Min Li

Zhengyuan Shi, Min Li, Sadaf Khan et al.

Test point insertion (TPI) is a widely used technique for testability enhancement, especially for logic built-in self-test (LBIST) due to its relatively low fault coverage. In this paper, we propose a novel TPI approach based on deep reinforcement learning (DRL), named DeepTPI. Unlike previous learning-based solutions that formulate the TPI task as a supervised-learning problem, we train a novel DRL agent, instantiated as the combination of a graph neural network (GNN) and a Deep Q-Learning network (DQN), to maximize the test coverage improvement. Specifically, we model circuits as directed graphs and design a graph-based value network to estimate the action values for inserting different test points. The policy of the DRL agent is defined as selecting the action with the maximum value. Moreover, we apply the general node embeddings from a pre-trained model to enhance node features, and propose a dedicated testability-aware attention mechanism for the value network. Experimental results on circuits with various scales show that DeepTPI significantly improves test coverage compared to the commercial DFT tool. The code of this work is available at https://github.com/cure-lab/DeepTPI.

Meng Wang, Chuqi Lei, Jianxin Wang et al.

Human leukocyte antigen (HLA) is an important molecule family in the field of human immunity, which recognizes foreign threats and triggers immune responses by presenting peptides to T cells. In recent years, the synthesis of tumor vaccines to induce specific immune responses has become the forefront of cancer treatment. Computationally modeling the binding patterns between peptide and HLA can greatly accelerate the development of tumor vaccines. However, most of the prediction methods performance is very limited and they cannot fully take advantage of the analysis of existing biological knowledge as the basis of modeling. In this paper, we propose TripHLApan, a novel pan-specific prediction model, for HLA molecular peptide binding prediction. TripHLApan exhibits powerful prediction ability by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. The comprehensive evaluations demonstrate the effectiveness of TripHLApan in predicting HLA-I and HLA-II peptide binding in different test environments. The predictive power of HLA-I is further demonstrated in the latest data set. In addition, we show that TripHLApan has strong binding reconstitution ability in the samples of a melanoma patient. In conclusion, TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines.

Zhiyuan Yan, Min Li, Zhengyuan Shi et al.

Boolean satisfiability problem (SAT) is fundamental to many applications. Existing works have used graph neural networks (GNNs) for (approximate) SAT solving. Typical GNN-based end-to-end SAT solvers predict SAT solutions concurrently. We show that for a group of symmetric SAT problems, the concurrent prediction is guaranteed to produce a wrong answer because it neglects the dependency among Boolean variables in SAT problems. % We propose AsymSAT, a GNN-based architecture which integrates recurrent neural networks to generate dependent predictions for variable assignments. The experiment results show that dependent variable prediction extends the solving capability of the GNN-based method as it improves the number of solved SAT instances on large test sets.

Huimin Zhu, Renyi Zhou, Jing Tang et al.

The rational design of novel molecules with desired bioactivity is a critical but challenging task in drug discovery, especially when treating a novel target family or understudied targets. Here, we propose PGMG, a pharmacophore-guided deep learning approach for bioactivate molecule generation. Through the guidance of pharmacophore, PGMG provides a flexible strategy to generate bioactive molecules with structural diversity in various scenarios using a trained variational autoencoder. We show that PGMG can generate molecules matching given pharmacophore models while maintaining a high level of validity, uniqueness, and novelty. In the case studies, we demonstrate the application of PGMG to generate bioactive molecules in ligand-based and structure-based drug de novo design, as well as in lead optimization scenarios. Overall, the flexibility and effectiveness of PGMG make it a useful tool for accelerating the drug discovery process.

Shuxian Niu, Qian Liu, Yang Zhou et al.

In this paper, we apply a Threshold-Decreasing Algorithm to maximize $k$-submodular functions under a matroid constraint, which reduces the query complexity of the algorithm compared to the greedy algorithm with little loss in approximation ratio. We give a $(\frac{1}{2} - ε)$-approximation algorithm for monotone $k$-submodular function maximization, and a $(\frac{1}{3} - ε)$-approximation algorithm for non-monotone case, with complexity $O(\frac{n(k\cdot EO + IO)}ε \log \frac{r}ε)$, where $r$ denotes the rank of the matroid, and $IO, EO$ denote the number of oracles to evaluate whether a subset is an independent set and to compute the function value of $f$, respectively. Since the constraint of total size can be looked as a special matroid, called uniform matroid, then we present the fast algorithm for maximizing $k$-submodular functions subject to a total size constraint as corollaries. corollaries.

Libo Qin, Qiguang Chen, Yuhang Zhou et al.

Multilingual Large Language Models are capable of using powerful Large Language Models to handle and respond to queries in multiple languages, which achieves remarkable success in multilingual natural language processing tasks. Despite these breakthroughs, there still remains a lack of a comprehensive survey to summarize existing approaches and recent developments in this field. To this end, in this paper, we present a thorough review and provide a unified perspective to summarize the recent progress as well as emerging trends in multilingual large language models (MLLMs) literature. The contributions of this paper can be summarized: (1) First survey: to our knowledge, we take the first step and present a thorough review in MLLMs research field according to multi-lingual alignment; (2) New taxonomy: we offer a new and unified perspective to summarize the current progress of MLLMs; (3) New frontiers: we highlight several emerging frontiers and discuss the corresponding challenges; (4) Abundant resources: we collect abundant open-source resources, including relevant papers, data corpora, and leaderboards. We hope our work can provide the community with quick access and spur breakthrough research in MLLMs.

Zihui Cheng, Qiguang Chen, Jin Zhang et al.

Large Vision-Language Models (LVLMs) have recently demonstrated amazing success in multi-modal tasks, including advancements in Multi-modal Chain-of-Thought (MCoT) reasoning. Despite these successes, current benchmarks still follow a traditional paradigm with multi-modal input and text-modal output, which leads to significant drawbacks such as missing visual operations and vague expressions. Motivated by this, we introduce a novel Chain of Multi-modal Thought (CoMT) benchmark to address these limitations. Different from the traditional MCoT benchmark, CoMT requires both multi-modal input and multi-modal reasoning output, aiming to mimic human-like reasoning that inherently integrates visual operation. Specifically, CoMT consists of four categories: (1) Visual Creation, (2) Visual Deletion, (3) Visual Update, and (4) Visual Selection to comprehensively explore complex visual operations and concise expression in real scenarios. We evaluate various LVLMs and strategies on CoMT, revealing some key insights into the capabilities and limitations of the current approaches. We hope that CoMT can inspire more research on introducing multi-modal generation into the reasoning process.

Hellina Hailu Nigatu, Min Li, Maartje ter Hoeve et al.

Knowledge Graphs represent real-world entities and the relationships between them. Multilingual Knowledge Graph Construction (mKGC) refers to the task of automatically constructing or predicting missing entities and links for knowledge graphs in a multilingual setting. In this work, we reformulate the mKGC task as a Question Answering (QA) task and introduce mRAKL: a Retrieval-Augmented Generation (RAG) based system to perform mKGC. We achieve this by using the head entity and linking relation in a question, and having our model predict the tail entity as an answer. Our experiments focus primarily on two low-resourced languages: Tigrinya and Amharic. We experiment with using higher-resourced languages Arabic and English for cross-lingual transfer. With a BM25 retriever, we find that the RAG-based approach improves performance over a no-context setting. Further, our ablation studies show that with an idealized retrieval system, mRAKL improves accuracy by 4.92 and 8.79 percentage points for Tigrinya and Amharic, respectively.

Tianyu Su, Zhiqiang Zou, Ali Luo et al.

Stellar flare forecasting, a critical research frontier in astronomy, offers profound insights into stellar activity. However, the field is constrained by both the sparsity of recorded flare events and the absence of domain-specific large-scale predictive models. To address these challenges, this study introduces StellarF (Stellar Flare Forecasting), a novel large model that leverages Low-Rank (LoRA) and Adapter techniques to parameter-efficient learning for stellar flare forecasting. At its core, StellarF integrates an flare statistical information module with a historical flare record module, enabling multi-scale pattern recognition from observational data. Extensive experiments on our self-constructed datasets (derived from Kepler and TESS light curves) demonstrate that StellarF achieves state-of-the-art performance compared to existing methods. The proposed prediction paradigm establishes a novel methodological framework for advancing astrophysical research and cross-disciplinary applications.

Ruwen Bai, Min Li, Bo Meng et al.

Graph convolutional networks (GCNs) have emerged as dominant methods for skeleton-based action recognition. However, they still suffer from two problems, namely, neighborhood constraints and entangled spatiotemporal feature representations. Most studies have focused on improving the design of graph topology to solve the first problem but they have yet to fully explore the latter. In this work, we design a disentangled spatiotemporal transformer (DSTT) block to overcome the above limitations of GCNs in three steps: (i) feature disentanglement for spatiotemporal decomposition;(ii) global spatiotemporal attention for capturing correlations in the global context; and (iii) local information enhancement for utilizing more local information. Thereon, we propose a novel architecture, named Hierarchical Graph Convolutional skeleton Transformer (HGCT), to employ the complementary advantages of GCN (i.e., local topology, temporal dynamics and hierarchy) and Transformer (i.e., global context and dynamic attention). HGCT is lightweight and computationally efficient. Quantitative analysis demonstrates the superiority and good interpretability of HGCT.

Yang Yang, Min Li, Bo Meng et al.

Object detection aims to localize and classify the objects in a given image, and these two tasks are sensitive to different object regions. Therefore, some locations predict high-quality bounding boxes but low classification scores, and some locations are quite the opposite. A misalignment exists between the two tasks, and their features are spatially entangled. In order to solve the misalignment problem, we propose a plug-in Spatial-disentangled and Task-aligned operator (SALT). By predicting two task-aware point sets that are located in each task's sensitive regions, SALT can reassign features from those regions and align them to the corresponding anchor point. Therefore, features for the two tasks are spatially aligned and disentangled. To minimize the difference between the two regression stages, we propose a Self-distillation regression (SDR) loss that can transfer knowledge from the refined regression results to the coarse regression results. On the basis of SALT and SDR loss, we propose SALT-Net, which explicitly exploits task-aligned point-set features for accurate detection results. Extensive experiments on the MS-COCO dataset show that our proposed methods can consistently boost different state-of-the-art dense detectors by $\sim$2 AP. Notably, SALT-Net with Res2Net-101-DCN backbone achieves 53.8 AP on the MS-COCO test-dev.

Yang Yang, Min Li, Bo Meng et al.

Object detection can be regarded as a pixel clustering task, and its boundary is determined by four extreme points (leftmost, top, rightmost, and bottom). However, most studies focus on the center or corner points of the object, which are actually conditional results of the extreme points. In this paper, we present an Extreme-Point-Prediction- Based object detector (EPP-Net), which directly regresses the relative displacement vector between each pixel and the four extreme points. We also propose a new metric to measure the similarity between two groups of extreme points, namely, Extreme Intersection over Union (EIoU), and incorporate this EIoU as a new regression loss. Moreover, we propose a novel branch to predict the EIoU between the ground-truth and the prediction results, and take it as the localization confidence to filter out poor detection results. On the MS-COCO dataset, our method achieves an average precision (AP) of 44.0% with ResNet-50 and an AP of 50.3% with ResNeXt-101-DCN. The proposed EPP-Net provides a new method to detect objects and outperforms state-of-the-art anchor-free detectors.

Yifan Wu, Min Gao, Min Zeng et al.

Motivation: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep learning methods extract features only from basic characteristics, such as protein sequences, molecule structures. Others achieve significant improvement by learning from not only sequences/molecules but the protein-protein and drug-drug associations (PPAs and DDAs). The PPAs and DDAs are generally obtained by using computational methods. However, existing computational methods have some limitations, resulting in low-quality PPAs and DDAs that hamper the prediction performance. Therefore, we hope to develop a novel supervised learning method to learn the PPAs and DDAs effectively and thereby improve the prediction performance of the specific task of DPI. Results: In this research, we propose a novel deep learning framework, namely BridgeDPI. BridgeDPI introduces a class of nodes named hyper-nodes, which bridge different proteins/drugs to work as PPAs and DDAs. The hyper-nodes can be supervised learned for the specific task of DPI since the whole process is an end-to-end learning. Consequently, such a model would improve prediction performance of DPI. In three real-world datasets, we further demonstrate that BridgeDPI outperforms state-of-the-art methods. Moreover, ablation studies verify the effectiveness of the hyper-nodes. Last, in an independent verification, BridgeDPI explores the candidate bindings among COVID-19's proteins and various antiviral drugs. And the predictive results accord with the statement of the World Health Organization and Food and Drug Administration, showing the validity and reliability of BridgeDPI.

Min Li, Sudeep Gaddam, Xiaolin Li et al.

The pervasive interstellar dust grains provide significant insights to understand the formation and evolution of the stars, planetary systems, and the galaxies, and may harbor the building blocks of life. One of the most effective way to analyze the dust is via their interaction with the light from background sources. The observed extinction curves and spectral features carry the size and composition information of dust. The broad absorption bump at 2175 Angstrom is the most prominent feature in the extinction curves. Traditionally, statistical methods are applied to detect the existence of the absorption bump. These methods require heavy preprocessing and the co-existence of other reference features to alleviate the influence from the noises. In this paper, we apply Deep Learning techniques to detect the broad absorption bump. We demonstrate the key steps for training the selected models and their results. The success of Deep Learning based method inspires us to generalize a common methodology for broader science discovery problems. We present our on-going work to build the DeepDis system for such kind of applications.