Jia Song

Changjian Zhou, Yuexi Qiu, Jia Song et al.

AI-assisted protein design has emerged as a critical tool for advancing biotechnology, as deep generative models have demonstrated their reliability in this domain. However, most existing models primarily utilize protein sequence or structural data for training, neglecting the physicochemical properties of proteins.Moreover, they are deficient to control the generation of proteins in intuitive conditions. To address these limitations,we propose CMADiff here, a novel framework that enables controllable protein generation by aligning the physicochemical properties of protein sequences with text-based descriptions through a latent diffusion process. Specifically, CMADiff employs a Conditional Variational Autoencoder (CVAE) to integrate physicochemical features as conditional input, forming a robust latent space that captures biological traits. In this latent space, we apply a conditional diffusion process, which is guided by BioAligner, a contrastive learning-based module that aligns text descriptions with protein features, enabling text-driven control over protein sequence generation. Validated by a series of evaluations including AlphaFold3, the experimental results indicate that CMADiff outperforms protein sequence generation benchmarks and holds strong potential for future applications. The implementation and code are available at https://github.com/HPC-NEAU/PhysChemDiff.

Changjian Zhou, Xin Zhang, Jiafeng Li et al.

Recent studies suggest that drug-drug interaction (DDI) prediction via computational approaches has significant importance for understanding the functions and co-prescriptions of multiple drugs. However, the existing silico DDI prediction methods either ignore the potential interactions among drug-drug pairs (DDPs), or fail to explicitly model and fuse the multi-scale drug feature representations for better prediction. In this study, we propose RGDA-DDI, a residual graph attention network (residual-GAT) and dual-attention based framework for drug-drug interaction prediction. A residual-GAT module is introduced to simultaneously learn multi-scale feature representations from drugs and DDPs. In addition, a dual-attention based feature fusion block is constructed to learn local joint interaction representations. A series of evaluation metrics demonstrate that the RGDA-DDI significantly improved DDI prediction performance on two public benchmark datasets, which provides a new insight into drug development.

Jiale Zhao, Wanru Zhuang, Jia Song et al.

In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing structure-based pre-trained models primarily focus on the residue level, i.e., alpha carbon atoms, while ignoring other atoms like side chain atoms. We argue that modeling proteins at both residue and atom levels is important since the side chain atoms can also be crucial for numerous downstream tasks, for example, molecular docking. Nevertheless, we find that naively combining residue and atom information during pre-training typically fails. We identify a key reason is the information leakage caused by the inclusion of atom structure in the input, which renders residue-level pre-training tasks trivial and results in insufficiently expressive residue representations. To address this issue, we introduce a span mask pre-training strategy on 3D protein chains to learn meaningful representations of both residues and atoms. This leads to a simple yet effective approach to learning protein representation suitable for diverse downstream tasks. Extensive experimental results on binding site prediction and function prediction tasks demonstrate our proposed pre-training approach significantly outperforms other methods. Our code will be made public.

Qingguo Hu, Ante Wang, Jia Song et al.

Large Vision-Language Models (LVLMs) have experienced significant advancements in recent years. However, their performance still falls short in tasks requiring deep visual perception, such as identifying subtle differences between images. A potential cause is the scarcity of visual knowledge in popular instruction-tuning corpora, resulting in inadequate visual perception and reasoning capabilities. To address this challenge, we introduce a self-improvement framework grounded in a novel visual knowledge-intensive task, \underline{C}ausality-driven \underline{V}isual object \underline{C}ompletion (CVC). This task requires LVLMs to infer the masked object in an image based on its \textit{causal} relationships with the other visible information. We first obtain rich examples cheaply through our automated instance construction pipeline, without relying on sophisticated LVLMs (\textit{e.g.}, GPT-4V) or human assistance. Then, LVLMs effectively self-improve through trial and error learning using these created instances. Our experiments demonstrate substantial gains across four challenging specialized tasks and four widely-used comprehensive benchmarks. Especially on specialized tasks, our method achieves an average improvement of 5.4\% and 4.0\% compared to the corresponding baselines when utilizing LLaVA-1.5-7B and LLaVA-1.5-13B, respectively. The code is available at https://github.com/XMUDeepLIT/CVC.

Zijun Min, Bingshuai Liu, Liang Zhang et al.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Beilin Chu, Weike You, Mengtao Li et al.

The rapid progress of GANs and Diffusion Models poses new challenges for detecting AI-generated images. Although CLIP-based detectors exhibit promising generalization, they often rely on semantic cues rather than generator artifacts, leading to brittle performance under distribution shifts. In this work, we revisit the nature of semantic bias and uncover that Patch Shuffle provides an unusually strong benefit for CLIP, that disrupts global semantic continuity while preserving local artifact cues, which reduces semantic entropy and homogenizes feature distributions between natural and synthetic images. Through a detailed layer-wise analysis, we further show that CLIP's deep semantic structure functions as a regulator that stabilizes cross-domain representations once semantic bias is suppressed. Guided by these findings, we propose SemAnti, a semantic-antagonistic fine-tuning paradigm that freezes the semantic subspace and adapts only artifact-sensitive layers under shuffled semantics. Despite its simplicity, SemAnti achieves state-of-the-art cross-domain generalization on AIGCDetectBenchmark and GenImage, demonstrating that regulating semantics is key to unlocking CLIP's full potential for robust AI-generated image detection.

Xuan Xu, Haolun Li, Zhongliang Yang et al.

Traditional topic models such as neural topic models rely on inference and generation networks to learn latent topic distributions. This paper explores a new paradigm for topic modeling in the era of large language models, framing TM as a long-form generation task whose definition is updated in this paradigm. We propose a simple but practical approach to implement LLM-based topic model tasks out of the box (sample a data subset, generate topics and representative text with our prompt, text assignment with keyword match). We then investigate whether the long-form generation paradigm can beat NTMs via zero-shot prompting. We conduct a systematic comparison between NTMs and LLMs in terms of topic quality and empirically examine the claim that "a majority of NTMs are outdated."

Binbin Xie, Jia Song, Liangying Shao et al.

Keyphrase prediction aims to generate phrases (keyphrases) that highly summarizes a given document. Recently, researchers have conducted in-depth studies on this task from various perspectives. In this paper, we comprehensively summarize representative studies from the perspectives of dominant models, datasets and evaluation metrics. Our work analyzes up to 167 previous works, achieving greater coverage of this task than previous surveys. Particularly, we focus highly on deep learning-based keyphrase prediction, which attracts increasing attention of this task in recent years. Afterwards, we conduct several groups of experiments to carefully compare representative models. To the best of our knowledge, our work is the first attempt to compare these models using the identical commonly-used datasets and evaluation metric, facilitating in-depth analyses of their disadvantages and advantages. Finally, we discuss the possible research directions of this task in the future.

Yu Zhao, Jia Song, Huali Feng et al.

Keyphrase provides accurate information of document content that is highly compact, concise, full of meanings, and widely used for discourse comprehension, organization, and text retrieval. Though previous studies have made substantial efforts for automated keyphrase extraction and generation, surprisingly, few studies have been made for \textit{keyphrase completion} (KPC). KPC aims to generate more keyphrases for document (e.g. scientific publication) taking advantage of document content along with a very limited number of known keyphrases, which can be applied to improve text indexing system, etc. In this paper, we propose a novel KPC method with an encoder-decoder framework. We name it \textit{deep keyphrase completion} (DKPC) since it attempts to capture the deep semantic meaning of the document content together with known keyphrases via a deep learning framework. Specifically, the encoder and the decoder in DKPC play different roles to make full use of the known keyphrases. The former considers the keyphrase-guiding factors, which aggregates information of known keyphrases into context. On the contrary, the latter considers the keyphrase-inhibited factor to inhibit semantically repeated keyphrase generation. Extensive experiments on benchmark datasets demonstrate the efficacy of our proposed model.

Kai Sun, Yingjie Hu, Jia Song et al.

Historical maps contain rich geographic information about the past of a region. They are sometimes the only source of information before the availability of digital maps. Despite their valuable content, it is often challenging to access and use the information in historical maps, due to their forms of paper-based maps or scanned images. It is even more time-consuming and labor-intensive to conduct an analysis that requires a synthesis of the information from multiple historical maps. To facilitate the use of the geographic information contained in historical maps, one way is to build a geographic knowledge graph (GKG) from them. This paper proposes a general workflow for completing one important step of building such a GKG, namely aligning the same geographic entities from different maps. We present this workflow and the related methods for implementation, and systematically evaluate their performances using two different datasets of historical maps. The evaluation results show that machine learning and deep learning models for matching place names are sensitive to the thresholds learned from the training data, and a combination of measures based on string similarity, spatial distance, and approximate topological relation achieves the best performance with an average F-score of 0.89.

Chenglizhao Chen, Jia Song, Chong Peng et al.

Previous video salient object detection (VSOD) approaches have mainly focused on designing fancy networks to achieve their performance improvements. However, with the slow-down in development of deep learning techniques recently, it may become more and more difficult to anticipate another breakthrough via fancy networks solely. To this end, this paper proposes a universal learning scheme to get a further 3\% performance improvement for all state-of-the-art (SOTA) methods. The major highlight of our method is that we resort the "motion quality"---a brand new concept, to select a sub-group of video frames from the original testing set to construct a new training set. The selected frames in this new training set should all contain high-quality motions, in which the salient objects will have large probability to be successfully detected by the "target SOTA method"---the one we want to improve. Consequently, we can achieve a significant performance improvement by using this new training set to start a new round of network training. During this new round training, the VSOD results of the target SOTA method will be applied as the pseudo training objectives. Our novel learning scheme is simple yet effective, and its semi-supervised methodology may have large potential to inspire the VSOD community in the future.

Di Qi, Lin Su, Jia Song et al.

In this paper, we introduce a new vision-language pre-trained model -- ImageBERT -- for image-text joint embedding. Our model is a Transformer-based model, which takes different modalities as input and models the relationship between them. The model is pre-trained on four tasks simultaneously: Masked Language Modeling (MLM), Masked Object Classification (MOC), Masked Region Feature Regression (MRFR), and Image Text Matching (ITM). To further enhance the pre-training quality, we have collected a Large-scale weAk-supervised Image-Text (LAIT) dataset from Web. We first pre-train the model on this dataset, then conduct a second stage pre-training on Conceptual Captions and SBU Captions. Our experiments show that multi-stage pre-training strategy outperforms single-stage pre-training. We also fine-tune and evaluate our pre-trained ImageBERT model on image retrieval and text retrieval tasks, and achieve new state-of-the-art results on both MSCOCO and Flickr30k datasets.