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1. Cross-Modal Center Loss for 3D Cross-Modal Retrieval

   Jing, L; Vahdani, E; Tan, J; Tian, Y. (June 2021, IEEE Conference on Computer Vision and Pattern Recognition (CVPR))

   null (Ed.)

   Cross-modal retrieval aims to learn discriminative and modal-invariant features for data from different modalities. Unlike the existing methods which usually learn from the features extracted by offline networks, in this paper, we pro- pose an approach to jointly train the components of cross- modal retrieval framework with metadata, and enable the network to find optimal features. The proposed end-to-end framework is updated with three loss functions: 1) a novel cross-modal center loss to eliminate cross-modal discrepancy, 2) cross-entropy loss to maximize inter-class variations, and 3) mean-square-error loss to reduce modality variations. In particular, our proposed cross-modal center loss minimizes the distances of features from objects belonging to the same class across all modalities. Extensive experiments have been conducted on the retrieval tasks across multi-modalities including 2D image, 3D point cloud and mesh data. The proposed framework significantly outperforms the state-of-the-art methods for both cross-modal and in-domain retrieval for 3D objects on the ModelNet10 and ModelNet40 datasets. 

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2. Multimodal deep learning approaches for single-cell multi-omics data integration

   https://doi.org/10.1093/bib/bbad313  

   Athaya, Tasbiraha; Ripan, Rony Chowdhury; Li, Xiaoman; Hu, Haiyan (August 2023, Briefings in Bioinformatics)

   Abstract Integrating single-cell multi-omics data is a challenging task that has led to new insights into complex cellular systems. Various computational methods have been proposed to effectively integrate these rapidly accumulating datasets, including deep learning. However, despite the proven success of deep learning in integrating multi-omics data and its better performance over classical computational methods, there has been no systematic study of its application to single-cell multi-omics data integration. To fill this gap, we conducted a literature review to explore the use of multimodal deep learning techniques in single-cell multi-omics data integration, taking into account recent studies from multiple perspectives. Specifically, we first summarized different modalities found in single-cell multi-omics data. We then reviewed current deep learning techniques for processing multimodal data and categorized deep learning-based integration methods for single-cell multi-omics data according to data modality, deep learning architecture, fusion strategy, key tasks and downstream analysis. Finally, we provided insights into using these deep learning models to integrate multi-omics data and better understand single-cell biological mechanisms. 

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3. scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection

   https://doi.org/10.1038/s41467-023-36066-2  

   Zhang, Ziqi; Sun, Haoran; Mariappan, Ragunathan; Chen, Xi; Chen, Xinyu; Jain, Mika S.; Efremova, Mirjana; Teichmann, Sarah A.; Rajan, Vaibhav; Zhang, Xiuwei (January 2023, Nature Communications)

   Abstract Single cell data integration methods aim to integrate cells across data batches and modalities, and data integration tasks can be categorized into horizontal, vertical, diagonal, and mosaic integration, where mosaic integration is the most general and challenging case with few methods developed. We propose scMoMaT, a method that is able to integrate single cell multi-omics data under the mosaic integration scenario using matrix tri-factorization. During integration, scMoMaT is also able to uncover the cluster specific bio-markers across modalities. These multi-modal bio-markers are used to interpret and annotate the clusters to cell types. Moreover, scMoMaT can integrate cell batches with unequal cell type compositions. Applying scMoMaT to multiple real and simulated datasets demonstrated these features of scMoMaT and showed that scMoMaT has superior performance compared to existing methods. Specifically, we show that integrated cell embedding combined with learned bio-markers lead to cell type annotations of higher quality or resolution compared to their original annotations. 

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4. Multi-Modal Contrastive Learning for Proteins by Combining Domain-Informed Views

   Xu, Haotian; You, Yuning; Shen, Yang (March 2024, Machine Learning for Genomics Explorations workshop at ICLR 2024)

   Proteins, often represented as multi-modal data of 1D sequences and 2D/3D structures, provide a motivating example for the communities of machine learning and computational biology to advance multi-modal representation learning. Protein language models over sequences and geometric deep learning over structures learn excellent single-modality representations for downstream tasks. It is thus desirable to fuse the single-modality models for better representation learning, but it remains an open question on how to fuse them effectively into multi-modal representation learning with a modest computational cost yet significant downstream performance gain. To answer the question, we propose to make use of separately pretrained single-modality models, integrate them in parallel connections, and continuously pretrain them end-to-end under the framework of multimodal contrastive learning. The technical challenge is to construct views for both intra- and inter-modality contrasts while addressing the heterogeneity of various modalities, particularly various levels of semantic robustness. We address the challenge by using domain knowledge of protein homology to inform the design of positive views, specifically protein classifications of families (based on similarities in sequences) and superfamilies (based on similarities in structures). We also assess the use of such views compared to, together with, and composed to other positive views such as identity and cropping. Extensive experiments on enzyme classification and protein function prediction benchmarks demonstrate the potential of domain-informed view construction and combination in multi-modal contrastive learning 

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5. MUTEX: Learning Unified Policies from Multimodal Task Specifications

   Shah, Rutav; Martín-Martín, Roberto; Zhu, Yuke (November 2023, Conference on Robot Learning)

   Humans use different modalities, such as speech, text, images, videos, etc., to communicate their intent and goals with teammates. For robots to become better assistants, we aim to endow them with the ability to follow instructions and understand tasks specified by their human partners. Most robotic policy learning methods have focused on one single modality of task specification while ignoring the rich cross-modal information. We present MUTEX, a unified approach to policy learning from multimodal task specifications. It trains a transformer-based architecture to facilitate cross-modal reasoning, combining masked modeling and cross-modal matching objectives in a two-stage training procedure. After training, MUTEX can follow a task specification in any of the six learned modalities (video demonstrations, goal images, text goal descriptions, text instructions, speech goal descriptions, and speech instructions) or a combination of them. We systematically evaluate the benefits of MUTEX in a newly designed dataset with 100 tasks in simulation and 50 tasks in the real world, annotated with multiple instances of task specifications in different modalities, and observe improved performance over methods trained specifically for any single modality. 

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