Zhengyang Wang

Weizhi Zhang, Xinyang Zhang, Chenwei Zhang et al.

Large Language Model (LLM) empowered agents have recently emerged as advanced paradigms that exhibit impressive capabilities in a wide range of domains and tasks. Despite their potential, current LLM agents often adopt a one-size-fits-all approach, lacking the flexibility to respond to users' varying needs and preferences. This limitation motivates us to develop PersonaAgent, the first personalized LLM agent framework designed to address versatile personalization tasks. Specifically, PersonaAgent integrates two complementary components - a personalized memory module that includes episodic and semantic memory mechanisms; a personalized action module that enables the agent to perform tool actions tailored to the user. At the core, the persona (defined as unique system prompt for each user) functions as an intermediary: it leverages insights from personalized memory to control agent actions, while the outcomes of these actions in turn refine the memory. Based on the framework, we propose a test-time user-preference alignment strategy that simulate the latest n interactions to optimize the persona prompt, ensuring real-time user preference alignment through textual loss feedback between simulated and ground-truth responses. Experimental evaluations demonstrate that PersonaAgent significantly outperforms other baseline methods by not only personalizing the action space effectively but also scaling during test-time real-world applications. These results underscore the feasibility and potential of our approach in delivering tailored, dynamic user experiences.

Bowen Jin, Hansi Zeng, Guoyin Wang et al.

Semantic identifier (ID) is an important concept in information retrieval that aims to preserve the semantics of objects such as documents and items inside their IDs. Previous studies typically adopt a two-stage pipeline to learn semantic IDs by first procuring embeddings using off-the-shelf text encoders and then deriving IDs based on the embeddings. However, each step introduces potential information loss, and there is usually an inherent mismatch between the distribution of embeddings within the latent space produced by text encoders and the anticipated distribution required for semantic indexing. It is non-trivial to design a method that can learn the document's semantic representations and its hierarchical structure simultaneously, given that semantic IDs are discrete and sequentially structured, and the semantic supervision is deficient. In this paper, we introduce LMIndexer, a self-supervised framework to learn semantic IDs with a generative language model. We tackle the challenge of sequential discrete ID by introducing a semantic indexer capable of generating neural sequential discrete representations with progressive training and contrastive learning. In response to the semantic supervision deficiency, we propose to train the model with a self-supervised document reconstruction objective. We show the high quality of the learned IDs and demonstrate their effectiveness on three tasks including recommendation, product search, and document retrieval on five datasets from various domains. Code is available at https://github.com/PeterGriffinJin/LMIndexer.

Wei Jin, Haitao Mao, Zheng Li et al.

Modeling customer shopping intentions is a crucial task for e-commerce, as it directly impacts user experience and engagement. Thus, accurately understanding customer preferences is essential for providing personalized recommendations. Session-based recommendation, which utilizes customer session data to predict their next interaction, has become increasingly popular. However, existing session datasets have limitations in terms of item attributes, user diversity, and dataset scale. As a result, they cannot comprehensively capture the spectrum of user behaviors and preferences. To bridge this gap, we present the Amazon Multilingual Multi-locale Shopping Session Dataset, namely Amazon-M2. It is the first multilingual dataset consisting of millions of user sessions from six different locales, where the major languages of products are English, German, Japanese, French, Italian, and Spanish. Remarkably, the dataset can help us enhance personalization and understanding of user preferences, which can benefit various existing tasks as well as enable new tasks. To test the potential of the dataset, we introduce three tasks in this work: (1) next-product recommendation, (2) next-product recommendation with domain shifts, and (3) next-product title generation. With the above tasks, we benchmark a range of algorithms on our proposed dataset, drawing new insights for further research and practice. In addition, based on the proposed dataset and tasks, we hosted a competition in the KDD CUP 2023 and have attracted thousands of users and submissions. The winning solutions and the associated workshop can be accessed at our website https://kddcup23.github.io/.

Yilun Yao, Xinyu Tan, Chao-Hsuan Liu et al.

LLM agents are increasingly deployed as executable systems that use tools, modify workspaces, and produce concrete artifacts. In such workflows, performance depends not only on the base model, but also on the harness: the system layer that manages context, tools, state, constraints, permissions, tracing, and recovery. However, existing benchmarks typically abstract away execution, compare complete agent systems, or hold the harness fixed, making execution-layer variation difficult to study. We introduce Harness-Bench, a diagnostic benchmark for evaluating configuration-level harness effects in realistic agent workflows. Harness-Bench evaluates representative harness configurations across multiple model backends under shared task environments, budgets, and evaluation protocols, while preserving each harness's native execution behavior. The benchmark contains 106 sandboxed offline tasks constructed from practical agent-use patterns and manually reviewed for realism, solvability, oracle-checkability, and integrity. Each run records final artifacts, execution traces, usage statistics, and validator outputs, enabling analysis beyond final completion. Across 5,194 execution trajectories, we observe substantial variation in completion, process quality, efficiency, and failure behavior across model-harness pairings. These results suggest that agent capability should be reported at the model-harness configuration level rather than attributed to the base model alone. Our analysis further identifies recurring execution-alignment failures, where plausible reasoning becomes decoupled from tool feedback, workspace state, evidence, or verifiable output contracts. Harness-Bench provides a reproducible foundation for diagnosing and improving reliable, efficient, and auditable agent execution stacks.

Jiachi Liu, Liwen Wang, Guanting Dong et al.

In real dialogue scenarios, as there are unknown input noises in the utterances, existing supervised slot filling models often perform poorly in practical applications. Even though there are some studies on noise-robust models, these works are only evaluated on rule-based synthetic datasets, which is limiting, making it difficult to promote the research of noise-robust methods. In this paper, we introduce a noise robustness evaluation dataset named Noise-SF for slot filling task. The proposed dataset contains five types of human-annotated noise, and all those noises are exactly existed in real extensive robust-training methods of slot filling into the proposed framework. By conducting exhaustive empirical evaluation experiments on Noise-SF, we find that baseline models have poor performance in robustness evaluation, and the proposed framework can effectively improve the robustness of models. Based on the empirical experimental results, we make some forward-looking suggestions to fuel the research in this direction. Our dataset Noise-SF will be released at https://github.com/dongguanting/Noise-SF.

Zijie Huang, Daheng Wang, Binxuan Huang et al.

Knowledge graph embeddings (KGE) have been extensively studied to embed large-scale relational data for many real-world applications. Existing methods have long ignored the fact many KGs contain two fundamentally different views: high-level ontology-view concepts and fine-grained instance-view entities. They usually embed all nodes as vectors in one latent space. However, a single geometric representation fails to capture the structural differences between two views and lacks probabilistic semantics towards concepts' granularity. We propose Concept2Box, a novel approach that jointly embeds the two views of a KG using dual geometric representations. We model concepts with box embeddings, which learn the hierarchy structure and complex relations such as overlap and disjoint among them. Box volumes can be interpreted as concepts' granularity. Different from concepts, we model entities as vectors. To bridge the gap between concept box embeddings and entity vector embeddings, we propose a novel vector-to-box distance metric and learn both embeddings jointly. Experiments on both the public DBpedia KG and a newly-created industrial KG showed the effectiveness of Concept2Box.

Kuan Wang, Alexander Bukharin, Haoming Jiang et al.

Instruction fine-tuning (IFT) elicits instruction following capabilities and steers the behavior of large language models (LLMs) via supervised learning. However, existing models trained on open-source IFT datasets only have the ability to follow instructions from users, and often fail to follow complex role and rules specified by developers, a.k.a. system prompts. The ability to follow these roles and rules is essential for deployment, as it ensures that the model safely interacts with users within developer defined guidelines. To improve such role and rule following ability, we propose \model, an automated data generation pipeline that generates diverse roles and rules from existing IFT instructions, along with corresponding responses. This data can then be used to train models that follow complex system prompts. The models are evaluated on our newly created benchmarks for role and rule following ability, as well as standard instruction-following benchmarks and general NLP tasks. Our framework significantly improves role and rule following capability in LLMs, as evidenced by over 25% increase in pass-rate on rule adherence, i.e. following all requirements, in our experiments with the Alpaca and Ultrachat datasets. Moreover, our models achieves this increase without any regression on popular instruction following benchmarks.

Weiqi Wang, Xin Liu, Binxuan Huang et al.

RLVR is now a standard way to train LLMs on reasoning tasks with verifiable outcomes, but when rollout generation dominates the cost, efficiency depends heavily on which prompts you sample and when. In practice, prompt pools are often static or only loosely tied to the model's learning progress, so uniform sampling can't keep up with the shifting capability frontier and ends up wasting rollouts on prompts that are already solved or still out of reach. Existing approaches improve efficiency through filtering, curricula, adaptive rollout allocation, or teacher guidance, but they typically assume a fixed pool-which makes it hard to support stable on-policy pool growth-or they add extra teacher cost and latency. We introduce HeaPA (Heap Sampling and On-Policy Query Augmentation), which maintains a bounded, evolving pool, tracks the frontier using heap-based boundary sampling, expands the pool via on-policy augmentation with lightweight asynchronous validation, and stabilizes correlated queries through topology-aware re-estimation of pool statistics and controlled reinsertion. Across two training corpora, two training recipes, and seven benchmarks, HeaPA consistently improves accuracy and reaches target performance with fewer computations while keeping wall-clock time comparable. Our analyses suggest these gains come from frontier-focused sampling and on-policy pool growth, with the benefits becoming larger as model scale increases. Our code is available at https://github.com/horizon-rl/HeaPA.

Ruijie Zhang, Yequan Zhao, Ziyue Liu et al.

The Muon optimizer has demonstrated promising performance in pre-training large language models through gradient (or momentum) orthogonalization. In this work, we propose a simple yet effective enhancement to Muon, namely Muon+, which introduces an additional normalization step after orthogonalization. We demonstrate the effectiveness of Muon+ through extensive pre-training experiments across a wide range of model scales and architectures. Our evaluation includes GPT-style models ranging from 130M to 774M parameters and LLaMA-style models ranging from 60M to 1B parameters. We comprehensively evaluate the effectiveness of Muon+ in the compute-optimal training regime and further extend the token-to-parameter (T2P) ratio to an industrial level of $\approx 200$. Experimental results show that Muon+ provides a consistent boost on training and validation perplexity over Muon. We provide our code here: https://github.com/K1seki221/MuonPlus.

Enyan Dai, Limeng Cui, Zhengyang Wang et al.

Graph Neural Networks (GNNs) have achieved great success in modeling graph-structured data. However, recent works show that GNNs are vulnerable to adversarial attacks which can fool the GNN model to make desired predictions of the attacker. In addition, training data of GNNs can be leaked under membership inference attacks. This largely hinders the adoption of GNNs in high-stake domains such as e-commerce, finance and bioinformatics. Though investigations have been made in conducting robust predictions and protecting membership privacy, they generally fail to simultaneously consider the robustness and membership privacy. Therefore, in this work, we study a novel problem of developing robust and membership privacy-preserving GNNs. Our analysis shows that Information Bottleneck (IB) can help filter out noisy information and regularize the predictions on labeled samples, which can benefit robustness and membership privacy. However, structural noises and lack of labels in node classification challenge the deployment of IB on graph-structured data. To mitigate these issues, we propose a novel graph information bottleneck framework that can alleviate structural noises with neighbor bottleneck. Pseudo labels are also incorporated in the optimization to minimize the gap between the predictions on the labeled set and unlabeled set for membership privacy. Extensive experiments on real-world datasets demonstrate that our method can give robust predictions and simultaneously preserve membership privacy.

Alexander Bukharin, Shiyang Li, Zhengyang Wang et al.

Recent works have shown that by curating high quality and diverse instruction tuning datasets, we can significantly improve instruction-following capabilities. However, creating such datasets is difficult and most works rely on manual curation or proprietary language models. Automatic data curation is difficult as it is still not clear how we can define diversity for instruction tuning, how diversity and quality depend on one other, and how we can optimize dataset quality and diversity. To resolve these issue, we propose a new algorithm, Quality-Diversity Instruction Tuning (QDIT). QDIT provides a simple method to simultaneously control dataset diversity and quality, allowing us to conduct an in-depth study on the effect of diversity and quality on instruction tuning performance. From this study we draw two key insights (1) there is a natural tradeoff between data diversity and quality and (2) increasing data diversity significantly improves the worst case instruction following performance, therefore improving robustness. We validate the performance of QDIT on several large scale instruction tuning datasets, where we find it can substantially improve worst and average case performance compared to quality-driven data selection.

Zhengyang Wang, Sanwoo Lee, Jiaxin Wang et al.

Multi-trait essay scoring aims to provide fine-grained evaluation of writing quality across multiple dimensions. However, how to effectively post-train autoregressive scoring models remains underexplored. In this paper, we propose Trait-Aware Policy Optimization (TAPO), a post-training framework tailored to autoregressive multi-trait scoring. Our method decomposes rewards along both the sample and trait dimensions, combining global scoring consistency, trait-level accuracy, format validity, and inter-trait dependency preservation. In addition, we enhance supervised fine-tuning with enhanced prompts, allowing the model to internalize trait semantics before preference optimization. Experiments across multiple backbone models show that our method consistently improves multi-trait scoring performance over supervised fine-tuning and scalar-reward optimization baselines, demonstrating the effectiveness and transferability of trait-aware post-training for essay scoring.

Kewei Cheng, Jingfeng Yang, Haoming Jiang et al.

Reasoning encompasses two typical types: deductive reasoning and inductive reasoning. Despite extensive research into the reasoning capabilities of Large Language Models (LLMs), most studies have failed to rigorously differentiate between inductive and deductive reasoning, leading to a blending of the two. This raises an essential question: In LLM reasoning, which poses a greater challenge - deductive or inductive reasoning? While the deductive reasoning capabilities of LLMs, (i.e. their capacity to follow instructions in reasoning tasks), have received considerable attention, their abilities in true inductive reasoning remain largely unexplored. To investigate into the true inductive reasoning capabilities of LLMs, we propose a novel framework, SolverLearner. This framework enables LLMs to learn the underlying function (i.e., $y = f_w(x)$), that maps input data points $(x)$ to their corresponding output values $(y)$, using only in-context examples. By focusing on inductive reasoning and separating it from LLM-based deductive reasoning, we can isolate and investigate inductive reasoning of LLMs in its pure form via SolverLearner. Our observations reveal that LLMs demonstrate remarkable inductive reasoning capabilities through SolverLearner, achieving near-perfect performance with ACC of 1 in most cases. Surprisingly, despite their strong inductive reasoning abilities, LLMs tend to relatively lack deductive reasoning capabilities, particularly in tasks involving ``counterfactual'' reasoning.

Jiayi Tian, Seyedarmin Azizi, Yequan Zhao et al.

Large reasoning models (LRMs) often cost significant key-value (KV) cache overhead, due to their linear growth with the verbose chain-of-thought (CoT) reasoning process. This costs both memory and throughput bottleneck limiting their efficient deployment. Towards reducing KV cache size during inference, we first investigate the effectiveness of existing KV cache eviction methods for CoT reasoning. Interestingly, we find that due to unstable token-wise scoring and the reduced effective KV budget caused by padding tokens, state-of-the-art (SoTA) eviction methods fail to maintain accuracy in the multi-batch setting. Additionally, these methods often generate longer sequences than the original model, as semantic-unaware token-wise eviction leads to repeated revalidation during reasoning. To address these issues, we present \textbf{SkipKV}, a \textbf{\textit{training-free}} KV compression method for selective \textit{eviction} and \textit{generation} operating at a coarse-grained sentence-level sequence removal for efficient CoT reasoning. In specific, it introduces a \textit{sentence-scoring metric} to identify and remove highly similar sentences while maintaining semantic coherence. To suppress redundant generation, SkipKV dynamically adjusts a steering vector to update the hidden activation states during inference enforcing the LRM to generate concise response. Extensive evaluations on multiple reasoning benchmarks demonstrate the effectiveness of SkipKV in maintaining up to $\mathbf{26.7}\%$ improved accuracy compared to the alternatives, at a similar compression budget. Additionally, compared to SoTA, SkipKV yields up to $\mathbf{1.6}\times$ fewer generation length while improving throughput up to $\mathbf{1.7}\times$.

Yilun Jin, Zheng Li, Chenwei Zhang et al.

Online shopping is a complex multi-task, few-shot learning problem with a wide and evolving range of entities, relations, and tasks. However, existing models and benchmarks are commonly tailored to specific tasks, falling short of capturing the full complexity of online shopping. Large Language Models (LLMs), with their multi-task and few-shot learning abilities, have the potential to profoundly transform online shopping by alleviating task-specific engineering efforts and by providing users with interactive conversations. Despite the potential, LLMs face unique challenges in online shopping, such as domain-specific concepts, implicit knowledge, and heterogeneous user behaviors. Motivated by the potential and challenges, we propose Shopping MMLU, a diverse multi-task online shopping benchmark derived from real-world Amazon data. Shopping MMLU consists of 57 tasks covering 4 major shopping skills: concept understanding, knowledge reasoning, user behavior alignment, and multi-linguality, and can thus comprehensively evaluate the abilities of LLMs as general shop assistants. With Shopping MMLU, we benchmark over 20 existing LLMs and uncover valuable insights about practices and prospects of building versatile LLM-based shop assistants. Shopping MMLU can be publicly accessed at https://github.com/KL4805/ShoppingMMLU. In addition, with Shopping MMLU, we host a competition in KDD Cup 2024 with over 500 participating teams. The winning solutions and the associated workshop can be accessed at our website https://amazon-kddcup24.github.io/.

Ziyue Liu, Ruijie Zhang, Zhengyang Wang et al.

Muon has emerged as a promising optimizer for large-scale foundation model pre-training by exploiting the matrix structure of neural network updates through iterative orthogonalization. However, its practical efficiency is limited by the need for multiple Newton--Schulz (NS) iterations per optimization step, which introduces non-trivial computation and communication overhead. We propose Muon$^2$, an extension of Muon that applies Adam-style adaptive second-moment preconditioning before orthogonalization. Our key insight is that the core challenge of polar approximation in Muon lies in the ill-conditioned momentum matrix, of which the spectrum is substantially improved by Muon$^2$, leading to faster convergence toward a practically sufficient orthogonalization. We further characterize the practical orthogonalization quality via directional alignment, under which Muon$^2$ demonstrates dramatic improvement over Muon at each polar step. Across GPT and LLaMA pre-training experiments from 60M to 1.3B parameters, Muon$^2$ consistently outperforms Muon and recent Muon variants while reducing NS iterations by 40\%. We further introduce Muon$^2$-F, a memory-efficient factorized variant that preserves most of the gains of Muon$^2$ with negligible memory overhead.

Zongyue Qin, Chen Luo, Zhengyang Wang et al.

Large language models (LLMs) excel in many natural language processing (NLP) tasks. However, since LLMs can only incorporate new knowledge through training or supervised fine-tuning processes, they are unsuitable for applications that demand precise, up-to-date, and private information not available in the training corpora. This precise, up-to-date, and private information is typically stored in relational databases. Thus, a promising solution is to augment LLMs with the inclusion of relational databases as external memory. This can ensure the timeliness, correctness, and consistency of data, and assist LLMs in performing complex arithmetic operations beyond their inherent capabilities. However, bridging the gap between LLMs and relational databases is challenging. It requires the awareness of databases and data values stored in databases to select correct databases and issue correct SQL queries. Besides, it is necessary for the external memory to be independent of the LLM to meet the needs of real-world applications. We introduce a novel LLM-agnostic memory architecture comprising a database selection memory, a data value memory, and relational databases. And we design an elegant pipeline to retrieve information from it. Besides, we carefully design the prompts to instruct the LLM to maximize the framework's potential. To evaluate our method, we compose a new dataset with various types of questions. Experimental results show that our framework enables LLMs to effectively answer database-related questions, which is beyond their direct ability.

Chi Han, Xin Liu, Haodong Wang et al.

Despite significant achievements in improving the instruction-following capabilities of large language models (LLMs), the ability to process multiple potentially entangled or conflicting instructions remains a considerable challenge. Real-world scenarios often require consistency across multiple instructions over time, such as secret privacy, personal preferences, and prioritization, which demand sophisticated abilities to integrate multiple turns and carefully balance competing objectives when instructions intersect or conflict. This work presents a systematic investigation of LLMs' capabilities in handling multiple turns of instructions, covering three levels of difficulty: (1) retrieving information from instructions, (2) tracking and reasoning across turns, and (3) resolving conflicts among instructions. We construct MultiTurnInstruct~with $\sim$1.1K high-quality multi-turn conversations through the human-in-the-loop approach and result in nine capability categories, including statics and dynamics, reasoning, and multitasking. Our finding reveals an intriguing trade-off between different capabilities. While GPT models demonstrate superior memorization, they show reduced effectiveness in privacy-protection tasks requiring selective information withholding. Larger models exhibit stronger reasoning capabilities but still struggle with resolving conflicting instructions. Importantly, these performance gaps cannot be attributed solely to information loss, as models demonstrate strong BLEU scores on memorization tasks. Still, their attention mechanisms fail to integrate multiple related instructions effectively. These findings highlight critical areas for improvement in complex real-world tasks involving multi-turn instructions. Data and codes are released at https://github.com/Glaciohound/Multi-Turn-Instruct.

Yuchen Zhuang, Jingfeng Yang, Haoming Jiang et al.

Due to the scarcity of agent-oriented pre-training data, LLM-based autonomous agents typically rely on complex prompting or extensive fine-tuning, which often fails to introduce new capabilities while preserving strong generalizability. We introduce Hephaestus-Forge, the first large-scale pre-training corpus designed to enhance the fundamental capabilities of LLM agents in API function calling, intrinsic reasoning and planning, and adapting to environmental feedback. Hephaestus-Forge comprises 103B agent-specific data encompassing 76,537 APIs, including both tool documentation to introduce knowledge of API functions and function calling trajectories to strengthen intrinsic reasoning. To explore effective training protocols, we investigate scaling laws to identify the optimal recipe in data mixing ratios. By continual pre-training on Hephaestus-Forge, Hephaestus outperforms small- to medium-scale open-source LLMs and rivals commercial LLMs on three agent benchmarks, demonstrating the effectiveness of our pre-training corpus in enhancing fundamental agentic capabilities and generalization of LLMs to new tasks or environments.

Ruijie Zhang, Yequan Zhao, Ziyue Liu et al.

The Muon optimizer has demonstrated strong empirical performance in pre-training large language models by performing matrix-level gradient (or momentum) orthogonalization in each layer independently. In this work, we propose TEON, a principled generalization of Muon that extends orthogonalization beyond individual layers by modeling the gradients of a neural network as a structured higher-order tensor. We present TEON's improved convergence guarantee over layer-wise Muon, and further develop a practical instantiation of TEON based on the theoretical analysis with corresponding ablation. We evaluate our approach on two widely adopted architectures: GPT-style models, ranging from 130M to 774M parameters, and LLaMA-style models, ranging from 60M to 1B parameters. Experimental results show that TEON consistently improves training and validation perplexity across model scales and exhibits strong robustness under various approximate SVD schemes.

Zihang Li, Yangdong Ruan, Wenjun Liu et al.

Although retrieval-augmented generation(RAG) significantly improves generation quality by retrieving external knowledge bases and integrating generated content, it faces computational efficiency bottlenecks, particularly in knowledge retrieval tasks involving hierarchical structures for Tree-RAG. This paper proposes a Tree-RAG acceleration method based on the improved Cuckoo Filter, which optimizes entity localization during the retrieval process to achieve significant performance improvements. Tree-RAG effectively organizes entities through the introduction of a hierarchical tree structure, while the Cuckoo Filter serves as an efficient data structure that supports rapid membership queries and dynamic updates. The experiment results demonstrate that our method is much faster than naive Tree-RAG while maintaining high levels of generative quality. When the number of trees is large, our method is hundreds of times faster than naive Tree-RAG. Our work is available at https://github.com/TUPYP7180/CFT-RAG-2025.

Ziyue Liu, Zhengyang Wang, Ruijie Zhang et al.

Pre-training large language models on massive GPU clusters has made hardware faults routine rather than rare, driving the need for resilient training systems. Yet existing frameworks either focus on specific parallelism schemes or risk drifting away from a failure-free training trajectory. We propose ReCoVer, a resilient LLM pre-training system that upholds a single invariant: each iteration keeps the number of microbatches constant, ensuring per-iteration gradients remain stochastically equivalent to a failure-free run. The framework is organized as three decoupled protocol layers: (1) Fault-tolerant collectives that isolate faults from propagating across replicas; (2) in-step fine-grained recovery that preserves intra-iteration progress and prevents gradient corruption; (3) versatile-workload policy that dynamically redistributes microbatch quotas across the survivors. The design is parallelism-agnostic, integrating directly with both 3D parallelism and Hybrid Sharded Data Parallel (HSDP) as a drop-in substrate. We evaluate our implementation on end-to-end pre-training tasks for up to 512 GPUs, ReCoVer successfully preserves the training trajectory from a failure-free reference despite of 256 GPUs lost spread across the run. For comparison with checkpoint-and-restart baselines, ReCoVer demonstrates $2.23\times$ higher effective throughput after successive failures. This advantage results in ReCoVer processing 74.9% more tokens at 234 GPU-hours, with the gap widening as the training prolongs.

Xiaoshuai Song, Muxi Diao, Guanting Dong et al.

Large language models (LLMs) have demonstrated significant potential in advancing various fields of research and society. However, the current community of LLMs overly focuses on benchmarks for analyzing specific foundational skills (e.g. mathematics and code generation), neglecting an all-round evaluation of the computer science field. To bridge this gap, we introduce CS-Bench, the first multilingual (English, Chinese, French, German) benchmark dedicated to evaluating the performance of LLMs in computer science. CS-Bench comprises approximately 10K meticulously curated test samples, covering 26 subfields across 4 key areas of computer science, encompassing various task forms and divisions of knowledge and reasoning. Utilizing CS-Bench, we conduct a comprehensive evaluation of over 30 mainstream LLMs, revealing the relationship between CS performance and model scales. We also quantitatively analyze the reasons for failures in existing LLMs and highlight directions for improvements, including knowledge supplementation and CS-specific reasoning. Further cross-capability experiments show a high correlation between LLMs' capabilities in computer science and their abilities in mathematics and coding. Moreover, expert LLMs specialized in mathematics and coding also demonstrate strong performances in several CS subfields. Looking ahead, we envision CS-Bench serving as a cornerstone for LLM applications in the CS field and paving new avenues in assessing LLMs' diverse reasoning capabilities. The CS-Bench data and evaluation code are available at https://github.com/csbench/csbench.

Xinyi Xu, Zhengyang Wang, Cheng Deng et al.

Grouping has been commonly used in deep metric learning for computing diverse features. However, current methods are prone to overfitting and lack interpretability. In this work, we propose an improved and interpretable grouping method to be integrated flexibly with any metric learning framework. Our method is based on the attention mechanism with a learnable query for each group. The query is fully trainable and can capture group-specific information when combined with the diversity loss. An appealing property of our method is that it naturally lends itself interpretability. The attention scores between the learnable query and each spatial position can be interpreted as the importance of that position. We formally show that our proposed grouping method is invariant to spatial permutations of features. When used as a module in convolutional neural networks, our method leads to translational invariance. We conduct comprehensive experiments to evaluate our method. Our quantitative results indicate that the proposed method outperforms prior methods consistently and significantly across different datasets, evaluation metrics, base models, and loss functions. For the first time to the best of our knowledge, our interpretation results clearly demonstrate that the proposed method enables the learning of distinct and diverse features across groups. The code is available on https://github.com/XinyiXuXD/DGML-master.

Yaochen Xie, Zhengyang Wang, Shuiwang Ji

Self-supervised frameworks that learn denoising models with merely individual noisy images have shown strong capability and promising performance in various image denoising tasks. Existing self-supervised denoising frameworks are mostly built upon the same theoretical foundation, where the denoising models are required to be J-invariant. However, our analyses indicate that the current theory and the J-invariance may lead to denoising models with reduced performance. In this work, we introduce Noise2Same, a novel self-supervised denoising framework. In Noise2Same, a new self-supervised loss is proposed by deriving a self-supervised upper bound of the typical supervised loss. In particular, Noise2Same requires neither J-invariance nor extra information about the noise model and can be used in a wider range of denoising applications. We analyze our proposed Noise2Same both theoretically and experimentally. The experimental results show that our Noise2Same remarkably outperforms previous self-supervised denoising methods in terms of denoising performance and training efficiency. Our code is available at https://github.com/divelab/Noise2Same.

Zhengyang Wang, Nuttapong Rochanavibhata, Yuxiao Ren et al.

In the early design stage of Japanese detached houses, the lack of a unified design representation among clients, sales representatives, and designers leads to design drift and inefficient feedback. Usually, sketches handed off by sales representatives may lose details for quick drawing, which reduces the fidelity of subsequent 3D generation using generative AI models. The generated 3D model typically takes the form of a single unified mesh, preventing component-level editing. To solve these issues, we propose a multi-stage 3D generative design framework capable of producing architectural models from rough design sketches. The framework combines generative and retrieval-based methods to enable component-level editing and personalized customization. It adopts a multimodal representation for 3D model generation and applies component segmentation to localize architectural components such as windows and doors and uses retrieval to support targeted replacement of components. Experiments show that the work enables modular customization which is thought to be suitable for personalized architectural design. This work introduces a multi-stage sketch-to-3D framework for Japanese detached houses, provides facade and component datasets, and shows effectiveness through quantitative and expert evaluations.

Warissara Booranamaitree, Xusheng Du, Yushu Cai et al.

Facade renovation offers a more sustainable alternative to full demolition, yet producing design proposals that preserve existing structures while expressing new intent remains challenging. Current workflows typically require detailed as-built modelling before design, which is time-consuming, labour-intensive, and often involves repeated revisions. To solve this issue, we propose a three-stage framework combining generative artificial intelligence (AI) and vision-language models (VLM) that directly processes rough structural sketch and textual descriptions to produce consistent renovation proposals. First, the input sketch is used by a fine-tuned VLM model to predict bounding boxes specifying where modifications are needed and which components should be added. Next, a stable diffusion model generates detailed sketches of new elements, which are merged with the original outline through a generative inpainting pipeline. Finally, ControlNet is employed to refine the result into a photorealistic image. Experiments on datasets and real industrial buildings indicate that the proposed framework can generate renovation proposals that preserve the original structure while improving facade detail quality. This approach effectively bypasses the need for detailed as-built modelling, enabling architects to rapidly explore design alternatives, iterate on early-stage concepts, and communicate renovation intentions with greater clarity.

Tianxin Wei, Bowen Jin, Ruirui Li et al.

Developing a universal model that can effectively harness heterogeneous resources and respond to a wide range of personalized needs has been a longstanding community aspiration. Our daily choices, especially in domains like fashion and retail, are substantially shaped by multi-modal data, such as pictures and textual descriptions. These modalities not only offer intuitive guidance but also cater to personalized user preferences. However, the predominant personalization approaches mainly focus on the ID or text-based recommendation problem, failing to comprehend the information spanning various tasks or modalities. In this paper, our goal is to establish a Unified paradigm for Multi-modal Personalization systems (UniMP), which effectively leverages multi-modal data while eliminating the complexities associated with task- and modality-specific customization. We argue that the advancements in foundational generative modeling have provided the flexibility and effectiveness necessary to achieve the objective. In light of this, we develop a generic and extensible personalization generative framework, that can handle a wide range of personalized needs including item recommendation, product search, preference prediction, explanation generation, and further user-guided image generation. Our methodology enhances the capabilities of foundational language models for personalized tasks by seamlessly ingesting interleaved cross-modal user history information, ensuring a more precise and customized experience for users. To train and evaluate the proposed multi-modal personalized tasks, we also introduce a novel and comprehensive benchmark covering a variety of user requirements. Our experiments on the real-world benchmark showcase the model's potential, outperforming competitive methods specialized for each task.

Weihong Lin, Lin Sun, Qilong Shi et al.

Model merging has emerged as a promising paradigm for composing the capabilities of large language models by directly operating in weight space, enabling the integration of specialized models without costly retraining. However, existing merging methods largely rely on parameter-space heuristics, which often introduce severe interference, leading to degraded generalization and unstable generation behaviors such as repetition and incoherent outputs. In this work, we propose Sparse Complementary Fusion with reverse KL (SCF-RKL), a novel model merging framework that explicitly controls functional interference through sparse, distribution-aware updates. Instead of assuming linear additivity in parameter space, SCF-RKL measures the functional divergence between models using reverse Kullback-Leibler divergence and selectively incorporates complementary parameters. This mode-seeking, sparsity-inducing design effectively preserves stable representations while integrating new capabilities. We evaluate SCF-RKL across a wide range of model scales and architectures, covering both reasoning-focused and instruction-tuned models. Extensive experiments on 24 benchmarks spanning advanced reasoning, general reasoning and knowledge, instruction following, and safety demonstrate, vision classification that SCF-RKL consistently outperforms existing model merging methods while maintaining strong generalization and generation stability.

Haoyu Wang, Ruirui Li, Haoming Jiang et al.

Retrieval-augmented Large Language Models (LLMs) offer substantial benefits in enhancing performance across knowledge-intensive scenarios. However, these methods often face challenges with complex inputs and encounter difficulties due to noisy knowledge retrieval, notably hindering model effectiveness. To address this issue, we introduce BlendFilter, a novel approach that elevates retrieval-augmented LLMs by integrating query generation blending with knowledge filtering. BlendFilter proposes the blending process through its query generation method, which integrates both external and internal knowledge augmentation with the original query, ensuring comprehensive information gathering. Additionally, our distinctive knowledge filtering module capitalizes on the intrinsic capabilities of the LLM, effectively eliminating extraneous data. We conduct extensive experiments on three open-domain question answering benchmarks, and the findings clearly indicate that our innovative BlendFilter surpasses state-of-the-art baselines significantly.

Yangyi Chen, Binxuan Huang, Yifan Gao et al.

Precise estimation of downstream performance in large language models (LLMs) prior to training is essential for guiding their development process. Scaling laws analysis utilizes the statistics of a series of significantly smaller sampling language models (LMs) to predict the performance of the target LLM. For downstream performance prediction, the critical challenge lies in the emergent abilities in LLMs that occur beyond task-specific computational thresholds. In this work, we focus on the pre-training loss as a more computation-efficient metric for performance estimation. Our two-stage approach FLP consists of first estimating a function that maps computational resources (e.g., FLOPs) to the pre-training Loss using a series of fully-converged sampling models, followed by mapping the pre-training loss to downstream task Performance using the intermediate models with emerged performance. In our experiments, this FLP solution accurately predicts the performance of LLMs with 7B and 13B parameters using a series of sampling LMs up to 3B, achieving error margins of 5% and 10%, respectively, and significantly outperforming the FLOPs-to-Performance approach. Further, we present FLP-M, a fundamental approach for performance prediction that addresses the practical need to integrate datasets from multiple sources during pre-training. FLP-M extends the power law analytical function to predict domain-specific pre-training loss based on FLOPs across data sources, and employs a two-layer neural network to model the non-linear relationship between multiple domain-specific loss and downstream performance. By utilizing a 3B LLM trained on a specific ratio and a series of smaller sampling LMs, FLP-M can effectively forecast the performance of 3B and 7B LLMs across various data mixtures for most benchmarks within 10% error margins.

Fengran Mo, Yifan Gao, Chuan Meng et al.

The rapid advancement of conversational search systems revolutionizes how information is accessed by enabling the multi-turn interaction between the user and the system. Existing conversational search systems are usually built with two different models. This separation restricts the system from leveraging the intrinsic knowledge of the models simultaneously, which cannot ensure the effectiveness of retrieval benefiting the generation. The existing studies for developing unified models cannot fully address the aspects of understanding conversational context, managing retrieval independently, and generating responses. In this paper, we explore how to unify dense retrieval and response generation for large language models in conversation. We conduct joint fine-tuning with different objectives and design two mechanisms to reduce the inconsistency risks while mitigating data discrepancy. The evaluations on five conversational search datasets demonstrate that our unified model can mutually improve both tasks and outperform the existing baselines.

Ziyue Liu, Ruijie Zhang, Zhengyang Wang et al.

The full-size MLPs and the projection layers in attention introduce tremendous model sizes of large language models (LLMs), consuming extensive computational resources in pre-training. We empirically observe that the activations of pre-trained LLMs exhibit low-rank property. Motivated by such observations, we propose CoLA and its memory-efficient implementation, CoLA-M, to replace these full-size layers with compute-efficient auto-encoders that naturally enforce low-rank activations throughout training. This fundamental architectural change eliminates the activation redundancy and significantly boosts model capacity and training efficiency. Experiments on LLaMA models with 60 million to 7 billion parameters show that CoLA reduces the computing cost by $\bf 2\pmb{\times}$ and improves training throughput by $\bf 1.86\pmb{\times}$ while maintaining full-rank level performance. CoLA-M further squeezes memory cost without sacrificing throughput, offering a pre-training approach with collectively superior parameter, computing, and memory efficiency. The LLMs produced are also $\bf 2\pmb{\times}$ smaller, enabling faster inference with lower memory cost on resource-constrained platforms.

Xiaoshuai Song, Zhengyang Wang, Keqing He et al.

Knowledge editing (KE) aims to efficiently and precisely modify the behavior of large language models (LLMs) to update specific knowledge without negatively influencing other knowledge. Current research primarily focuses on white-box LLMs editing, overlooking an important scenario: black-box LLMs editing, where LLMs are accessed through interfaces and only textual output is available. In this paper, we first officially introduce KE on black-box LLMs and then propose a comprehensive evaluation framework to overcome the limitations of existing evaluations that are not applicable to black-box LLMs editing and lack comprehensiveness. To tackle privacy leaks of editing data and style over-editing in current methods, we introduce a novel postEdit framework, resolving privacy concerns through downstream post-processing and maintaining textual style consistency via fine-grained editing to original responses. Experiments and analysis on two benchmarks demonstrate that postEdit outperforms all baselines and achieves strong generalization, especially with huge improvements on style retention (average $+20.82\%\uparrow$).

Hy Dang, Tianyi Liu, Zhuofeng Wu et al.

Large language models (LLMs) have demonstrated strong reasoning and tool-use capabilities, yet they often fail in real-world tool-interactions due to incorrect parameterization, poor tool selection, or misinterpretation of user intent. These issues often stem from an incomplete understanding of user goals and inadequate comprehension of tool documentation. While Chain-of-Thought (CoT) prompting has proven effective for enhancing reasoning in general contexts, our analysis reveals that free-form CoT is insufficient and sometimes counterproductive for structured function-calling tasks. To address this, we introduce a curriculum-inspired framework that leverages structured reasoning templates to guide LLMs through more deliberate step-by-step instructions for generating function callings. Experimental results show that our method reduces tool-use errors, achieving 3-12% relative improvements over strong baselines across diverse model series and approaches. Moreover, our framework enhances the robustness, interpretability, and transparency of tool-using agents, advancing the development of more reliable AI assistants for real-world applications.

Xusheng Du, Ruihan Gui, Zhengyang Wang et al.

In the early stages of architectural design, shoebox models are typically used as a simplified representation of building structures but require extensive operations to transform them into detailed designs. Generative artificial intelligence (AI) provides a promising solution to automate this transformation, but ensuring multi-view consistency remains a significant challenge. To solve this issue, we propose a novel three-stage consistent image generation framework using generative AI models to generate architectural designs from shoebox model representations. The proposed method enhances state-of-the-art image generation diffusion models to generate multi-view consistent architectural images. We employ ControlNet as the backbone and optimize it to accommodate multi-view inputs of architectural shoebox models captured from predefined perspectives. To ensure stylistic and structural consistency across multi-view images, we propose an image space loss module that incorporates style loss, structural loss and angle alignment loss. We then use depth estimation method to extract depth maps from the generated multi-view images. Finally, we use the paired data of the architectural images and depth maps as inputs to improve the multi-view consistency via the depth-aware 3D attention module. Experimental results demonstrate that the proposed framework can generate multi-view architectural images with consistent style and structural coherence from shoebox model inputs.

Hongye Jin, Pei Chen, Jingfeng Yang et al.

Large Language Models (LLMs) have demonstrated remarkable performance across a wide range of natural language processing tasks. However, they are often distracted by irrelevant or noisy context in input sequences that degrades output quality. This problem affects both long- and short-context scenarios, such as retrieval-augmented generation, table question-answering, and in-context learning. We reveal that LLMs can implicitly identify whether input sequences contain useful information at early layers, prior to token generation. Leveraging this insight, we introduce Early Noise Dropping (\textsc{END}), a novel approach to mitigate this issue without requiring fine-tuning the LLMs. \textsc{END} segments input sequences into chunks and employs a linear prober on the early layers of LLMs to differentiate between informative and noisy chunks. By discarding noisy chunks early in the process, \textsc{END} preserves critical information, reduces distraction, and lowers computational overhead. Extensive experiments demonstrate that \textsc{END} significantly improves both performance and efficiency across different LLMs on multiple evaluation datasets. Furthermore, by investigating LLMs' implicit understanding to the input with the prober, this work also deepens understanding of how LLMs do reasoning with contexts internally.

Hao Jin, Hengyuan Chang, Xiaoxuan Xie et al.

Designing stylized cinemagraphs is challenging due to the difficulty in customizing complex and expressive flow motions. To achieve intuitive and detailed control of the generated cinemagraphs, freehand sketches can provide a better solution to convey personalized design requirements than only text inputs. In this paper, we propose Sketch2Cinemagraph, a sketch-guided framework that enables the conditional generation of stylized cinemagraphs from freehand sketches. Sketch2Cinemagraph adopts text prompts for initial content generation and provides hand-drawn sketch controls for both spatial and motion cues. The latent diffusion model is adopted to generate target stylized landscape images along with realistic versions. Then, a pre-trained object detection model is utilized to segment and obtain masks for the flow regions. We proposed a novel latent motion diffusion model to estimate the motion field in the fluid regions of the generated landscape images. The input motion sketches serve as the conditions to control the generated vector fields in the masked fluid regions with the prompt. To synthesize the cinemagraph frames, the pixels within fluid regions are subsequently warped to the target locations for each timestep using a frame generator. The results verified that Sketch2Cinemagraph can generate high-fidelity and aesthetically appealing stylized cinemagraphs with continuous temporal flow from intuitive sketch inputs. We showcase the advantages of Sketch2Cinemagraph through quantitative comparisons against the state-of-the-art generation approaches.

Zhengyang Wang, Ziyue Liu, Ruijie Zhang et al.

The scale of transformer model pre-training is constrained by the increasing computation and communication cost. Low-rank bottleneck architectures offer a promising solution to significantly reduce the training time and memory footprint with minimum impact on accuracy. Despite algorithmic efficiency, bottleneck architectures scale poorly under standard tensor parallelism. Simply applying 3D parallelism designed for full-rank methods leads to excessive communication and poor GPU utilization. To address this limitation, we propose BOOST, an efficient training framework tailored for large-scale low-rank bottleneck architectures. BOOST introduces a novel Bottleneck-aware Tensor Parallelism, and combines optimizations such as online-RMSNorm, linear layer grouping, and low-rank activation checkpointing to achieve end-to-end training speedup. Evaluations on different low-rank bottleneck architectures demonstrate that BOOST achieves 1.46-1.91$\times$ speedup over full-rank model baselines and 1.87-2.27$\times$ speedup over low-rank model with naively integrated 3D parallelism, with improved GPU utilization and reduced communication overhead.

Chao Yi, Dian Chen, Gaoyang Guo et al.

Recommender systems are among the most impactful applications of artificial intelligence, serving as critical infrastructure connecting users, merchants, and platforms. However, most current industrial systems remain heavily reliant on historical co-occurrence patterns and log-fitting objectives, i.e., optimizing for past user interactions without explicitly modeling user intent. This log-fitting approach often leads to overfitting to narrow historical preferences, failing to capture users' evolving and latent interests. As a result, it reinforces filter bubbles and long-tail phenomena, ultimately harming user experience and threatening the sustainability of the whole recommendation ecosystem. To address these challenges, we rethink the overall design paradigm of recommender systems and propose RecGPT, a next-generation framework that places user intent at the center of the recommendation pipeline. By integrating large language models (LLMs) into key stages of user interest mining, item retrieval, and explanation generation, RecGPT transforms log-fitting recommendation into an intent-centric process. To effectively align general-purpose LLMs to the above domain-specific recommendation tasks at scale, RecGPT incorporates a multi-stage training paradigm, which integrates reasoning-enhanced pre-alignment and self-training evolution, guided by a Human-LLM cooperative judge system. Currently, RecGPT has been fully deployed on the Taobao App. Online experiments demonstrate that RecGPT achieves consistent performance gains across stakeholders: users benefit from increased content diversity and satisfaction, merchants and the platform gain greater exposure and conversions. These comprehensive improvement results across all stakeholders validates that LLM-driven, intent-centric design can foster a more sustainable and mutually beneficial recommendation ecosystem.

Ruijie Zhang, Ziyue Liu, Zhengyang Wang et al.

Training foundation models such as ViTs and LLMs requires tremendous computing cost. Low-rank matrix or tensor factorization offers a parameter-efficient alternative, but often downgrades performance due to the restricted parameter space. In this work, we introduce {\textbf{Latent Crossing (LaX)}} -- a simple yet effective plug-and-play module that enhances the capacity of low-rank models by enabling information flow across low-rank subspaces. We extensively validate the benefits of LaX on pre-training tasks with ViT-Base/Large and LLaMA-like models ranging from 60M to 1B parameters. LaX boosts low-rank model performance to match or exceed the full-rank baselines while using 2-3\(\times\) fewer parameters. When equipped with low-rank adapters (i.e., LoRA) for fine-tuning LLaMA-7/13B, LaX consistently improves performance on arithmetic and common sense reasoning tasks with negligible cost.

Yinglun Xu, Tarun Suresh, Rohan Gumaste et al.

Preference-based reinforcement learning (PBRL) in the offline setting has succeeded greatly in industrial applications such as chatbots. A two-step learning framework where one applies a reinforcement learning step after a reward modeling step has been widely adopted for the problem. However, such a method faces challenges from the risk of reward hacking and the complexity of reinforcement learning. To overcome the challenge, our insight is that both challenges come from the state-actions not supported in the dataset. Such state-actions are unreliable and increase the complexity of the reinforcement learning problem at the second step. Based on the insight, we develop a novel two-step learning method called PRC: preference-based reinforcement learning with constrained actions. The high-level idea is to limit the reinforcement learning agent to optimize over a constrained action space that excludes the out-of-distribution state-actions. We empirically verify that our method has high learning efficiency on various datasets in robotic control environments.

Xin Liu, Zheng Li, Yifan Gao et al.

The goal of session-based recommendation in E-commerce is to predict the next item that an anonymous user will purchase based on the browsing and purchase history. However, constructing global or local transition graphs to supplement session data can lead to noisy correlations and user intent vanishing. In this work, we propose the Frequent Attribute Pattern Augmented Transformer (FAPAT) that characterizes user intents by building attribute transition graphs and matching attribute patterns. Specifically, the frequent and compact attribute patterns are served as memory to augment session representations, followed by a gate and a transformer block to fuse the whole session information. Through extensive experiments on two public benchmarks and 100 million industrial data in three domains, we demonstrate that FAPAT consistently outperforms state-of-the-art methods by an average of 4.5% across various evaluation metrics (Hits, NDCG, MRR). Besides evaluating the next-item prediction, we estimate the models' capabilities to capture user intents via predicting items' attributes and period-item recommendations.

Peifeng Wang, Zhengyang Wang, Zheng Li et al.

Large language models (LMs) beyond a certain scale, demonstrate the emergent capability of generating free-text rationales for their predictions via chain-of-thought (CoT) prompting. While CoT can yield dramatically improved performance, such gains are only observed for sufficiently large LMs. Even more concerning, there is little guarantee that the generated rationales are consistent with LM's predictions or faithfully justify the decisions. In this work, we propose a faithful knowledge distillation method to learn a small, self-consistent CoT model from a teacher model that is orders of magnitude larger. To form better supervision, we elicit rationales supporting the gold answers from a large LM (teacher) by contrastive decoding, which encourages the teacher to generate tokens that become more plausible only when the answer is considered. To ensure faithful distillation, we use the teacher-generated rationales to learn a student LM with a counterfactual reasoning objective, which prevents the student from ignoring the rationales to make inconsistent predictions. Experiments show that, while yielding comparable end-task performance, our method can generate CoT rationales that are more faithful than baselines do. Further analysis suggests that such a model respects the rationales more when making decisions; thus, we can improve its performance more by refining its rationales.

Yaochen Xie, Zhao Xu, Jingtun Zhang et al.

Deep models trained in supervised mode have achieved remarkable success on a variety of tasks. When labeled samples are limited, self-supervised learning (SSL) is emerging as a new paradigm for making use of large amounts of unlabeled samples. SSL has achieved promising performance on natural language and image learning tasks. Recently, there is a trend to extend such success to graph data using graph neural networks (GNNs). In this survey, we provide a unified review of different ways of training GNNs using SSL. Specifically, we categorize SSL methods into contrastive and predictive models. In either category, we provide a unified framework for methods as well as how these methods differ in each component under the framework. Our unified treatment of SSL methods for GNNs sheds light on the similarities and differences of various methods, setting the stage for developing new methods and algorithms. We also summarize different SSL settings and the corresponding datasets used in each setting. To facilitate methodological development and empirical comparison, we develop a standardized testbed for SSL in GNNs, including implementations of common baseline methods, datasets, and evaluation metrics.

Chen Wei, Kexin Lou, Zhengyang Wang et al.

EEG source localization is an important technical issue in EEG analysis. Despite many numerical methods existed for EEG source localization, they all rely on strong priors and the deep sources are intractable. Here we propose a deep learning framework using spatial basis function decomposition for EEG source localization. This framework combines the edge sparsity prior and Gaussian source basis, called Edge Sparse Basis Network (ESBN). The performance of ESBN is validated by both synthetic data and real EEG data during motor tasks. The results suggest that the supervised ESBN outperforms the traditional numerical methods in synthetic data and the unsupervised fine-tuning provides more focal and accurate localizations in real data. Our proposed deep learning framework can be extended to account for other source priors, and the real-time property of ESBN can facilitate the applications of EEG in brain-computer interfaces and clinics.

Zhengyang Wang, Meng Liu, Youzhi Luo et al.

Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep learning methods, computational approaches for predicting molecular properties are gaining increasing momentum. However, there lacks customized and advanced methods and comprehensive tools for this task currently. Here we develop a suite of comprehensive machine learning methods and tools spanning different computational models, molecular representations, and loss functions for molecular property prediction and drug discovery. Specifically, we represent molecules as both graphs and sequences. Built on these representations, we develop novel deep models for learning from molecular graphs and sequences. In order to learn effectively from highly imbalanced datasets, we develop advanced loss functions that optimize areas under precision-recall curves. Altogether, our work not only serves as a comprehensive tool, but also contributes towards developing novel and advanced graph and sequence learning methodologies. Results on both online and offline antibiotics discovery and molecular property prediction tasks show that our methods achieve consistent improvements over prior methods. In particular, our methods achieve #1 ranking in terms of both ROC-AUC and PRC-AUC on the AI Cures Open Challenge for drug discovery related to COVID-19. Our software is released as part of the MoleculeX library under AdvProp.

Lei Cai, Zhengyang Wang, Rob Kulathinal et al.

Predictive modeling is useful but very challenging in biological image analysis due to the high cost of obtaining and labeling training data. For example, in the study of gene interaction and regulation in Drosophila embryogenesis, the analysis is most biologically meaningful when in situ hybridization (ISH) gene expression pattern images from the same developmental stage are compared. However, labeling training data with precise stages is very time-consuming even for evelopmental biologists. Thus, a critical challenge is how to build accurate computational models for precise developmental stage classification from limited training samples. In addition, identification and visualization of developmental landmarks are required to enable biologists to interpret prediction results and calibrate models. To address these challenges, we propose a deep two-step low-shot learning framework to accurately classify ISH images using limited training images. Specifically, to enable accurate model training on limited training samples, we formulate the task as a deep low-shot learning problem and develop a novel two-step learning approach, including data-level learning and feature-level learning. We use a deep residual network as our base model and achieve improved performance in the precise stage prediction task of ISH images. Furthermore, the deep model can be interpreted by computing saliency maps, which consist of pixel-wise contributions of an image to its prediction result. In our task, saliency maps are used to assist the identification and visualization of developmental landmarks. Our experimental results show that the proposed model can not only make accurate predictions, but also yield biologically meaningful interpretations. We anticipate our methods to be easily generalizable to other biological image classification tasks with small training datasets.

Zhengyang Wang, Bunyamin Sisman, Hao Wei et al.

Entity linkage (EL) is a critical problem in data cleaning and integration. In the past several decades, EL has typically been done by rule-based systems or traditional machine learning models with hand-curated features, both of which heavily depend on manual human inputs. With the ever-increasing growth of new data, deep learning (DL) based approaches have been proposed to alleviate the high cost of EL associated with the traditional models. Existing exploration of DL models for EL strictly follows the well-known twin-network architecture. However, we argue that the twin-network architecture is sub-optimal to EL, leading to inherent drawbacks of existing models. In order to address the drawbacks, we propose a novel and generic contrastive DL framework for EL. The proposed framework is able to capture both syntactic and semantic matching signals and pays attention to subtle but critical differences. Based on the framework, we develop a contrastive DL approach for EL, called CorDEL, with three powerful variants. We evaluate CorDEL with extensive experiments conducted on both public benchmark datasets and a real-world dataset. CorDEL outperforms previous state-of-the-art models by 5.2% on public benchmark datasets. Moreover, CorDEL yields a 2.4% improvement over the current best DL model on the real-world dataset, while reducing the number of training parameters by 97.6%.

Zhengyang Wang, Yaochen Xie, Shuiwang Ji

Advances in deep learning have led to remarkable success in augmented microscopy, enabling us to obtain high-quality microscope images without using expensive microscopy hardware and sample preparation techniques. However, current deep learning models for augmented microscopy are mostly U-Net based neural networks, thus sharing certain drawbacks that limit the performance. In this work, we introduce global voxel transformer networks (GVTNets), an advanced deep learning tool for augmented microscopy that overcomes intrinsic limitations of the current U-Net based models and achieves improved performance. GVTNets are built on global voxel transformer operators (GVTOs), which are able to aggregate global information, as opposed to local operators like convolutions. We apply the proposed methods on existing datasets for three different augmented microscopy tasks under various settings. The performance is significantly and consistently better than previous U-Net based approaches.