Haitao Lin

Min Xiao, Junnan Zhu, Haitao Lin et al.

Multimodal summarization usually suffers from the problem that the contribution of the visual modality is unclear. Existing multimodal summarization approaches focus on designing the fusion methods of different modalities, while ignoring the adaptive conditions under which visual modalities are useful. Therefore, we propose a novel Coarse-to-Fine contribution network for multimodal Summarization (CFSum) to consider different contributions of images for summarization. First, to eliminate the interference of useless images, we propose a pre-filter module to abandon useless images. Second, to make accurate use of useful images, we propose two levels of visual complement modules, word level and phrase level. Specifically, image contributions are calculated and are adopted to guide the attention of both textual and visual modalities. Experimental results have shown that CFSum significantly outperforms multiple strong baselines on the standard benchmark. Furthermore, the analysis verifies that useful images can even help generate non-visual words which are implicitly represented in the image.

Jinyu Zhang, Yongchong Gu, Jianxiong Gao et al.

This paper addresses the challenge of perceiving complete object shapes through visual perception. While prior studies have demonstrated encouraging outcomes in segmenting the visible parts of objects within a scene, amodal segmentation, in particular, has the potential to allow robots to infer the occluded parts of objects. To this end, this paper introduces a new framework that explores amodal segmentation for robotic grasping in cluttered scenes, thus greatly enhancing robotic grasping abilities. Initially, we use a conventional segmentation algorithm to detect the visible segments of the target object, which provides shape priors for completing the full object mask. Particularly, to explore how to utilize semantic features from RGB images and geometric information from depth images, we propose a Linear-fusion Attention-guided Convolutional Network (LAC-Net). LAC-Net utilizes the linear-fusion strategy to effectively fuse this cross-modal data, and then uses the prior visible mask as attention map to guide the network to focus on target feature locations for further complete mask recovery. Using the amodal mask of the target object provides advantages in selecting more accurate and robust grasp points compared to relying solely on the visible segments. The results on different datasets show that our method achieves state-of-the-art performance. Furthermore, the robot experiments validate the feasibility and robustness of this method in the real world. Our code and demonstrations are available on the project page: https://jrryzh.github.io/LAC-Net.

Haitao Lin, Odin Zhang, Huifeng Zhao et al.

Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored. To fill the gap, we propose a target-aware peptide design method called \textsc{PPFlow}, based on conditional flow matching on torus manifolds, to model the internal geometries of torsion angles for the peptide structure design. Besides, we establish a protein-peptide binding dataset named PPBench2024 to fill the void of massive data for the task of structure-based peptide drug design and to allow the training of deep learning methods. Extensive experiments show that PPFlow reaches state-of-the-art performance in tasks of peptide drug generation and optimization in comparison with baseline models, and can be generalized to other tasks including docking and side-chain packing.

Lirong Wu, Haitao Lin, Yufei Huang et al.

Antibodies are Y-shaped proteins that protect the host by binding to specific antigens, and their binding is mainly determined by the Complementary Determining Regions (CDRs) in the antibody. Despite the great progress made in CDR design, existing computational methods still encounter several challenges: 1) poor capability of modeling complex CDRs with long sequences due to insufficient contextual information; 2) conditioned on pre-given antigenic epitopes and their static interaction with the target antibody; 3) neglect of specificity during antibody optimization leads to non-specific antibodies. In this paper, we take into account a variety of node features, edge features, and edge relations to include more contextual and geometric information. We propose a novel Relation-Aware Antibody Design (RAAD) framework, which dynamically models antigen-antibody interactions for co-designing the sequences and structures of antigen-specific CDRs. Furthermore, we propose a new evaluation metric to better measure antibody specificity and develop a contrasting specificity-enhancing constraint to optimize the specificity of antibodies. Extensive experiments have demonstrated the superior capability of RAAD in terms of antibody modeling, generation, and optimization across different CDR types, sequence lengths, pre-training strategies, and input contexts.

Lirong Wu, Yunfan Liu, Haitao Lin et al.

The proteins that exist today have been optimized over billions of years of natural evolution, during which nature creates random mutations and selects them. The discovery of functionally promising mutations is challenged by the limited evolutionary accessible regions, i.e., only a small region on the fitness landscape is beneficial. There have been numerous priors used to constrain protein evolution to regions of landscapes with high-fitness variants, among which the change in binding free energy (DDG) of protein complexes upon mutations is one of the most commonly used priors. However, the huge mutation space poses two challenges: (1) how to improve the efficiency of DDG prediction for fast mutation screening; and (2) how to explain mutation preferences and efficiently explore accessible evolutionary regions. To address these challenges, we propose a lightweight DDG predictor (Light-DDG), which adopts a structure-aware Transformer as the backbone and enhances it by knowledge distilled from existing powerful but computationally heavy DDG predictors. Additionally, we augmented, annotated, and released a large-scale dataset containing millions of mutation data for pre-training Light-DDG. We find that such a simple yet effective Light-DDG can serve as a good unsupervised antibody optimizer and explainer. For the target antibody, we propose a novel Mutation Explainer to learn mutation preferences, which accounts for the marginal benefit of each mutation per residue. To further explore accessible evolutionary regions, we conduct preference-guided antibody optimization and evaluate antibody candidates quickly using Light-DDG to identify desirable mutations.

Jingyang Huo, Qiang Sun, Boyan Jiang et al.

Most existing works solving Room-to-Room VLN problem only utilize RGB images and do not consider local context around candidate views, which lack sufficient visual cues about surrounding environment. Moreover, natural language contains complex semantic information thus its correlations with visual inputs are hard to model merely with cross attention. In this paper, we propose GeoVLN, which learns Geometry-enhanced visual representation based on slot attention for robust Visual-and-Language Navigation. The RGB images are compensated with the corresponding depth maps and normal maps predicted by Omnidata as visual inputs. Technically, we introduce a two-stage module that combine local slot attention and CLIP model to produce geometry-enhanced representation from such input. We employ V&L BERT to learn a cross-modal representation that incorporate both language and vision informations. Additionally, a novel multiway attention module is designed, encouraging different phrases of input instruction to exploit the most related features from visual input. Extensive experiments demonstrate the effectiveness of our newly designed modules and show the compelling performance of the proposed method.

Lirong Wu, Haitao Lin, Zhangyang Gao et al.

Recent years have witnessed great success in handling node classification tasks with Graph Neural Networks (GNNs). However, most existing GNNs are based on the assumption that node samples for different classes are balanced, while for many real-world graphs, there exists the problem of class imbalance, i.e., some classes may have much fewer samples than others. In this case, directly training a GNN classifier with raw data would under-represent samples from those minority classes and result in sub-optimal performance. This paper presents GraphMixup, a novel mixup-based framework for improving class-imbalanced node classification on graphs. However, directly performing mixup in the input space or embedding space may produce out-of-domain samples due to the extreme sparsity of minority classes; hence we construct semantic relation spaces that allows the Feature Mixup to be performed at the semantic level. Moreover, we apply two context-based self-supervised techniques to capture both local and global information in the graph structure and then propose Edge Mixup specifically for graph data. Finally, we develop a \emph{Reinforcement Mixup} mechanism to adaptively determine how many samples are to be generated by mixup for those minority classes. Extensive experiments on three real-world datasets show that GraphMixup yields truly encouraging results for class-imbalanced node classification tasks.

Zhangyang Gao, Haitao Lin, Stan. Z Li

Convolution and pooling are the key operations to learn hierarchical representation for graph classification, where more expressive $k$-order($k>1$) method requires more computation cost, limiting the further applications. In this paper, we investigate the strategy of selecting $k$ via neighborhood information gain and propose light $k$-order convolution and pooling requiring fewer parameters while improving the performance. Comprehensive and fair experiments through six graph classification benchmarks show: 1) the performance improvement is consistent to the $k$-order information gain. 2) the proposed convolution requires fewer parameters while providing competitive results. 3) the proposed pooling outperforms SOTA algorithms in terms of efficiency and performance.

Siyuan Li, Haitao Lin, Zelin Zang et al.

Dimension reduction (DR) aims to learn low-dimensional representations of high-dimensional data with the preservation of essential information. In the context of manifold learning, we define that the representation after information-lossless DR preserves the topological and geometric properties of data manifolds formally, and propose a novel two-stage DR method, called invertible manifold learning (inv-ML) to bridge the gap between theoretical information-lossless and practical DR. The first stage includes a homeomorphic sparse coordinate transformation to learn low-dimensional representations without destroying topology and a local isometry constraint to preserve local geometry. In the second stage, a linear compression is implemented for the trade-off between the target dimension and the incurred information loss in excessive DR scenarios. Experiments are conducted on seven datasets with a neural network implementation of inv-ML, called i-ML-Enc. Empirically, i-ML-Enc achieves invertible DR in comparison with typical existing methods as well as reveals the characteristics of the learned manifolds. Through latent space interpolation on real-world datasets, we find that the reliability of tangent space approximated by the local neighborhood is the key to the success of manifold-based DR algorithms.