Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring alignment between generated drugs and their pharmacological properties, remains a critical challenge. To address these challenges, we propose MolChord, which integrates two key techniques: (1) to align protein and molecule structures with their textual descriptions and sequential representations (e.g., FASTA for proteins and SMILES for molecules), we leverage NatureLM, an autoregressive model unifying text, small molecules, and proteins, as the molecule generator, alongside a diffusion-based structure encoder; and (2) to guide molecules toward desired properties, we curate a property-aware dataset by integrating preference data and refine the alignment process using Direct Preference Optimization (DPO). Experimental results on CrossDocked2020 demonstrate that our approach achieves state-of-the-art performance on key evaluation metrics, highlighting its potential as a practical tool for SBDD.

These tokens serve as an effective protein structure representation.

Graph foundation models (GFMs) have recently emerged as a promising paradigm for achieving broad generalization across various graph data. However, existing GFMs are often trained on datasets that may not fully reflect real-world graphs, limiting their generalization performance. In contrast, tabular foundation models (TFMs) not only excel at classical tabular prediction tasks but have also shown strong applicability in other domains such as time series forecasting, natural language processing, and computer vision. Motivated by this, we take an alternative view to the standard perspective of GFMs and reformulate node classification as a tabular problem. In this reformulation, each node is represented as a row with feature, structure, and label information as columns, enabling TFMs to directly perform zero-shot node classification via in-context learning. In this work, we introduce TAG, a tabular approach for graph learning that first converts a graph into a table via feature and structural encoders, applies multiple TFMs to diversely subsampled tables, and then aggregates their outputs through ensemble selection. Experiments on 28 real-world datasets demonstrate that TAG consistently improves upon task-specific GNNs and state-of-the-art GFMs, highlighting the potential of the tabular reformulation for scalable and generalizable graph learning.

Understanding biological processes, drug development, and biotechnological advancements requires detailed analysis of protein structures and sequences, a task in protein research that is inherently complex and time-consuming when performed manually. To streamline this process, we introduce ProteinGPT, a state-of-the-art multi-modal protein chat system, that allows users to upload protein sequences and/or structures for comprehensive protein analysis and responsive inquiries. ProteinGPT seamlessly integrates protein sequence and structure encoders with linear projection layers for precise representation adaptation, coupled with a large language model (LLM) to generate accurate and contextually relevant responses. To train ProteinGPT, we construct a large-scale dataset of 132,092 proteins with annotations, and optimize the instruction-tuning process using GPT-4o. This innovative system ensures accurate alignment between the user-uploaded data and prompts, simplifying protein analysis. Experiments show that ProteinGPT can produce promising responses to proteins and their corresponding questions.

Hierarchical text classification (HTC) is a special sub-task of multi-label classification (MLC) whose taxonomy is constructed as a tree and each sample is assigned with at least one path in the tree. Latest HTC models contain three modules: a text encoder, a structure encoder and a multi-label classification head. Specially, the structure encoder is designed to encode the hierarchy of taxonomy. However, the structure encoder has scale problem. As the taxonomy size increases, the learnable parameters of recent HTC works grow rapidly. Recursive regularization is another widely-used method to introduce hierarchical information but it has collapse problem and generally relaxed by assigning with a small weight (ie. 1e-6). In this paper, we propose a Hierarchy-aware Light Global model with Hierarchical local conTrastive learning (HiLight), a lightweight and efficient global model only consisting of a text encoder and a multi-label classification head. We propose a new learning task to introduce the hierarchical information, called Hierarchical Local Contrastive Learning (HiLCL). Extensive experiments are conducted on two benchmark datasets to demonstrate the effectiveness of our model.

Existing self-supervised methods in natural language processing (NLP), especially hierarchical text classification (HTC), mainly focus on self-supervised contrastive learning, extremely relying on human-designed augmentation rules to generate contrastive samples, which can potentially corrupt or distort the original information. In this paper, we tend to investigate the feasibility of a contrastive learning scheme in which the semantic and syntactic information inherent in the input sample is adequately reserved in the contrastive samples and fused during the learning process. Specifically, we propose an information lossless contrastive learning strategy for HTC, namely \textbf{H}ierarchy-aware \textbf{I}nformation \textbf{L}ossless contrastive \textbf{L}earning (HILL), which consists of a text encoder representing the input document, and a structure encoder directly generating the positive sample. The structure encoder takes the document embedding as input, extracts the essential syntactic information inherent in the label hierarchy with the principle of structural entropy minimization, and injects the syntactic information into the text representation via hierarchical representation learning. Experiments on three common datasets are conducted to verify the superiority of HILL.

Multimodal knowledge graphs (MKGs), which intuitively organize information in various modalities, can benefit multiple practical downstream tasks, such as recommendation systems, and visual question answering. However, most MKGs are still far from complete, which motivates the flourishing of MKG reasoning models. Recently, with the development of general artificial architectures, the pretrained transformer models have drawn increasing attention, especially for multimodal scenarios. However, the research of multimodal pretrained transformer (MPT) for knowledge graph reasoning (KGR) is still at an early stage. As the biggest difference between MKG and other multimodal data, the rich structural information underlying the MKG still cannot be fully leveraged in existing MPT models. Most of them only utilize the graph structure as a retrieval map for matching images and texts connected with the same entity. This manner hinders their reasoning performances. To this end, we propose the graph Structure Guided Multimodal Pretrained Transformer for knowledge graph reasoning, termed SGMPT. Specifically, the graph structure encoder is adopted for structural feature encoding. Then, a structure-guided fusion module with two different strategies, i.e., weighted summation and alignment constraint, is first designed to inject the structural information into both the textual and visual features. To the best of our knowledge, SGMPT is the first MPT model for multimodal KGR, which mines the structural information underlying the knowledge graph. Extensive experiments on FB15k-237-IMG and WN18-IMG, demonstrate that our SGMPT outperforms existing state-of-the-art models, and prove the effectiveness of the designed strategies.

Hierarchical text classification (HTC) is a challenging subtask of multi-label classification as the labels form a complex hierarchical structure. Existing dual-encoder methods in HTC achieve weak performance gains with huge memory overheads and their structure encoders heavily rely on domain knowledge. Under such observation, we tend to investigate the feasibility of a memory-friendly model with strong generalization capability that could boost the performance of HTC without prior statistics or label semantics. In this paper, we propose Hierarchy-aware Tree Isomorphism Network (HiTIN) to enhance the text representations with only syntactic information of the label hierarchy. Specifically, we convert the label hierarchy into an unweighted tree structure, termed coding tree, with the guidance of structural entropy. Then we design a structure encoder to incorporate hierarchy-aware information in the coding tree into text representations. Besides the text encoder, HiTIN only contains a few multi-layer perceptions and linear transformations, which greatly saves memory. We conduct experiments on three commonly used datasets and the results demonstrate that HiTIN could achieve better test performance and less memory consumption than state-of-the-art (SOTA) methods.

Relational pooling is a framework for building more expressive and permutation-invariant graph neural networks. However, there is limited understanding of the exact enhancement in the expressivity of RP and its connection with the Weisfeiler Lehman hierarchy. Starting from RP, we propose to explicitly assign labels to nodes as additional features to improve expressive power of message passing neural networks. The method is then extended to higher dimensional WL, leading to a novel $k,l$-WL algorithm, a more general framework than $k$-WL. Theoretically, we analyze the expressivity of $k,l$-WL with respect to $k$ and $l$ and unifies it with a great number of subgraph GNNs. Complexity reduction methods are also systematically discussed to build powerful and practical $k,l$-GNN instances. We theoretically and experimentally prove that our method is universally compatible and capable of improving the expressivity of any base GNN model. Our $k,l$-GNNs achieve superior performance on many synthetic and real-world datasets, which verifies the effectiveness of our framework.