Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change when binding with ligand molecules, leading to a big gap with real-world scenarios and inferior generation qualities (e.g., many steric clashes). To bridge the gap, we propose FlexSBDD, a deep generative model capable of accurately modeling the flexible protein-ligand complex structure for ligand molecule generation. FlexSBDD adopts an efficient flow matching framework and leverages E(3)-equivariant network with scalar-vector dual representation to model dynamic structural changes. Moreover, novel data augmentation schemes based on structure relaxation/sidechain repacking are adopted to boost performance. Extensive experiments demonstrate that FlexS-BDD achieves state-of-the-art performance in generating high-affinity molecules and effectively modeling the protein's conformation change to increase favorable protein-ligand interactions (e.g., Hydrogen bonds) and decrease steric clashes.

As the deep integration of machine learning and intelligent education, Computerized Adaptive Testing (CAT) has received more and more research attention. Compared to traditional paper-and-pencil tests, CAT can deliver both personalized and interactive assessments by automatically adjusting testing questions according to the performance of students during the test process. Therefore, CAT has been recognized as an efficient testing methodology capable of accurately estimating a student's ability with a minimal number of questions, leading to its widespread adoption in mainstream selective exams such as the GMAT and GRE. However, just improving the accuracy of ability estimation is far from satisfactory in the real-world scenarios, since an accurate ranking of students is usually more important (e.g., in high-stakes exams). Considering the shortage of existing CAT solutions in student ranking, this paper emphasizes the importance of aligning test outcomes (student ranks) with the true underlying abilities of students. Along this line, different from the conventional independent testing paradigm among students, we propose a novel collaborative framework, Collaborative Computerized Adaptive Testing (CCAT), that leverages inter-student information to enhance student ranking. By using collaborative students as anchors to assist in ranking test-takers, CCAT can give both theoretical guarantees and experimental validation for ensuring ranking consistency.

Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein pockets, the protein interface binding with the ligand. Current approaches to pocket generation often suffer from time-intensive physical computations or template-based methods, as well as compromised generation quality due to the overlooking of domain knowledge. To tackle these challenges, we propose PocketFlow, a generative model that incorporates protein-ligand interaction priors based on flow matching. During training, PocketFlow learns to model key types of protein-ligand interactions, such as hydrogen bonds. In the sampling, PocketFlow leverages multi-granularity guidance (overall binding affinity and interaction geometry constraints) to facilitate generating high-affinity and valid pockets. Extensive experiments show that PocketFlow outperforms baselines on multiple benchmarks, e.g., achieving an average improvement of 1.29 in Vina Score and 0.05 in scRMSD. Moreover, modeling interactions make PocketFlow a generalized generative model across multiple ligand modalities, including small molecules, peptides, and RNA.

Two-stage recommender systems play a crucial role in efficiently identifying relevant items and personalizing recommendations from a vast array of options. This paper, based on an error decomposition framework, analyzes the generalization error for two-stage recommender systems with a tree structure, which consist of an efficient tree-based retriever and a more precise yet time-consuming ranker. We use the Rademacher complexity to establish the generalization upper bound for various tree-based retrievers using beam search, as well as for different ranker models under a shifted training distribution. Both theoretical insights and practical experiments on real-world datasets indicate that increasing the branches in tree-based retrievers and harmonizing distributions across stages can enhance the generalization performance of two-stage recommender systems.

Since some brand-new methods utilize post-processing, such as calibration stacking [5] or domain detector [2, 12], to alleviate the domain shift problem, we report the results of our Dual Progressive Prototype Network (DPPN) with post-processing in Table 3 of the main paper for fair comparison. In this part, we further compare our DPPN with recent methods that clearly report their results without post-processing, of which the comparison results are shown in Table 1. APN [15] only reports their results with calibration stacking. Our DPPN outperforms the best one by respectively 15.3%, 8.8%, and 7.3% for H on CUB, AWA2, and aPY datasets, and obtains comparable performance on SUN dataset. This demonstrates the effectiveness of learning representations that progressively explore category discrimination and attribute-region correspondence.

Generalized Zero-Shot Learning (GZSL) aims to recognize new categories with auxiliary semantic information, e.g., category attributes. In this paper, we handle the critical issue of domain shift problem, i.e., confusion between seen and unseen categories, by progressively improving cross-domain transferability and category discriminability of visual representations. Our approach, named Dual Progressive Prototype Network (DPPN), constructs two types of prototypes that record prototypical visual patterns for attributes and categories, respectively. With attribute prototypes, DPPN alternately searches attribute-related local regions and updates corresponding attribute prototypes to progressively explore accurate attribute-region correspondence. This enables DPPN to produce visual representations with accurate attribute localization ability, which benefts the semantic-visual alignment and representation transferability. Besides, along with progressive attribute localization, DPPN further projects category prototypes into multiple spaces to progressively repel visual representations from different categories, which boosts category discriminability. Both attribute and category prototypes are collaboratively learned in a unifed framework, which makes visual representations of DPPN transferable and distinctive. Experiments on four benchmarks prove that DPPN effectively alleviates the domain shift problem in GZSL.

Learners sharing similar implicit cognitive states often display comparable observable problem-solving performances. Leveraging collaborative connections among such similar learners proves valuable in comprehending human learning. Motivated by the success of collaborative modeling in various domains, such as recommender systems, we aim to investigate how collaborative signals among learners contribute to the diagnosis of human cognitive states (i.e., knowledge proficiency) in the context of intelligent education. The primary challenges lie in identifying implicit collaborative connections and disentangling the entangled cognitive factors of learners for improved explainability and controllability in learner Cognitive Diagnosis (CD). However, there has been no work on CD capable of simultaneously modeling collaborative and disentangled cognitive states. To address this gap, we present Coral, a Collaborative cognitive diagnosis model with disentangled representation learning. Specifically, Coral first introduces a disentangled state encoder to achieve the initial disentanglement of learners' states. Subsequently, a meticulously designed collaborative representation learning procedure captures collaborative signals.

In this paper, we introduce DeAR (Decompose-Analyze-Rethink), a framework that iteratively builds a reasoning tree to tackle intricate problems within a single large language model (LLM). Unlike approaches that extend or search for rationales, DeAR is featured by 1) adopting a tree-based question decomposition manner to plan the organization of rationales, which mimics the logical planning inherent in human cognition; 2) globally updating the rationales at each reasoning step through natural language feedback. Specifically, the Decompose stage decomposes the question into simpler sub-questions, storing them as new nodes; the Analyze stage generates and self-checks rationales for sub-questions at each node level; and the Rethink stage updates parent-node rationales based on feedback from their child nodes. By generating and updating the reasoning process from a more global perspective, DeAR constructs more adaptive and accurate logical structures for complex problems, facilitating timely error correction compared to rationale-extension and search-based approaches such as Tree-of-Thoughts (ToT) and Graph-of-Thoughts (GoT). We conduct extensive experiments on three reasoning benchmarks, including ScienceQA, StrategyQA, and GSM8K, which cover a variety of reasoning tasks, demonstrating that our approach significantly reduces logical errors and enhances performance across various LLMs. Furthermore, we validate that DeAR is an efficient method that achieves a superior trade-off between accuracy and reasoning time compared to ToT and GoT.

This work studies the evaluation of explaining graph neural networks (GNNs), which is crucial to the credibility of post-hoc explainability in practical usage. Conventional evaluation metrics, and even explanation methods -- which mainly follow the paradigm of feeding the explanatory subgraph to the model and measuring output difference -- mostly suffer from the notorious out-of-distribution (OOD) issue. Hence, in this work, we endeavor to confront this issue by introducing a novel evaluation metric, termed OOD-resistant Adversarial Robustness (OAR). Specifically, we draw inspiration from adversarial robustness and evaluate post-hoc explanation subgraphs by calculating their robustness under attack. On top of that, an elaborate OOD reweighting block is inserted into the pipeline to confine the evaluation process to the original data distribution. For applications involving large datasets, we further devise a Simplified version of OAR (SimOAR), which achieves a significant improvement in computational efficiency at the cost of a small amount of performance.

User modeling techniques profile users' latent characteristics (e.g., preference) from their observed behaviors, and play a crucial role in decision-making. Unfortunately, traditional user models may unconsciously capture biases related to sensitive attributes (e.g., gender) from behavior data, even when this sensitive information is not explicitly provided. This can lead to unfair issues and discrimination against certain groups based on these sensitive attributes. Recent studies have been proposed to improve fairness by explicitly decorrelating user modeling results and sensitive attributes. However, most existing approaches assume that fully sensitive attribute labels are available in the training set, which is unrealistic due to collection limitations like privacy concerns, and hence bear the limitation of performance.