arXiv subjects

Zijun Yao

Publications and source records attributed to Zijun Yao.

At least 19 recordsLinked to original sources

arXiv2026

City Editing: Hierarchical Agentic Execution for Dependency-Aware Urban Geospatial Modification

Urban renewal requires incremental modifications to existing geospatial plans, yet manually updating complex layouts under spatial constraints is labor-intensive and error-prone. To tackle this, we propose CEAE, a hierarchical agentic framework that formulates urban renewal as machine-executable GeoJSON editing from natural-language instructions. CEAE decomposes instructions into hierarchical geometric intents, executing edits from coarse to fine while preserving spatial consistency through a self-reflective execution-validation loop. Experimental results show that CEAE outperforms baselines in execution validity, robustness, and geometric accuracy.

cs.MA↗

arXiv2026

REFINE: LLM Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation

Learning rich medical concept representations is essential for EHR prediction. Text-attributed knowledge graphs (TKGs) provide a natural foundation by organizing heterogeneous medical relations together with textual semantics. However, most existing encoders process concepts uniformly across patients, despite the fact that a code's meaning and predictive value depend on patient-specific clinical context and trajectory. Learning patient-personalized concept representations from TKGs introduces two key challenges: (1) deciding how much KG context to incorporate for each observed code, and (2) aligning semantic information with the patient-specific relational structure. We propose REFINE, a KG-aware budgeted LLM graph refinement framework for patient-personalized medical concept encoding. Starting from a global TKG, REFINE constructs patient-specific temporal graphs. A sequential reinforcement learning policy selects a personalized KG expansion budget for each observed code. The resulting patient graph is processed by a heterogeneous GNN to capture relation-aware structural dependencies, while a frozen LLM uses graph-aware soft prompts to semantically refine concept representations. Experiments on MIMIC-III and MIMIC-IV show that REFINE consistently improves diverse EHR backbones, outperforms strong baselines, and demonstrates robust gains across component ablation, KG selection, and data insufficiency.

cs.LG↗

arXiv2026

From Base Rollouts to RL Reasoning: A Budgeted Search Perspective

Reinforcement learning with verifiable rewards (RLVR) improves language-model reasoning, but how these gains relate to inference-time decoding and search remains unclear. Does RL create reasoning the base model lacks, or shift the rollout distribution toward trajectories it can already reach but rarely samples? We study this behaviorally with a Unified Decoding Framework (UDF), which expresses token-level sampling, beam-like search, tree search, and sequence-level resampling as executable policies over a shared budgeted operating space, scored post hoc with pass@$k$, self-consistency, best-of-$N$, and first-finish success. Using paired Base/RL checkpoints from SimpleRL-Zoo, we ask whether an RL default-policy curve can be approximated by a structured path of Base operating points. On Math500, AIME, GPQA, and IFEval, the pass@$k$ recovery path follows a Budgeted Operating-Point Transition Rule (BOPTR), $N_{\mathrm{Base}} \approx αN_{\mathrm{RL}}^β$, with benchmark-conditioned exponents. On Qwen2.5-7B, BOPTR gives the lowest transfer error among the non-oracle rules we test, 3.41 pp (95% CI [2.32, 5.53]); a three-seed replication gives 3.07 $\pm$ 0.39 pp. The rule extends to ten models across four families (3.28 to 4.87 pp on checkpoints added after fitting), to four benchmarks it was never fitted on (5.03 pp vs. 4.44 pp in fit), and holds without an RL checkpoint for the target model (4.19 pp) or without RL supervision of any kind (5.08 pp). These results support a qualified internalized-search reading: under the recipe we test, much of the measured RL gain corresponds to a change in sampling efficiency toward operating points the base model can already reach under search. We treat the scaling patterns as descriptive of this recipe and cohort, report where they break down, and use UDF and BOPTR as behavioral diagnostics rather than evidence of parameter-level equivalence.

cs.CL↗

arXiv2026

Import What You Need: Learning When and How to Augment EHR Graphs with External Knowledge

Longitudinal prediction from electronic health records (EHRs) is limited by the sparsity and irregularity in patient trajectories, and knowledge augmentation with external knowledge graphs (KGs) offers a promising way to alleviate these issues. However, most existing methods perform fixed, context-agnostic topology augmentation by adding the same KG nodes and edges regardless of a patient's evolving state. We propose ReTA, a Reinforcement learning-based dynamic Topology Augmentation framework that casts KG import as a per-visit, budget-aware policy. ReTA first constructs an offline refined pool of KG-grounded templates, then learns a policy to select one augment action per visit from three options: Soft Import, which enriches node features without modifying graph topology, Hard Import, which grafts a compact KG subgraph onto the visit graph to create message-passing shortcuts, and Skip, which leaves the visit unaugmented when the base encoder is already confident. To stabilize learning, ReTA employs a decoupled encoder that processes semantic and structural signals in separate channels and fuses them via adaptive gating. Experiments on MIMIC-III and MIMIC-IV across diagnosis prediction, mortality, and readmission show that ReTA consistently outperforms strong baselines while remaining efficient, transfers across datasets and knowledge graphs, and yields interpretable augmentation patterns. The robust gains under sparse supervision highlight the advantage of ReTA's dynamic decision to import knowledge, boosting accuracy while curbing costs.

cs.LG↗

arXiv2026

Where Steering Signals Come From: Activation Source Selection in Activation Steering

Activation steering controls language models by adding vectors or features to hidden states at inference time, but the upstream source of these steering signals is often treated as a secondary detail. We study this source choice as activation source selection: the combination of source context and activation readout policy used to collect the hidden states from which a steering signal is built. Holding the downstream intervention fixed, we show across three instruction-tuned models and four steering task families that changing only the source activations substantially changes steering success. We further find that effective steering is not explained simply by whether the desired behavior appears in the source text. Instead, strong signals come from execution-boundary states, where the model is about to produce or continue the target behavior. This pre-/post-realization distinction explains why answer-based sources sometimes work: their useful component aligns with execution-boundary directions rather than target appearance alone. Building on this view, we introduce tail subtraction, which removes shared prompt and continuation semantics from boundary states and yields cleaner, more stable steering signals. Overall, our results suggest that steering depends on representations of what the model is about to do, not merely on what has already appeared.

cs.CL↗

arXiv2026

SAEVerbalizer: Generating Explanations for Sparse Autoencoder Features via Representation Verbalization

Sparse autoencoders (SAEs) are proposed to extract numerous features from large language model (LLM) representations, yet explaining these features still relies primarily on external observation. This reliance leads to superficial explanations inferred from observed model behavior and computational inefficiency from collecting such behavioral evidence at scale. We introduce SAEVerbalizer, a framework that injects SAE decoder directions into an LLM's representations and fine-tunes the LLM's downstream layers to generate natural-language explanations of the injected features. Once trained, the resulting verbalizer explains SAE features directly from decoder directions, addressing both limitations. Our experiments show that the learned verbalization capability generalizes to unseen features, transfers across separately trained SAE dictionaries, and, with a lightweight adapter, extends to SAE features from different LLMs. Intervention experiments show that injecting multiple directions yields an explanation combining their meanings, while reversing individual directions produces corresponding meaning shifts.

cs.CL↗

arXiv2026

EurekAgent: Agent Environment Engineering is All You Need For Autonomous Scientific Discovery

LLM-based agents have shown increasing potential in automating scientific discovery. Given an optimizable metric and an execution environment, they can propose, validate, and iterate scientific solutions, and have produced results that outperform human-designed approaches. As model capabilities continue to improve, we argue that the bottleneck for autonomous scientific discovery is shifting from prescribing agent workflows to designing agent environments: the resources, constraints, and interfaces that shape agent behavior. We frame this as environment engineering: building environments that amplify productive behaviors, such as open-ended exploration, systematic artifact management, and inter-agent collaboration, while suppressing harmful behaviors, such as reward hacking and high-friction human oversight. We present EurekAgent, an environment-engineered agent system for metric-driven autonomous scientific discovery. EurekAgent engineers the environment along four dimensions: permissions engineering for bounded agent execution and isolated evaluation; artifact engineering for filesystem and Git-based collaboration; budget engineering for budget-aware exploration; and human-in-the-loop engineering for easy human supervision and intervention. EurekAgent sets new state-of-the-art results on multiple mathematics, kernel engineering, and machine learning tasks, including new state-of-the-art 26-circle packing results discovered with less than $11 in total API cost. We open-source our code and results, and call for environment engineering as a core research direction for developing reliable autonomous research agents.

cs.AI↗

arXiv2026

Automatic bioinformatic software named entity recognition from literature

Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale. The lack of a comprehensive and up-to-date catalog of bioinformatics resources hinders efforts toward automated biomedical knowledge extraction and streamlined data analysis. Here we present SNAIL, a hybrid named entity recognition framework designed to automatically identify bioinformatics software and database (SW/DB) names from biomedical texts. SNAIL integrates complementary lexical and semantic modeling strategies. The lexical component captures orthographic patterns and contextual cues characteristic of SW/DB names, while the semantic component leverages contextual embeddings generated by transformer-based language models such as SciBERT, combined with an explicit token-masking strategy to enhance entity-focused representations. A large training corpus was constructed automatically through a hybrid pipeline that integrates citation-hinted extraction with large language model-assisted distillation. Evaluation on two independent benchmark datasets and real-world research articles demonstrates that SNAIL substantially outperforms existing approaches, including domain-specific methods such as bioNerDS2 and general-purpose large language models such as ChatGPT, Gemini, Grok and Claude. Applying SNAIL to large-scale literature analysis further reveals distinct journal-level preferences across bioinformatics subfields. These results demonstrate that SNAIL provides an accurate and scalable solution for identifying bioinformatics resources in scientific texts and enables systematic meta-analysis of tool usage and research trends.

cs.CL↗

arXiv2026

Guiding LLM Post-training Data Engineering with Model Internals from Sparse Autoencoders

Model internals encode rich information about how a large language model (LLM) processes its training data; however, post-training data engineering largely relies on external signals and ignores rich intrinsic signals lying in model internals. We propose SAERL, a data engineering framework for LLM reinforcement learning (RL). It models three intrinsic data properties: diversity, difficulty, and quality, using model internals extracted with Sparse Autoencoder (SAE), an advanced mechanistic interpretability tool. Each property grounds a concrete data engineering operation: SAE-space clustering with moderate batch mixing for batch diversity control, a difficulty proxy for easy-to-hard curriculum ordering, and a quality probe for data filtering. SAERL improves average accuracy by 3.00% over vanilla GRPO and reaches target accuracy with 20% fewer training steps on Qwen2.5-Math-1.5B, with consistent gains across model scales and RL algorithms. Experiments show that SAE transfers effectively across model families and scales, serving as a lightweight and reusable data engineering tool. These results demonstrate that model internals are a powerful and practical source of signals for post-training data engineering.

cs.LG↗

arXiv2026

Iterative Feature Space Optimization through Incremental Adaptive Evaluation

Iterative feature space optimization involves systematically evaluating and adjusting the feature space to improve downstream task performance. However, existing works suffer from three key limitations:1) overlooking differences among data samples leads to evaluation bias; 2) tailoring feature spaces to specific machine learning models results in overfitting and poor generalization; 3) requiring the evaluator to be retrained from scratch during each optimization iteration significantly reduces the overall efficiency of the optimization process. To bridge these gaps, we propose a gEneralized Adaptive feature Space Evaluator (EASE) to efficiently produce optimal and generalized feature spaces. This framework consists of two key components: Feature-Sample Subspace Generator and Contextual Attention Evaluator. The first component aims to decouple the information distribution within the feature space to mitigate evaluation bias. To achieve this, we first identify features most relevant to prediction tasks and samples most challenging for evaluation based on feedback from the subsequent evaluator. This decoupling strategy makes the evaluator consistently target the most challenging aspects of the feature space. The second component intends to incrementally capture evolving patterns of the feature space for efficient evaluation. We propose a weighted-sharing multi-head attention mechanism to encode key characteristics of the feature space into an embedding vector for evaluation. Moreover, the evaluator is updated incrementally, retaining prior evaluation knowledge while incorporating new insights, as consecutive feature spaces during the optimization process share partial information. Extensive experiments on fourteen real-world datasets demonstrate the effectiveness of the proposed framework. Our code and data are publicly available.

cs.LG↗

arXiv2026

Text-Attributed Knowledge Graph Enrichment with Large Language Models for Medical Concept Representation

In electronic health record (EHR) mining, learning high-quality representations of medical concepts (e.g., standardized diagnosis, medication, and procedure codes) is fundamental for downstream clinical prediction. However, ro bust concept representation learning is hindered by two key challenges: (i) clinically important cross-type dependencies (e.g., diagnosis medication and medication-procedure relations) are often missing or incomplete in existing ontology resources, limiting the ability to model complex EHR patterns; and (ii) rich clinical semantics are often missing from structured resources, and even when available as text, are difficult to integrate with KG structure for representation learning. To address these challenges, we present MedCo, an LLM empowered graph learning framework for medical concept representation. MedCo first builds a global knowledge graph (KG) over medical codes by combining statistically reliable associations mined from EHRs with type-constrained LLM prompting to infer semantic relations. It then utilizes LLMs to enrich the KG into a text-attributed graph by generating node descriptions and edge rationales, providing semantic signals for both concepts and their relationships. Finally, MedCo jointly trains a LoRA-tuned LLaMA text encoder with a heterogeneous GNN, fusing text semantics and graph structure into unified concept embeddings. Extensive experiments on MIMIC-III and MIMIC-IV show that MedCo consistently improves prediction performance and serves as an effective plug-in concept encoder for standard EHR pipelines.

cs.LG↗

arXiv2026

Understanding the Mechanism of Altruism in Large Language Models

Altruism is fundamental to human societies, fostering cooperation and social cohesion. Recent studies suggest that large language models (LLMs) can display human-like prosocial behavior, but the internal computations that produce such behavior remain poorly understood. We investigate the mechanisms underlying LLM altruism using sparse autoencoders (SAEs). In a standard Dictator Game, minimal-pair prompts that differ only in social stance (generous versus selfish) induce large, economically meaningful shifts in allocations. Leveraging this contrast, we identify a set of SAE features (0.024% of all features across the model's layers) whose activations are strongly associated with the behavioral shift. To interpret these features, we use benchmark tasks motivated by dual-process theories to classify a subset as primarily heuristic (System 1) or primarily deliberative (System 2). Causal interventions validate their functional role: activation patching and continuous steering of this feature direction reliably shift allocation distributions, with System 2 features exerting a more proximal influence on the model's final output than System 1 features. The same steering direction generalizes across multiple social-preference games. Together, these results enhance our understanding of artificial cognition by translating altruistic behaviors into identifiable network states and provide a framework for aligning LLM behavior with human values, thereby informing more transparent and value-aligned deployment.

econ.GN↗

arXiv2026

RePrompT: Recurrent Prompt Tuning for Integrating Structured EHR Encoders with Large Language Models

Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured EHRs (e.g., standardized diagnosis and medication codes) presents two key challenges. First, translating time-stamped EHR sequences into plain text can obscure both temporal structure and code identities, weakening the ability to capture code co-occurrence and longitudinal regularities. Second, unlike cohort-trained predictive models that learn a shared, task-aligned representation space across patients, LLMs are often applied in a case-isolated inference setting where each patient is processed independently without leveraging population-level patterns. To address these challenges, we introduce RePrompT, a time-aware LLM framework that integrates structured EHR encoders through prompt tuning, without modifying underlying architectures. Specifically, RePrompT recurrently incorporates latent states from prior visits to preserve longitudinal information, and injects population-level information through trainable prompt tokens derived from a cohort-trained, task-aligned EHR encoder. Experiments on MIMIC-III and MIMIC-IV demonstrate that RePrompT consistently outperforms both EHR-based and LLM-based baselines across multiple clinical prediction tasks.

cs.CL↗

arXiv2026

AgentOS: From Application Silos to a Natural Language-Driven Data Ecosystem

The rapid emergence of open-source, locally hosted intelligent agents marks a critical inflection point in human-computer interaction. Systems such as OpenClaw demonstrate that Large Language Model (LLM)-based agents can autonomously operate local computing environments, orchestrate workflows, and integrate external tools. However, within the current paradigm, these agents remain conventional applications running on legacy operating systems originally designed for Graphical User Interfaces (GUIs) or Command Line Interfaces (CLIs). This architectural mismatch leads to fragmented interaction models, poorly structured permission management (often described as "Shadow AI"), and severe context fragmentation. This paper proposes a new paradigm: a Personal Agent Operating System (AgentOS). In AgentOS, traditional GUI desktops are replaced by a Natural User Interface (NUI) centered on a unified natural language or voice portal. The system core becomes an Agent Kernel that interprets user intent, decomposes tasks, and coordinates multiple agents, while traditional applications evolve into modular Skills-as-Modules enabling users to compose software through natural language rules. We argue that realizing AgentOS fundamentally becomes a Knowledge Discovery and Data Mining (KDD) problem. The Agent Kernel must operate as a real-time engine for intent mining and knowledge discovery. Viewed through this lens, the operating system becomes a continuous data mining pipeline involving sequential pattern mining for workflow automation, recommender systems for skill retrieval, and dynamically evolving personal knowledge graphs. These challenges define a new research agenda for the KDD community in building the next generation of intelligent computing systems.

cs.AI↗

arXiv2026

DT-BEHRT: Disease Trajectory-aware Transformer for Interpretable Patient Representation Learning

The growing adoption of electronic health record (EHR) systems has provided unprecedented opportunities for predictive modeling to guide clinical decision making. Structured EHRs contain longitudinal observations of patients across hospital visits, where each visit is represented by a set of medical codes. While sequence-based, graph-based, and graph-enhanced sequence approaches have been developed to capture rich code interactions over time or within the same visits, they often overlook the inherent heterogeneous roles of medical codes arising from distinct clinical characteristics and contexts. To this end, in this study we propose the Disease Trajectory-aware Transformer for EHR (DT-BEHRT), a graph-enhanced sequential architecture that disentangles disease trajectories by explicitly modeling diagnosis-centric interactions within organ systems and capturing asynchronous progression patterns. To further enhance the representation robustness, we design a tailored pre-training methodology that combines trajectory-level code masking with ontology-informed ancestor prediction, promoting semantic alignment across multiple modeling modules. Extensive experiments on multiple benchmark datasets demonstrate that DT-BEHRT achieves strong predictive performance and provides interpretable patient representations that align with clinicians' disease-centered reasoning. The source code is publicly accessible at https://github.com/GatorAIM/DT-BEHRT.git.

cs.LG↗

arXiv2026

StockBench: Can LLM Agents Trade Stocks Profitably In Real-world Markets?

Large language models (LLMs) demonstrate strong potential as autonomous agents, with promising capabilities in reasoning, tool use, and sequential decision-making. While prior benchmarks have evaluated LLM agents in various domains, the financial domain remains underexplored, despite its significant economic value and complex reasoning requirements. Most existing financial benchmarks focus on static question-answering, failing to capture the dynamics of real-market trading. To address this gap, we introduce STOCKBENCH, a contamination-free benchmark designed to evaluate LLM agents in realistic, multi-month stock trading environments. Agents receive daily market signals -- including prices, fundamentals, and news -- and make sequential buy, sell, or hold decisions. Performance is measured using financial metrics such as cumulative return, maximum drawdown, and the Sortino ratio, capturing both profitability and risk management. We evaluate a wide range of state-of-the-art proprietary and open-source LLMs. Surprisingly, most models struggle to outperform the simple buy-and-hold baseline, while some models demonstrate the potential to achieve higher returns and stronger risk management. These findings highlight both the challenges and opportunities of LLM-based trading agents, showing that strong performance on static financial question-answering do not necessarily translate into effective trading behavior. We release STOCKBENCH as an open-source benchmark to enable future research on LLM-driven financial agents.

cs.LG↗

arXiv2026

Continuous Optimization for Feature Selection with Permutation-Invariant Embedding and Policy-Guided Search

Feature selection removes redundant features to enhanc performance and computational efficiency in downstream tasks. Existing works often struggle to capture complex feature interactions and adapt to diverse scenarios. Recent advances in this domain have incorporated generative intelligence to address these drawbacks by uncovering intricate relationships between features. However, two key limitations remain: 1) embedding feature subsets in a continuous space is challenging due to permutation sensitivity, as changes in feature order can introduce biases and weaken the embedding learning process; 2) gradient-based search in the embedding space assumes convexity, which is rarely guaranteed, leading to reduced search effectiveness and suboptimal subsets. To address these limitations, we propose a new framework that can: 1) preserve feature subset knowledge in a continuous embedding space while ensuring permutation invariance; 2) effectively explore the embedding space without relying on strong convex assumptions. For the first objective, we develop an encoder-decoder paradigm to preserve feature selection knowledge into a continuous embedding space. This paradigm captures feature interactions through pairwise relationships within the subset, removing the influence of feature order on the embedding. Moreover, an inducing point mechanism is introduced to accelerate pairwise relationship computations. For the second objective, we employ a policy-based reinforcement learning (RL) approach to guide the exploration of the embedding space. The RL agent effectively navigates the space by balancing multiple objectives. By prioritizing high-potential regions adaptively and eliminating the reliance on convexity assumptions, the RL agent effectively reduces the risk of converging to local optima. Extensive experiments demonstrate the effectiveness, efficiency, robustness and explicitness of our model.

cs.LG↗

arXiv2026

Robust and Efficient Tool Orchestration via Layered Execution Structures with Reflective Correction

Tool invocation is a core capability of agentic systems, yet failures often arise not from individual tool calls but from how multiple tools are organized and executed together. Existing approaches tightly couple tool execution with stepwise language reasoning or explicit planning, leading to brittle behavior and high execution overhead. To overcome these limitations, we revisit tool invocation from the perspective of tool orchestration. Our key insight is that effective orchestration does not require precise dependency graphs or fine-grained planning. Instead, a coarse-grained layer structure suffices to provide global guidance, while execution-time errors can be corrected locally. Specifically, we model tool orchestration as learning a layered execution structure that captures high-level tool dependencies, inducing layer-wise execution through context constraints. To handle execution-time failures, we introduce a schema-aware reflective correction mechanism that detects and repairs errors locally. This design confines errors to individual tool calls and avoids re-planning entire execution trajectories. This structured execution paradigm enables a lightweight and reusable orchestration component for agentic systems. Experimental results show that our approach achieves robust tool execution while reducing execution complexity and overhead. Code will be made publicly available.

cs.AI↗