partial perception of an underlying latent state and performs availability-aware representation learning directly from the observed modalities. This combination of neighbor-based latent alignment and availability-aware modality fusion enables robust multimodal prediction under partial observation, while avoiding error propagation from explicit reconstruction of missing modalities. We evaluate the proposed framework on real-world incomplete multi-omics benchmarks and demonstrate that it provides an effective approach to downstream tasks such as cancer phenotype classification and survival prediction.

Latent reasoning enables reasoning over continuous hidden states rather than explicit tokens, avoiding the language bottleneck and inference overhead of chain-of-thought for medical VQA. However, existing methods suffer from modality collapse, insufficient visual supervision, and train-inference mismatch. Moreover, their opaque latent states offer no interpretability, which is critical in clinical applications. We propose VITAL, a latent-space reasoning framework for medical MLLMs with visual-semantic dual supervision: an auxiliary text decoder reconstructs reasoning chains from latent states, while a visual projector regresses ROI features from a frozen, independent medical vision encoder. Both modules are discarded at inference with zero overhead, yet can be re-attached post-hoc for dual interpretability, providing textual and visual explanations of the reasoning process without sacrificing efficiency. We construct a 61K dataset spanning 9 imaging modalities, exceeding prior medical visual latent reasoning datasets by an order of magnitude. Experiments on 7 benchmarks show that VITAL consistently and substantially outperforms the backbone, all latent reasoning baselines, and medical MLLMs trained on far larger data, achieving state-of-the-art results competitive with trillion-parameter proprietary models.