Xuying Ning

Zihao Li, Kaifeng Jin, Yuanchen Bei et al.

Time series are often embedded in rich contexts that are essential for holistic modeling. Moreover, real-world practitioners often require end-to-end workflows for analyzing temporal dynamics, where widely studied tasks such as forecasting are only one step in a broader solution loop. While generalist AI agents offer a promising interface for such workflows under complex contexts, they still operate primarily in textual spaces that are not fully aligned with structured temporal signals. In this work, we introduce TimeClaw, an agentic harness framework for time series that equips generalist LLM agents with the time series-native runtime support needed for contextualized temporal reasoning. TimeClaw integrates executable temporal tools for grounded and auditable analysis, experience-driven capability evolution for creating reusable analytical routines, and episodic multimodal memory for retrieving relevant reasoning traces. Together, these components unlock harnessed open-ended temporal reasoning with contextual information. Extensive evaluation on multiple benchmarks covering diverse tasks across energy, finance, weather, traffic, and other real-world domains demonstrates improved performance of TimeClaw. Code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/TimeClaw.

Yanjun Zhao, Tianxin Wei, Jiaru Zou et al.

Understanding scientific papers requires more than answering isolated questions or summarizing content. It involves an integrated reasoning process that grounds textual and visual information, interprets experimental evidence, synthesizes information across sources, and critically evaluates scientific claims. However, existing benchmarks typically assess these abilities in isolation, making it difficult to evaluate scientific paper understanding as a unified set of interacting cognitive abilities. In this work, we introduce PAPERMIND, a benchmark designed to evaluate integrated and agent-oriented scientific reasoning over research papers. PAPERMIND is constructed from real scientific papers across seven domains, including agriculture, biology, chemistry, computer science, medicine, physics, and economics. It comprises four complementary task families that collectively operationalize distinct cognitive facets of scientific paper reasoning, including multimodal grounding, experimental interpretation, cross-source evidence reasoning, and critical assessment. By analyzing model behavior across multiple tasks, PAPERMIND enables a diagnostic evaluation of integrated scientific reasoning behaviors that are difficult to assess through isolated task evaluations. Extensive experiments on both opensource and closed-source multimodal LLMs reveal consistent performance gaps across tasks, highlighting persistent challenges in integrated scientific reasoning and critique. Our benchmark and dataset are available at https:// github.com/Yanjun-Zhao/PaperMind.

Xuying Ning, Dongqi Fu, Tianxin Wei et al.

With the increasing demand for step-wise, cross-modal, and knowledge-grounded reasoning, multimodal large language models (MLLMs) are evolving beyond the traditional fixed retrieve-then-generate paradigm toward more sophisticated agentic multimodal retrieval-augmented generation (MM-RAG). Existing benchmarks, however, mainly focus on simplified QA with short retrieval chains, leaving adaptive planning and multimodal reasoning underexplored. We present MC-Search, the first benchmark for agentic MM-RAG with long, step-wise annotated reasoning chains spanning five representative reasoning structures. Each example specifies sub-questions, retrieval modalities, supporting facts, and intermediate answers, with fidelity ensured by HAVE (Hop-wise Attribution and Verification of Evidence), resulting in 3,333 high-quality examples averaging 3.7 hops. Beyond answer accuracy, MC-Search introduces new process-level metrics for reasoning quality, stepwise retrieval and planning accuracy. By developing a unified agentic MM-RAG pipeline, we benchmark six leading MLLMs and reveal systematic issues such as over- and under-retrieval and modality-misaligned planning. Finally, we introduce Search-Align, a process-supervised fine-tuning framework leveraging verified reasoning chains, showing that our data not only enables faithful evaluation but also improves planning and retrieval fidelity in open-source MLLMs.

Chengming Cui, Tianxin Wei, Ziyi Chen et al.

Large language models (LLMs) exhibit complementary strengths arising from differences in pretraining data, model architectures, and decoding behaviors. Inference-time ensembling provides a practical way to combine these capabilities without retraining. However, existing ensemble approaches suffer from fundamental limitations. Most rely on fixed fusion granularity, which lacks the flexibility required for mid-generation adaptation and fails to adapt to different generation characteristics across tasks. To address these challenges, we propose AdaFuse, an adaptive ensemble decoding framework that dynamically selects semantically appropriate fusion units during generation. Rather than committing to a fixed granularity, AdaFuse adjusts fusion behavior on the fly based on the decoding context, with words serving as basic building blocks for alignment. To be specific, we introduce an uncertainty-based criterion to decide whether to apply ensembling at each decoding step. Under confident decoding states, the model continues generation directly. In less certain states, AdaFuse invokes a diversity-aware scaling strategy to explore alternative candidate continuations and inform ensemble decisions. This design establishes a synergistic interaction between adaptive ensembling and test-time scaling, where ensemble decisions guide targeted exploration, and the resulting diversity in turn strengthens ensemble quality. Experiments on open-domain question answering, arithmetic reasoning, and machine translation demonstrate that AdaFuse consistently outperforms strong ensemble baselines, achieving an average relative improvement of 6.88%. The code is available at https://github.com/CCM0111/AdaFuse.

Xiao Lin, Zhicheng Tang, Weilin Cong et al.

Sequential recommendation has rapidly advanced in click-through rate prediction due to its ability to model dynamic user interests. A key challenge, however, lies in modeling long sequences: users often exhibit significant interest shifts, introducing substantial irrelevant or misleading information. Our empirical analysis corroborates this challenge and uncovers a recurring behavioral pattern in long sequences (\textit{session hopping}): user interests remain stable within short temporal spans (\textit{sessions}) but shift drastically across sessions and may reappear after multiple sessions. To address this challenge, we propose the Mixture of Sequence (MoS) framework, a model-agnostic MoE approach that achieves accurate predictions by extracting theme-specific and multi-scale subsequences from noisy raw user sequences. First, MoS employs a theme-aware routing mechanism to adaptively learn the latent themes of user sequences and organizes these sequences into multiple coherent subsequences. Each subsequence contains only sessions aligned with a specific theme, thereby effectively filtering out irrelevant or even misleading information introduced by user interest shifts in session hopping. In addition, to alleviate potential information loss, we introduce a multi-scale fusion mechanism, which leverages three types of experts to capture global sequence characteristics, short-term user behaviors, and theme-specific semantic patterns. Together, these two mechanisms endow MoS with the ability to deliver accurate recommendations from multi-faceted and multi-scale perspectives. Experimental results demonstrate that MoS consistently achieves the SOTA performance while introducing fewer FLOPs compared with other MoE counterparts, providing strong evidence of its excellent balance between utility and efficiency. The code is available at https://github.com/xiaolin-cs/MoS.

Wujiang Xu, Xuying Ning, Wenfang Lin et al.

Cross-domain sequential recommendation (CDSR) aims to address the data sparsity problems that exist in traditional sequential recommendation (SR) systems. The existing approaches aim to design a specific cross-domain unit that can transfer and propagate information across multiple domains by relying on overlapping users with abundant behaviors. However, in real-world recommender systems, CDSR scenarios usually consist of a majority of long-tailed users with sparse behaviors and cold-start users who only exist in one domain. This leads to a drop in the performance of existing CDSR methods in the real-world industry platform. Therefore, improving the consistency and effectiveness of models in open-world CDSR scenarios is crucial for constructing CDSR models (\textit{1st} CH). Recently, some SR approaches have utilized auxiliary behaviors to complement the information for long-tailed users. However, these multi-behavior SR methods cannot deliver promising performance in CDSR, as they overlook the semantic gap between target and auxiliary behaviors, as well as user interest deviation across domains (\textit{2nd} CH).

Rui Cai, Xuying Ning, Peter N. Belhumeur

In the post-pandemic era, wearing face masks has posed great challenge to the ordinary face recognition. In the previous study, researchers has applied pretrained VGG16, and ResNet50 to extract features on the elaborate curated existing masked face recognition (MFR) datasets, RMFRD and SMFRD. To make the model more adaptable to the real world situation where the sample size is smaller and the camera environment has greater changes, we created a more challenging masked face dataset ourselves, by selecting 50 identities with 1702 images from Labelled Faces in the Wild (LFW) Dataset, and simulated face masks through key point detection. The another part of our study is to solve the masked face recognition problem, and we chose models by referring to the former state of the art results, instead of directly using pretrained models, we fine tuned the model on our new dataset and use the last linear layer to do the classification directly. Furthermore, we proposed using data augmentation strategy to further increase the test accuracy, and fine tuned a new networks beyond the former study, one of the most SOTA networks, Inception ResNet v1. The best test accuracy on 50 identity MFR has achieved 95%.

Zhichen Zeng, Wenxuan Bao, Xiao Lin et al.

Vision-language models (VLMs), despite their extraordinary zero-shot capabilities, are vulnerable to distribution shifts. Test-time adaptation (TTA) emerges as a predominant strategy to adapt VLMs to unlabeled test data on the fly. However, existing TTA methods heavily rely on zero-shot predictions as pseudo-labels for self-training, which can be unreliable under distribution shifts and misguide adaptation due to two fundamental limitations. First (Modality Gap), distribution shifts induce gaps between visual and textual modalities, making cross-modal relations inaccurate. Second (Visual Nuisance), visual embeddings encode rich but task-irrelevant noise that often overwhelms task-specific semantics under distribution shifts. To address these limitations, we propose SubTTA, which aligns the semantic subspaces of both modalities to enhance zero-shot predictions to better guide the TTA process. To bridge the modality gap, SubTTA extracts the principal subspaces of both modalities and aligns the visual manifold to the textual semantic anchor by minimizing their chordal distance. To eliminate visual nuisance, SubTTA projects the aligned visual features onto the task-specific textual subspace, which filters out task-irrelevant noise by constraining visual embeddings within the valid semantic span, and standard TTA is further performed on the purified space to refine the decision boundaries. Extensive experiments on various benchmarks and VLM architectures demonstrate the effectiveness of SubTTA, yielding an average improvement of 2.24% over state-of-the-art TTA methods.

Xuying Ning, Katherine Tieu, Dongqi Fu et al.

Recent large language models (LLMs) have demonstrated strong capabilities in understanding and generating code, from competitive programming to repository-level software engineering. In emerging agentic systems, code is no longer only a target output. It increasingly serves as an operational substrate for agent reasoning, acting, environment modeling, and execution-based verification. We frame this shift through the lens of agent harnesses and introduce code as agent harness: a unified view that centers code as the basis for agent infrastructure. To systematically study this perspective, we organize the survey around three connected layers. First, we study the harness interface, where code connects agents to reasoning, action, and environment modeling. Second, we examine harness mechanisms: planning, memory, and tool use for long-horizon execution, together with feedback-driven control and optimization that make harness reliable and adaptive. Third, we discuss scaling the harness from single-agent systems to multi-agent settings, where shared code artifacts support multi-agent coordination, review, and verification. Across these layers, we summarize representative methods and practical applications of code as agent harness, spanning coding assistants, GUI/OS automation, embodied agents, scientific discovery, personalization and recommendation, DevOps, and enterprise workflows. We further outline open challenges for harness engineering, including evaluation beyond final task success, verification under incomplete feedback, regression-free harness improvement, consistent shared state across multiple agents, human oversight for safety-critical actions, and extensions to multimodal environments. By centering code as the harness of agentic AI, this survey provides a unified roadmap toward executable, verifiable, and stateful AI agent systems.

Yuanchen Bei, Tianxin Wei, Xuying Ning et al.

Long-term memory is a critical capability for multimodal large language model (MLLM) agents, particularly in conversational settings where information accumulates and evolves over time. However, existing benchmarks either evaluate multi-session memory in text-only conversations or assess multimodal understanding within localized contexts, failing to evaluate how multimodal memory is preserved, organized, and evolved across long-term conversational trajectories. Thus, we introduce Mem-Gallery, a new benchmark for evaluating multimodal long-term conversational memory in MLLM agents. Mem-Gallery features high-quality multi-session conversations grounded in both visual and textual information, with long interaction horizons and rich multimodal dependencies. Building on this dataset, we propose a systematic evaluation framework that assesses key memory capabilities along three functional dimensions: memory extraction and test-time adaptation, memory reasoning, and memory knowledge management. Extensive benchmarking across thirteen memory systems reveals several key findings, highlighting the necessity of explicit multimodal information retention and memory organization, the persistent limitations in memory reasoning and knowledge management, as well as the efficiency bottleneck of current models.

Xiao Lin, Philip Li, Zhichen Zeng et al.

Despite rich safety alignment strategies, large language models (LLMs) remain highly susceptible to jailbreak attacks, which compromise safety guardrails and pose serious security risks. Existing detection methods mainly detect jailbreak status relying on jailbreak templates present in the training data. However, few studies address the more realistic and challenging zero-shot jailbreak detection setting, where no jailbreak templates are available during training. This setting better reflects real-world scenarios where new attacks continually emerge and evolve. To address this challenge, we propose a layer-wise, module-wise, and token-wise amplification framework that progressively magnifies internal feature discrepancies between benign and jailbreak prompts. We uncover safety-relevant layers, identify specific modules that inherently encode zero-shot discriminative signals, and localize informative safety tokens. Building upon these insights, we introduce ALERT (Amplification-based Jailbreak Detector), an efficient and effective zero-shot jailbreak detector that introduces two independent yet complementary classifiers on amplified representations. Extensive experiments on three safety benchmarks demonstrate that ALERT achieves consistently strong zero-shot detection performance. Specifically, (i) across all datasets and attack strategies, ALERT reliably ranks among the top two methods, and (ii) it outperforms the second-best baseline by at least 10% in average Accuracy and F1-score, and sometimes by up to 40%.

Tianxin Wei, Xuying Ning, Xuxing Chen et al.

In web environments, user preferences are often refined progressively as users move from browsing broad categories to exploring specific items. However, existing generative recommenders overlook this natural refinement process. Generative recommendation formulates next-item prediction as autoregressive generation over tokenized user histories, where each item is represented as a sequence of discrete tokens. Prior models typically fuse heterogeneous attributes such as ID, category, title, and description into a single embedding before quantization, which flattens the inherent semantic hierarchy of items and fails to capture the gradual evolution of user intent during web interactions. To address this limitation, we propose CoFiRec, a novel generative recommendation framework that explicitly incorporates the Coarse-to-Fine nature of item semantics into the tokenization process. Instead of compressing all attributes into a single latent space, CoFiRec decomposes item information into multiple semantic levels, ranging from high-level categories to detailed descriptions and collaborative filtering signals. Based on this design, we introduce the CoFiRec Tokenizer, which tokenizes each level independently while preserving structural order. During autoregressive decoding, the language model is instructed to generate item tokens from coarse to fine, progressively modeling user intent from general interests to specific item-level interests. Experiments across multiple public benchmarks and backbones demonstrate that CoFiRec outperforms existing methods, offering a new perspective for generative recommendation. Theoretically, we prove that structured tokenization leads to lower dissimilarity between generated and ground truth items, supporting its effectiveness in generative recommendation. Our code is available at https://github.com/YennNing/CoFiRec.

Zihao Li, Zhichen Zeng, Xiao Lin et al.

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

Zihao Li, Jiaru Zou, Feihao Fang et al.

Agentic large language model systems have demonstrated strong capabilities. However, their reliance on language as the universal interface fundamentally limits their applicability to many real-world problems, especially in scientific domains where domain-specific foundation models have been developed to address specialized tasks beyond natural language. In this work, we introduce Eywa, a heterogeneous agentic framework designed to extend language-centric systems to a broader class of scientific foundation models. The key idea of Eywa is to augment domain-specific foundation models with a language-model-based reasoning interface, enabling language models to guide inference over non-linguistic data modalities. This design allows predictive foundation models, which are typically optimized for specialized data and tasks, to participate in higher-level reasoning and decision-making processes within agentic systems. Eywa can serve as a drop-in replacement for a single-agent pipeline (EywaAgent) or be integrated into existing multi-agent systems by replacing traditional agents with specialized agents (EywaMAS). We further investigate a planning-based orchestration framework in which a planner dynamically coordinates traditional agents and Eywa agents to solve complex tasks across heterogeneous data modalities (EywaOrchestra). We evaluate Eywa across a diverse set of scientific domains spanning physical, life, and social sciences. Experimental results demonstrate that Eywa improves performance on tasks involving structured and domain-specific data, while reducing reliance on language-based reasoning through effective collaboration with specialized foundation models.

Junyu Zhang, Runpei Dong, Han Wang et al.

This paper presents AlphaOne ($α$1), a universal framework for modulating reasoning progress in large reasoning models (LRMs) at test time. $α$1 first introduces $α$ moment, which represents the scaled thinking phase with a universal parameter $α$. Within this scaled pre-$α$ moment phase, it dynamically schedules slow thinking transitions by modeling the insertion of reasoning transition tokens as a Bernoulli stochastic process. After the $α$ moment, $α$1 deterministically terminates slow thinking with the end-of-thinking token, thereby fostering fast reasoning and efficient answer generation. This approach unifies and generalizes existing monotonic scaling methods by enabling flexible and dense slow-to-fast reasoning modulation. Extensive empirical studies on various challenging benchmarks across mathematical, coding, and scientific domains demonstrate $α$1's superior reasoning capability and efficiency. Project page: https://alphaone-project.github.io/

Xuying Ning, Dongqi Fu, Tianxin Wei et al.

Real-world multimodal data usually exhibit complex structural relationships beyond traditional one-to-one mappings like image-caption pairs. Entities across modalities interact in intricate ways, with images and text forming diverse interconnections through contextual dependencies and co-references. Graphs provide powerful structural information for modeling intra-modal and inter-modal relationships. However, previous works fail to distinguish multi-hop neighbors and treat the graph as a standalone modality, which fragments the overall understanding. This limitation presents two key challenges in multimodal learning: (1) integrating structural information from multi-hop neighbors into foundational models, and (2) fusing modality-specific information in a principled manner. To address these challenges, we revisit the role of graphs in multimodal learning within the era of foundation models and propose Graph4MM, a graph-based multimodal learning framework. To be specific, we introduce Hop-Diffused Attention, which integrates multi-hop structural information into self-attention through causal masking and hop diffusion. Furthermore, we design MM-QFormer, a multi-mapping querying transformer for cross-modal fusion. Through theoretical and empirical analysis, we show that leveraging structures to integrate both intra- and inter-modal interactions improves multimodal understanding beyond treating them as a standalone modality. Experiments on both generative and discriminative tasks show that Graph4MM outperforms larger VLMs, LLMs, and multimodal graph baselines, achieving a 6.93% average improvement.

Wujiang Xu, Yunxiao Shi, Zujie Liang et al.

Traditional recommender systems usually take the user-platform paradigm, where users are directly exposed under the control of the platform's recommendation algorithms. However, the defect of recommendation algorithms may put users in very vulnerable positions under this paradigm. First, many sophisticated models are often designed with commercial objectives in mind, focusing on the platform's benefits, which may hinder their ability to protect and capture users' true interests. Second, these models are typically optimized using data from all users, which may overlook individual user's preferences. Due to these shortcomings, users may experience several disadvantages under the traditional user-platform direct exposure paradigm, such as lack of control over the recommender system, potential manipulation by the platform, echo chamber effects, or lack of personalization for less active users due to the dominance of active users during collaborative learning. Therefore, there is an urgent need to develop a new paradigm to protect user interests and alleviate these issues. Recently, some researchers have introduced LLM agents to simulate user behaviors, these approaches primarily aim to optimize platform-side performance, leaving core issues in recommender systems unresolved. To address these limitations, we propose a new user-agent-platform paradigm, where agent serves as the protective shield between user and recommender system that enables indirect exposure.

Tianxin Wei, Noveen Sachdeva, Benjamin Coleman et al.

Statefulness is essential for large language model (LLM) agents to perform long-term planning and problem-solving. This makes memory a critical component, yet its management and evolution remain largely underexplored. Existing evaluations mostly focus on static conversational settings, where memory is passively retrieved from dialogue to answer queries, overlooking the dynamic ability to accumulate and reuse experience across evolving task streams. In real-world environments such as interactive problem assistants or embodied agents, LLMs are required to handle continuous task streams, yet often fail to learn from accumulated interactions, losing valuable contextual insights, a limitation that calls for test-time evolution, where LLMs retrieve, integrate, and update memory continuously during deployment. To bridge this gap, we introduce Evo-Memory, a comprehensive streaming benchmark and framework for evaluating self-evolving memory in LLM agents. Evo-Memory structures datasets into sequential task streams, requiring LLMs to search, adapt, and evolve memory after each interaction. We unify and implement over ten representative memory modules and evaluate them across 10 diverse multi-turn goal-oriented and single-turn reasoning and QA datasets. To better benchmark experience reuse, we provide a baseline method, ExpRAG, for retrieving and utilizing prior experience, and further propose ReMem, an action-think-memory refine pipeline that tightly integrates reasoning, task actions, and memory updates to achieve continual improvement.

Zhichen Zeng, Qi Yu, Xiao Lin et al.

Different large language models (LLMs) exhibit diverse strengths and weaknesses, and LLM ensemble serves as a promising approach to integrate their complementary capabilities. Despite substantial progress in improving ensemble quality, limited attention has been paid to the robustness of ensembles against potential erroneous signals, which often arise from heterogeneous tokenization schemes and varying model expertise. Our analysis shows that ensemble failures typically arise from both the token level and the model level: the former reflects severe disagreement in token predictions, while the latter involves low confidence and pronounced disparities among models. In light of this, we propose CoRE, a plug-and-play technique that harnesses model consistency for robust LLM ensemble, which can be seamlessly integrated with diverse ensemble methods. Token-level consistency captures fine-grained disagreements by applying a low-pass filter to downweight uncertain tokens with high inconsistency, often due to token misalignment, thereby improving robustness at a granular level. Model-level consistency models global agreement by promoting model outputs with high self-confidence and minimal divergence from others, enhancing robustness at a coarser level. Extensive experiments across diverse benchmarks, model combinations, and ensemble strategies demonstrate that CoRE consistently improves ensemble performance and robustness.