Di Wu

Di Wu, Jiaxin Fan, Junzhe Zang et al.

Embodied planning requires agents to make coherent multi-step decisions based on dynamic visual observations and natural language goals. While recent vision-language models (VLMs) excel at static perception tasks, they struggle with the temporal reasoning, spatial understanding, and commonsense grounding needed for planning in interactive environments. In this work, we introduce a reinforcement fine-tuning framework that brings R1-style reasoning enhancement into embodied planning. We first distill a high-quality dataset from a powerful closed-source model and perform supervised fine-tuning (SFT) to equip the model with structured decision-making priors. We then design a rule-based reward function tailored to multi-step action quality and optimize the policy via Generalized Reinforced Preference Optimization (GRPO). Our approach is evaluated on Embench, a recent benchmark for interactive embodied tasks, covering both in-domain and out-of-domain scenarios. Experimental results show that our method significantly outperforms models of similar or larger scale, including GPT-4o-mini and 70B+ open-source baselines, and exhibits strong generalization to unseen environments. This work highlights the potential of reinforcement-driven reasoning to advance long-horizon planning in embodied AI.

Mostafa Karimi, Di Wu, Zhangyang Wang et al.

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and interpretability. Results: We present a seamless integration of domain knowledges and learning-based approaches. Under novel representations of structurally-annotated protein sequences, a semi-supervised deep learning model that unifies recurrent and convolutional neural networks has been proposed to exploit both unlabeled and labeled data, for jointly encoding molecular representations and predicting affinities. Our representations and models outperform conventional options in achieving relative error in IC$_{50}$ within 5-fold for test cases and 20-fold for protein classes not included for training. Performances for new protein classes with few labeled data are further improved by transfer learning. Furthermore, separate and joint attention mechanisms are developed and embedded to our model to add to its interpretability, as illustrated in case studies for predicting and explaining selective drug-target interactions. Lastly, alternative representations using protein sequences or compound graphs and a unified RNN/GCNN-CNN model using graph CNN (GCNN) are also explored to reveal algorithmic challenges ahead. Availability: Data and source codes are available at https://github.com/Shen-Lab/DeepAffinity Supplementary Information: Supplementary data are available at http://shen-lab.github.io/deep-affinity-bioinf18-supp-rev.pdf

Shuaidong Pan, Di Wu

This study addresses the reliability of automatic summarization in high-risk scenarios and proposes a large language model framework that integrates uncertainty quantification and risk-aware mechanisms. Starting from the demands of information overload and high-risk decision-making, a conditional generation-based summarization model is constructed, and Bayesian inference is introduced during generation to model uncertainty in the parameter space, which helps avoid overconfident predictions. The uncertainty level of the generated content is measured using predictive distribution entropy, and a joint optimization of entropy regularization and risk-aware loss is applied to ensure that key information is preserved and risk attributes are explicitly expressed during information compression. On this basis, the model incorporates risk scoring and regulation modules, allowing summaries to cover the core content accurately while enhancing trustworthiness through explicit risk-level prompts. Comparative experiments and sensitivity analyses verify that the proposed method significantly improves the robustness and reliability of summarization in high-risk applications while maintaining fluency and semantic integrity. This research provides a systematic solution for trustworthy summarization and demonstrates both scalability and practical value at the methodological level.

Bozhi Dan, Di Wu, Ji Xu et al.

In the intensive care setting, sepsis continues to be a major contributor to patient illness and death; however, its timely detection is hindered by the complex, sparse, and heterogeneous nature of electronic health record (EHR) data. We propose Triplet-GCN, a single-branch graph convolutional model that represents each encounter as patient-feature-value triplets, constructs a bipartite EHR graph, and learns patient embeddings via a Graph Convolutional Network (GCN) followed by a lightweight multilayer perceptron (MLP). The pipeline applies type-specific preprocessing -- median imputation and standardization for numeric variables, effect coding for binary features, and mode imputation with low-dimensional embeddings for rare categorical attributes -- and initializes patient nodes with summary statistics, while retaining measurement values on edges to preserve "who measured what and by how much". In a retrospective, multi-center Chinese cohort (N = 648; 70/30 train-test split) drawn from three tertiary hospitals, Triplet-GCN consistently outperforms strong tabular baselines (KNN, SVM, XGBoost, Random Forest) across discrimination and balanced error metrics, yielding a more favorable sensitivity-specificity trade-off and improved overall utility for early warning. These findings indicate that encoding EHR as triplets and propagating information over a patient-feature graph produce more informative patient representations than feature-independent models, offering a simple, end-to-end blueprint for deployable sepsis risk stratification.

Di Wu, Chengshuai Shi, Ruida Zhou et al.

Pure exploration is one of the fundamental problems in multi-armed bandits (MAB). However, existing works mostly focus on specific pure exploration tasks, without a holistic view of the general pure exploration problem. This work fills this gap by introducing a versatile framework to study pure exploration, with a focus on identifying the pairwise relationships between targeted arm pairs. Moreover, unlike existing works that only optimize the stopping time (i.e., sample complexity), this work considers that arms are associated with potentially different costs and targets at optimizing the cumulative cost that occurred during learning. Under the general framework of pairwise pure exploration with arm-specific costs, a performance lower bound is derived. Then, a novel algorithm, termed CAET (Cost-Aware Pairwise Exploration Task), is proposed. CAET builds on the track-and-stop principle with a novel design to handle the arm-specific costs, which can potentially be zero and thus represent a very challenging case. Theoretical analyses prove that the performance of CAET approaches the lower bound asymptotically. Special cases are further discussed, including an extension to regret minimization, which is another major focus of MAB. The effectiveness and efficiency of CAET are also verified through experimental results under various settings.

Mostafa Karimi, Di Wu, Zhangyang Wang et al.

Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying affinities, our large-scale interpretability assessment finds commonly-used attention mechanisms inadequate. We thus formulate a hierarchical multi-objective learning problem whose predicted contacts form the basis for predicted affinities. We further design a physics-inspired deep relational network, DeepRelations, with intrinsically explainable architecture. Specifically, various atomic-level contacts or "relations" lead to molecular-level affinity prediction. And the embedded attentions are regularized with predicted structural contexts and supervised with partially available training contacts. DeepRelations shows superior interpretability to the state-of-the-art: without compromising affinity prediction, it boosts the AUPRC of contact prediction 9.5, 16.9, 19.3 and 5.7-fold for the test, compound-unique, protein-unique, and both-unique sets, respectively. Our study represents the first dedicated model development and systematic model assessment for interpretable machine learning of compound-protein affinity.

Di Wu, Chao Wang, Yong Wu et al.

In recent years, person re-identification (PReID) has become a hot topic in computer vision duo to it is an important part in intelligent surveillance. Many state-of-the-art PReID methods are attention-based or multi-scale feature learning deep models. However, introducing attention mechanism may lead to some important feature information losing issue. Besides, most of the multi-scale models embedding the multi-scale feature learning block into the feature extraction deep network, which reduces the efficiency of inference network. To address these issue, in this study, we introduce an attention deep architecture with multi-scale deep supervision for PReID. Technically, we contribute a reverse attention block to complement the attention block, and a novel multi-scale layer with deep supervision operator for training the backbone network. The proposed block and operator are only used for training, and discard in test phase. Experiments have been performed on Market-1501, DukeMTMC-reID and CUHK03 datasets. All the experiment results show that the proposed model significantly outperforms the other competitive state-of-the-art methods.

Di Wu, Hong-Wei Yang, De-Shuang Huang

Person re-identification (PReID) has received increasing attention due to it is an important part in intelligent surveillance. Recently, many state-of-the-art methods on PReID are part-based deep models. Most of them focus on learning the part feature representation of person body in horizontal direction. However, the feature representation of body in vertical direction is usually ignored. Besides, the spatial information between these part features and the different feature channels is not considered. In this study, we introduce a multi-branches deep model for PReID. Specifically, the model consists of five branches. Among the five branches, two of them learn the local feature with spatial information from horizontal or vertical orientations, respectively. The other one aims to learn interdependencies knowledge between different feature channels generated by the last convolution layer. The remains of two other branches are identification and triplet sub-networks, in which the discriminative global feature and a corresponding measurement can be learned simultaneously. All the five branches can improve the representation learning. We conduct extensive comparative experiments on three PReID benchmarks including CUHK03, Market-1501 and DukeMTMC-reID. The proposed deep framework outperforms many state-of-the-art in most cases.