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.

Vision-language models (VLMs) have demonstrated remarkable zero-shot capabilities yet remain sensitive to real-world distribution shifts during inference. Although significant efforts are devoted to adapting VLMs at test time, they rely heavily on noisy pseudo-labels predicted directly from raw embedding similarities during inference, which are unreliable under distribution shift and mislead the adaptation. To avoid noise amplification, existing works craft coarse-grained surrogate objectives during adaptation, which fail to explicitly model sample-level relationships across different modalities, creating objective mismatch with inference, thus leading to marginal performance improvement. In this work, we aim to bridge the detached objectives of inference and adaptation for VLMs, and propose a principled VLM TTA method called . For VLM inference, we formulate the zero-shot image classification task as a cross-modal alignment problem encoded via a Wasserstein OT formulation, providing robust pseudo-labels at the sample-level to effectively adapt VLMs. For VLM adaptation, we adopt a soft-label InfoNCE loss to adapt VLMs based on the OT-induced pseudo-labels, leveraging fine-grained supervisions to explicitly model relationships of individual image-text pairs via contrastive learning, which empowers accurate inference at the same granularity. Moreover, we theoretically reveal that the InfoNCE loss can be neatly reformulated as a Wasserstein OT formulation, thereby unifying the objectives of the inference and adaptation of VLMs to achieve their mutual benefits. Extensive experiments demonstrate the effectiveness and efficiency of our methods, outperforming the best-performing methods by up to 7

Alignment plays a fundamental role in many machine learning problems, such as multi-network analysis, multimodal learning, and point cloud registration. Recent works increasingly leverage optimal transport (OT) for distributional alignment, whose effectiveness largely depends on sparse supervision that is hard or costly to obtain in practice. Existing works, however, largely overlook how to actively acquire high-quality supervision to improve their alignment performance under OT frameworks. In this paper, we propose a principled active alignment framework for optimal transport alignment called AvAtar. We quantify the informativeness of a candidate by measuring its gradient-based impact on the global alignment result, computed as the gradient propagation from the global alignment result to all possible supervisions of the candidate through the entropy-regularized OT formulation. While differentiating through OT is challenging given its constrained nature, we leverage the adjoint-state method to reformulate the computation to a linear system solvable by the conjugate gradient method with linear complexity and guaranteed convergence. By encoding the global alignment result via effective utility functions, AvAtar is applicable to general alignment problems under the OT framework. Extensive experiments on three representative alignment tasks demonstrate the effectiveness, scalability, and generalizability of the proposed AvAtar.

Network alignment (NA) aims to identify node correspondence across different networks and serves as a critical cornerstone behind various downstream multi-network learning tasks. Despite growing research in NA, there lacks a comprehensive library that facilitates the systematic development and benchmarking of NA methods. In this work, we introduce PLANETALIGN, a comprehensive Python library for network alignment that features a rich collection of built-in datasets, methods, and evaluation pipelines with easy-to-use APIs. Specifically, PLANETALIGN integrates 18 datasets and 14 NA methods with extensible APIs for easy use and development of NA methods. Our standardized evaluation pipeline encompasses a wide range of metrics, enabling a systematic assessment of the effectiveness, scalability, and robustness of NA methods. Through extensive comparative studies, we reveal practical insights into the strengths and limitations of existing NA methods. We hope that PLANETALIGN can foster a deeper understanding of the NA problem and facilitate the development and benchmarking of more effective, scalable, and robust methods in the future. The The source code of PLANETALIGN is available at https://anonymous.4open.science/r/PlanetAlign-E9BA

Time series data are integral to critical applications across domains such as finance, healthcare, transportation, and environmental science. While recent work has begun to explore multi-task time series question answering (QA), current benchmarks remain limited to forecasting and anomaly detection tasks. We introduce TSAQA, a novel unified benchmark designed to broaden task coverage and evaluate diverse temporal analysis capabilities. TSAQA integrates six diverse tasks under a single framework ranging from conventional analysis, including anomaly detection and classification, to advanced analysis, such as characterization, comparison, data transformation, and temporal relationship analysis. Spanning 210k samples across 13 domains, the dataset employs diverse formats, including true-or-false (TF), multiple-choice (MC), and a novel puzzling (PZ), to comprehensively assess time series analysis. Zero-shot evaluation demonstrates that these tasks are challenging for current Large Language Models (LLMs): the best-performing commercial LLM, Gemini-2.5-Flash, achieves an average score of only 65.08. Although instruction tuning boosts open-source performance: the best-performing open-source model, LLaMA-3.1-8B, shows significant room for improvement, highlighting the complexity of temporal analysis for LLMs.

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.

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

Graph neural networks, despite their impressive performance, are highly vulnerable to distribution shifts on graphs. Existing graph domain adaptation (graph DA) methods often implicitly assume a mild shift between source and target graphs, limiting their applicability to real-world scenarios with large shifts. Gradual domain adaptation (GDA) has emerged as a promising approach for addressing large shifts by gradually adapting the source model to the target domain via a path of unlabeled intermediate domains. Existing GDA methods exclusively focus on independent and identically distributed (IID) data with a predefined path, leaving their extension to non-IID graphs without a given path an open challenge. To bridge this gap, we present Gadget, the first GDA framework for non-IID graph data. First (theoretical foundation), the Fused Gromov-Wasserstein (FGW) distance is adopted as the domain discrepancy for non-IID graphs, based on which, we derive an error bound on node, edge and graph-level tasks, showing that the target domain error is proportional to the length of the path. Second (optimal path), guided by the error bound, we identify the FGW geodesic as the optimal path, which can be efficiently generated by our proposed algorithm. The generated path can be seamlessly integrated with existing graph DA methods to handle large shifts on graphs, improving state-of-the-art graph DA methods by up to 6.8

Reasoning is a fundamental cognitive process underlying inference, problem-solving, and decision-making. While large language models (LLMs) demonstrate strong reasoning capabilities in closed-world settings, they struggle in open-ended and dynamic environments. Agentic reasoning marks a paradigm shift by reframing LLMs as autonomous agents that plan, act, and learn through continual interaction. In this survey, we organize agentic reasoning along three complementary dimensions. First, we characterize environmental dynamics through three layers: foundational agentic reasoning, which establishes core single-agent capabilities including planning, tool use, and search in stable environments; self-evolving agentic reasoning, which studies how agents refine these capabilities through feedback, memory, and adaptation; and collective multi-agent reasoning, which extends intelligence to collaborative settings involving coordination, knowledge sharing, and shared goals. Across these layers, we distinguish in-context reasoning, which scales test-time interaction through structured orchestration, from post-training reasoning, which optimizes behaviors via reinforcement learning and supervised fine-tuning. We further review representative agentic reasoning frameworks across real-world applications and benchmarks, including science, robotics, healthcare, autonomous research, and mathematics. This survey synthesizes agentic reasoning methods into a unified roadmap bridging thought and action, and outlines open challenges and future directions, including personalization, long-horizon interaction, world modeling, scalable multi-agent training, and governance for real-world deployment.

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 QA, arithmetic reasoning, and machine translation demonstrate that AdaFuse consistently outperforms strong ensemble baselines, achieving an average relative improvement of 6.88%.

Low-rank adapters (LoRAs) are a parameter-efficient finetuning technique that injects trainable low-rank matrices into pretrained models to adapt them to new tasks. Mixture-of-LoRAs models expand neural networks efficiently by routing each layer input to a small subset of specialized LoRAs of the layer. Existing Mixture-of-LoRAs routers assign a learned routing weight to each LoRA to enable end-to-end training of the router. Despite their empirical promise, we observe that the routing weights are typically extremely imbalanced across LoRAs in practice, where only one or two LoRAs often dominate the routing weights. This essentially limits the number of effective LoRAs and thus severely hinders the expressive power of existing Mixture-of-LoRAs models. In this work, we attribute this weakness to the nature of learnable routing weights and rethink the fundamental design of the router. To address this critical issue, we propose a new router designed that we call Reinforcement Routing for Mixture-of-LoRAs (ReMix). Our key idea is using non-learnable routing weights to ensure all active LoRAs to be equally effective, with no LoRA dominating the routing weights. However, our routers cannot be trained directly via gradient descent due to our non-learnable routing weights. Hence, we further propose an unbiased gradient estimator for the router by employing the reinforce leave-one-out (RLOO) technique, where we regard the supervision loss as the reward and the router as the policy in reinforcement learning. Our gradient estimator also enables to scale up training compute to boost the predictive performance of our ReMix. Extensive experiments demonstrate that our proposed ReMix significantly outperform state-of-the-art parameter-efficient finetuning methods under a comparable number of activated parameters.

We present Speculative Rollout with Tree-Structured Cache (SRT), a simple, model-free approach to accelerate on-policy reinforcement learning (RL) for language models without sacrificing distributional correctness. SRT exploits the empirical similarity of rollouts for the same prompt across training steps by storing previously generated continuations in a per-prompt tree-structured cache. During generation, the current policy uses this tree as the draft model for performing speculative decoding. To keep the cache fresh and improve draft model quality, SRT updates trees online from ongoing rollouts and proactively performs run-ahead generation during idle GPU bubbles. Integrated into standard RL pipelines (e.g., PPO, GRPO and DAPO) and multi-turn settings, SRT consistently reduces generation and step latency and lowers per-token inference cost, achieving up to 2.08x wall-clock time speedup during rollout.

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

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

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 (session hopping): user interests remain stable within short temporal spans (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.

Specializing Large Language Models (LLMs) toward distinct abilities underpins successes ranging from personalized assistants to multi-agent systems (MAS). Single-agent paradigms rely on pre-defined personas or steering vectors to induce specialization, yet they impose a single fixed specialization that fails to adapt to diverse queries. Conversely, MAS achieves dynamic multi-perspective problem solving by orchestrating agents with distinct text-based roles, but fusing these specializations requires multi-turn interactions that inflate context length and inference cost. To address these limitations, we propose Mixture of Roles (MoRe), which adaptively composes multiple specializations into a single steering vector for single-turn inference. Specifically, MoRe learns a diversified codeboox of steering vectors, each of which encodes a latent role. A query-aware router dynamically fuses the codebook into a steering vector that encompasses multiple roles. By steering the backbone LLM with the composed vector, MoRe enables multi-perspective specialization in a single-agent, single-turn inference process. The proposed MoRe can be efficiently trained via a three-stage SFT curriculum and GRPO post-training, while the backbone LLM remains frozen. Experiments across reasoning and personality benchmarks show that MoRe outperforms single-agent baselines by 2.2

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, catalysis discovery, 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.

Fixed-point general matrix multiplication (GEMM) is pivotal in AI-accelerated computing for data centers and edge devices in GPU and NPU tensor processing engines (TPEs). This work exposes two critical limitations in typical spatial mixed-precision TPEs:. Redundant partial products (PPs) reduction in PE multipliers across temporal and spatial domains in MAC arrays.. Compute density imbalance: when the operand bit-width is reduced by one-half, the throughput of GEMM only doubles, which is half of the theoretical 4x improvement. To address these challenges. First, we design a multi-operand high-radix encoder based on vector inner products, which reduces PPs for vector reduction by half through decoding. Second, we establish a three-stage computational paradigm for TPE's microarchitecture, comprising bit-slice encoding, PPs generation, and PPs reduction, which enables bit-width reconfiguration in unified hardware. Our approach decomposes the mixed-precision mapping process in TPEs into two components: temporal mapping of multi-precision multiplicands and spatial mapping of multipliers,

Graph Self-Supervised Learning (SSL) has emerged as a pivotal area of research in recent years. By engaging in pretext tasks to learn the intricate topological structures and properties of graphs using unlabeled data, these graph SSL models achieve enhanced performance, improved generalization, and heightened robustness. Despite the remarkable achievements of these graph SSL methods, their current implementation poses significant challenges for beginners and practitioners due to the complex nature of graph structures, inconsistent evaluation metrics, and concerns regarding reproducibility hinder further progress in this field. Recognizing the growing interest within the research community, there is an urgent need for a comprehensive, beginner-friendly, and accessible toolkit consisting of the most representative graph SSL algorithms. To address these challenges, we present a Graph SSL toolkit named PyG-SSL, which is built upon PyTorch and is compatible with various deep learning and scientific computing backends. Within the toolkit, we offer a unified framework encompassing dataset loading, hyper-parameter configuration, model training, and comprehensive performance evaluation for diverse downstream tasks. Moreover, we provide beginner-friendly tutorials and the best hyper-parameters of each graph SSL algorithm on different graph datasets, facilitating the reproduction of results. The GitHub repository of the library is https://github.com/iDEA-iSAIL-Lab-UIUC/pyg-ssl.

Click-through rate (CTR) prediction, which predicts the probability of a user clicking an ad, is a fundamental task in recommender systems. The emergence of heterogeneous information, such as user profile and behavior sequences, depicts user interests from different aspects. A mutually beneficial integration of heterogeneous information is the cornerstone towards the success of CTR prediction. However, most of the existing methods suffer from two fundamental limitations, including (1) insufficient inter-mode interaction due to the unidirectional information flow between modes, and (2) aggressive information aggregation caused by early summarization, resulting in excessive information loss. To address the above limitations, we propose a novel module named InterFormer to learn heterogeneous information interaction in an interleaving style. To achieve better interaction learning, InterFormer enables bidirectional information flow for mutually beneficial learning across different modes. To avoid aggressive information aggregation, we retain complete information in each data mode and use a separate bridging arch for effective information selection and summarization. Our proposed InterFormer achieves state-of-the-art performance on three public datasets and a large-scale industrial dataset.