OpenRaiser/Intern-Atlas huggingface dataset:
ActorDB: A Unified Database Model Integrating Single-Writer Actors, Incremental View Maintenance, and Zero-Trust Messaging
Venue: arXiv cs.DB 2025
Year: 2025

This paper presents ActorDB ( Dekigoto ) , a novel database architecture that tightly integrates a single-writer actor model for writes, Incremental View Maintenance (IVM), and a zero-trust security model as a core component. The primary contribution of this work is the unification of these powerful but complex concepts into a single, cohesive system designed to reduce architectural complexity for developers of modern, data-intensive applications. We argue that by providing these capabilities out-of-the-box, ActorDB can offer a more robust, secure, and developer-friendly platform compared to solutions that require manual integration of separate systems for actor persistence, stream processing, and security. We present the core architecture, discuss the critical trade-offs in its design, and define the performance criteria for a Minimum Viable Product (MVP) to validate our approach.
Learning Relationships Between Separate Audio Tracks for Creative Applications
Venue: arXiv cs.SD 2025
Year: 2025

This paper presents the first step in a research project situated within the field of musical agents. The objective is to achieve, through training, the tuning of the desired musical relationship between a live musical input and a real-time generated musical output, through the curation of a database of separated tracks. We propose an architecture integrating a symbolic decision module capable of learning and exploiting musical relationships from such musical corpus. We detail an offline implementation of this architecture employing Transformers as the decision module, associated with a perception module based on Wav2Vec 2.0, and concatenative synthesis as audio renderer. We present a quantitative evaluation of the decision module's ability to reproduce learned relationships extracted during training. We demonstrate that our decision module can predict a coherent track B when conditioned by its corresponding ''guide'' track A, based on a corpus of paired tracks (A, B).
Automatically Generating Web Applications from Requirements Via Multi-Agent Test-Driven Development
Venue: arXiv cs.SE 2025
Year: 2025

Developing full-stack web applications is complex and time-intensive, demanding proficiency across diverse technologies and frameworks. Although recent advances in multimodal large language models (MLLMs) enable automated webpage generation from visual inputs, current solutions remain limited to front-end tasks and fail to deliver fully functional applications. In this work, we introduce TDDev, the first test-driven development (TDD)-enabled LLM-agent framework for end-to-end full-stack web application generation. Given a natural language description or design image, TDDev automatically derives executable test cases, generates front-end and back-end code, simulates user interactions, and iteratively refines the implementation until all requirements are satisfied. Our framework addresses key challenges in full-stack automation, including underspecified user requirements, complex interdependencies among multiple files, and the need for both functional correctness and visual fidelity. Through extensive experiments on diverse application scenarios, TDDev achieves a 14.4% improvement on overall accuracy compared to state-of-the-art baselines, demonstrating its effectiveness in producing reliable, high-quality web applications without requiring manual intervention.
ID-RAG: Identity Retrieval-Augmented Generation for Long-Horizon Persona Coherence in Generative Agents
Venue: arXiv cs.AI 2025
Year: 2025

Generative agents powered by language models are increasingly deployed for long-horizon tasks. However, as long-term memory context grows over time, they struggle to maintain coherence. This deficiency leads to critical failures, including identity drift, ignoring established beliefs, and the propagation of hallucinations in multi-agent systems. To mitigate these challenges, this paper introduces Identity Retrieval-Augmented Generation (ID-RAG), a novel mechanism designed to ground an agent's persona and persistent preferences in a dynamic, structured identity model: a knowledge graph of core beliefs, traits, and values. During the agent's decision loop, this model is queried to retrieve relevant identity context, which directly informs action selection. We demonstrate this approach by introducing and implementing a new class of ID-RAG enabled agents called Human-AI Agents (HAis), where the identity model is inspired by the Chronicle structure used in Perspective-Aware AI, a dynamic knowledge graph learned from a real-world entity's digital footprint. In social simulations of a mayoral election, HAis using ID-RAG outperformed baseline agents in long-horizon persona coherence - achieving higher identity recall across all tested models by the fourth timestep - and reduced simulation convergence time by 19% (GPT-4o) and 58% (GPT-4o mini). By treating identity as an explicit, retrievable knowledge structure, ID-RAG offers a foundational approach for developing more temporally coherent, interpretable, and aligned generative agents. Our code is open-source and available at: https://github.com/flybits/humanai-agents.
Uncertainty-Aware Generative Oversampling Using an Entropy-Guided Conditional Variational Autoencoder
Venue: arXiv cs.LG 2025
Year: 2025

Class imbalance remains a major challenge in machine learning, especially for high-dimensional biomedical data where nonlinear manifold structures dominate. Traditional oversampling methods such as SMOTE rely on local linear interpolation, often producing implausible synthetic samples. Deep generative models like Conditional Variational Autoencoders (CVAEs) better capture nonlinear distributions, but standard variants treat all minority samples equally, neglecting the importance of uncertain, boundary-region examples emphasized by heuristic methods like Borderline-SMOTE and ADASYN. We propose Local Entropy-Guided Oversampling with a CVAE (LEO-CVAE), a generative oversampling framework that explicitly incorporates local uncertainty into both representation learning and data generation. To quantify uncertainty, we compute Shannon entropy over the class distribution in a sample's neighborhood: high entropy indicates greater class overlap, serving as a proxy for uncertainty. LEO-CVAE leverages this signal through two mechanisms: (i) a Local Entropy-Weighted Loss (LEWL) that emphasizes robust learning in uncertain regions, and (ii) an entropy-guided sampling strategy that concentrates generation in these informative, class-overlapping areas. Applied to clinical genomics datasets (ADNI and TCGA lung cancer), LEO-CVAE consistently improves classifier performance, outperforming both traditional oversampling and generative baselines. These results highlight the value of uncertainty-aware generative oversampling for imbalanced learning in domains governed by complex nonlinear structures, such as omics data.
VisualOverload: Probing Visual Understanding of VLMs in Really Dense Scenes
Venue: arXiv cs.CV 2025
Year: 2025

Is basic visual understanding really solved in state-of-the-art VLMs? We present VisualOverload, a slightly different visual question answering (VQA) benchmark comprising 2,720 question-answer pairs, with privately held ground-truth responses. Unlike prior VQA datasets that typically focus on near global image understanding, VisualOverload challenges models to perform simple, knowledge-free vision tasks in densely populated (or, overloaded) scenes. Our dataset consists of high-resolution scans of public-domain paintings that are populated with multiple figures, actions, and unfolding subplots set against elaborately detailed backdrops. We manually annotated these images with questions across six task categories to probe for a thorough understanding of the scene. We hypothesize that current benchmarks overestimate the performance of VLMs, and encoding and reasoning over details is still a challenging task for them, especially if they are confronted with densely populated scenes. Indeed, we observe that even the best model (o3) out of 37 tested models only achieves 19.6% accuracy on our hardest test split and overall 69.5% accuracy on all questions. Beyond a thorough evaluation, we complement our benchmark with an error analysis that reveals multiple failure modes, including a lack of counting skills, failure in OCR, and striking logical inconsistencies under complex tasks. Altogether, VisualOverload exposes a critical gap in current vision models and offers a crucial resource for the community to develop better models. Benchmark: http://paulgavrikov.github.io/visualoverload
SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces for Cellular Perturbation Prediction
Venue: arXiv cs.AI 2025
Year: 2025

Predicting cellular responses to genetic perturbations represents a fundamental challenge in systems biology, critical for advancing therapeutic discovery and virtual cell modeling. While large language models (LLMs) show promise for biological reasoning, their application to perturbation prediction remains underexplored due to challenges in adapting them to structured experimental data. We present SynthPert, a novel method that enhances LLM performance through supervised fine-tuning on synthetic reasoning traces generated by frontier models. Using the PerturbQA benchmark, we demonstrate that our approach not only achieves state-of-the-art performance but surpasses the capabilities of the frontier model that generated the training data. Our results reveal three key insights: (1) Synthetic reasoning traces effectively distill biological knowledge even when partially inaccurate, (2) This approach enables cross-cell-type generalization with 87% accuracy on unseen RPE1 cells, and (3) Performance gains persist despite using only 2% of quality-filtered training data. This work shows the effectiveness of synthetic reasoning distillation for enhancing domain-specific reasoning in LLMs.
Structural Reward Model: Enhancing Interpretability, Efficiency, and Scalability in Reward Modeling
Venue: arXiv cs.AI 2025
Year: 2025

Reward Models (RMs) are key components for evaluating and guiding language model outputs. However, traditional scalar RMs often struggle with incorporating contextual and background information during inference, leading to incomplete evaluations. Generative RMs (GRMs) attempt to address these limitations by generating intermediate reasoning steps. Yet, their uncontrolled black-box nature and inefficiency due to sequential decoding hinder their industrial deployment. Industrial scenarios, such as search and recommendation systems, often involve single-domain tasks requiring evaluation along specific dimensions. In such contexts, diagnosing "bad cases" necessitates structured feedback to identify and optimize dimension-specific issues. In this paper, we propose the Structural Reward Model (SRM), a modular and interpretable framework integrating side-branch models as auxiliary feature generators. By introducing fine-grained dimensions, SRMs enable interpretable and efficient evaluation, facilitating targeted diagnostics and optimization. This structured approach ensures adaptability and scalability for industrial applications. Through comprehensive experiments, we demonstrate that SRMs outperform scalar RMs and GRMs in robustness and alignment with human preferences. The modular design further supports efficient optimization for practical scenarios, allowing SRM to provide a practical reward modeling solution for industry.
Where LLM Agents Fail and How They can Learn From Failures
Venue: arXiv cs.AI 2025
Year: 2025

Large Language Model (LLM) agents, which integrate planning, memory, reflection, and tool-use modules, have shown promise in solving complex, multi-step tasks. Yet their sophisticated architectures amplify vulnerability to cascading failures, where a single root-cause error propagates through subsequent decisions, leading to task failure. Current systems lack a framework that can comprehensively understand agent error in a modular and systemic way, and therefore fail to detect these errors accordingly. We address this gap with three contributions. First, we introduce the AgentErrorTaxonomy, a modular classification of failure modes spanning memory, reflection, planning, action, and system-level operations. Second, we construct AgentErrorBench, the first dataset of systematically annotated failure trajectories from ALFWorld, GAIA, and WebShop, grounding error analysis in real-world agent rollouts. Third, we propose AgentDebug, a debugging framework that isolates root-cause failures and provides corrective feedback, enabling agents to recover and iteratively improve. Experiments on AgentErrorBench show that AgentDebug achieves 24% higher all-correct accuracy and 17% higher step accuracy compared to the strongest baseline. Beyond detection, the targeted feedback generated by AgentDebug enables LLM agents to iteratively recover from failures, yielding up to 26% relative improvements in task success across ALFWorld, GAIA, and WebShop. These results establish principled debugging as a pathway to more reliable and adaptive LLM agents. The code and data will be available at https://github.com/ulab-uiuc/AgentDebug
From Perception to Cognition: A Survey of Vision-Language Interactive Reasoning in Multimodal Large Language Models
Venue: arXiv cs.AI 2025
Year: 2025

Multimodal Large Language Models (MLLMs) strive to achieve a profound, human-like understanding of and interaction with the physical world, but often exhibit a shallow and incoherent integration when acquiring information (Perception) and conducting reasoning (Cognition). This disconnect leads to a spectrum of reasoning failures, with hallucination being the most prominent. Collectively, these issues expose a fundamental challenge: the ability to process pixels does not yet confer the ability to construct a coherent, credible internal world model. To systematically dissect and address this challenge, this survey introduces a novel and unified analytical framework: ``From Perception to Cognition." We deconstruct the complex process of vision-language interactive understanding into two interdependent layers: Perception, the foundational ability to accurately extract visual information and achieve fine-grained alignment with textual instructions; and Cognition, the higher-order capability for proactive, multi-step, goal-oriented reasoning built upon this perceptual foundation, the core of which is the formation of a dynamic observe-think-verify reasoning loop. Guided by this framework, this paper systematically analyzes the key bottlenecks of current MLLMs at both layers. It surveys the landscape of cutting-edge methods designed to address these challenges, spanning from techniques that enhance low-level visual representations to those that improve high-level reasoning paradigms. Furthermore, we review critical benchmarks and delineate future research directions. This survey aims to provide the research community with a clear, structured perspective for understanding the intrinsic limitations of current MLLMs and to illuminate the path toward building next-generation models capable of deep reasoning and a genuine understanding of the world.
Detecting and Fixing API Misuses of Data Science Libraries Using Large Language Models
Venue: arXiv cs.SE 2025
Year: 2025

Data science libraries, such as scikit-learn and pandas, specialize in processing and manipulating data. The data-centric nature of these libraries makes the detection of API misuse in them more challenging. This paper introduces DSCHECKER, an LLM-based approach designed for detecting and fixing API misuses of data science libraries. We identify two key pieces of information, API directives and data information, that may be beneficial for API misuse detection and fixing. Using three LLMs and misuses from five data science libraries, we experiment with various prompts. We find that incorporating API directives and data-specific details enhances Dschecker's ability to detect and fix API misuses, with the best-performing model achieving a detection F1-score of 61.18 percent and fixing 51.28 percent of the misuses. Building on these results, we implement Dschecker agent which includes an adaptive function calling mechanism to access information on demand, simulating a real-world setting where information about the misuse is unknown in advance. We find that Dschecker agent achieves 48.65 percent detection F1-score and fixes 39.47 percent of the misuses, demonstrating the promise of LLM-based API misuse detection and fixing in real-world scenarios.
Crowdsourcing Without People: Modelling Clustering Algorithms as Experts
Venue: arXiv cs.LG 2025
Year: 2025

This paper introduces mixsemble, an ensemble method that adapts the Dawid-Skene model to aggregate predictions from multiple model-based clustering algorithms. Unlike traditional crowdsourcing, which relies on human labels, the framework models the outputs of clustering algorithms as noisy annotations. Experiments on both simulated and real-world datasets show that, although the mixsemble is not always the single top performer, it consistently approaches the best result and avoids poor outcomes. This robustness makes it a practical alternative when the true data structure is unknown, especially for non-expert users.
Optimal Threshold Signatures in Bitcoin
Venue: arXiv cs.CR 2025
Year: 2025

We formulate the design of a threshold signature scheme as made possible on cryptocurrency protocols like Bitcoin. The funds are secured by an m-of-n threshold signature, where at least m signatures are needed to unlock the funds. A user designs this scheme knowing that a malicious attacker can also obtain the signatures with some probability. Higher thresholds offer more security, but also risk locking the user out of his own funds. The optimal threshold balances these twin effects. Interventions like increasing the security or usability of the signatures allow for higher thresholds. We model dynamic threshold signature schemes, where the probability of a user or attacker obtaining signatures decays with time. A dynamic threshold signature scheme is optimal, and increasing security or usability allows for higher thresholds and longer time locks.
From Faithfulness to Correctness: Generative Reward Models that Think Critically
Venue: arXiv cs.CL 2025
Year: 2025

Through reinforcement learning with verifiable rewards (RLVR), large language models have achieved substantial progress in domains with easily verifiable outcomes, such as mathematics and coding. However, when applied to more complex tasks like open-domain question answering, RLVR faces significant challenges due to the difficulty of verifying correctness. The nuanced and ambiguous nature of real-world knowledge makes it difficult to reliably evaluate correctness in these settings, necessitating further abilities that extend beyond mere logical consistency to encompass an understanding and assessment of both external and internal knowledge. Recent work has primarily focused on improving faithfulness, defined as semantic alignment with supporting documents, which can cause models to rely excessively on external sources and diminish their capacity for critical assessment. To address this, we propose the Thinking-supervised Reward Model (TRM), which incorporates sentence-level thinking supervision to endow reward models with critical thinking abilities. Given a query, answer, and supporting documents, TRM first assesses the faithfulness of each answer sentence to the supporting documents, and then applies a reasoning step to evaluate sentence-level correctness. By structuring reward modeling as a sequence of faithfulness, reasoning, and correctness evaluations, TRM encourages models to critically assess and leverage both external and internal knowledge. Experiments on reward signals demonstrate that TRM substantially improves the identification of incorrect sentences, and incorporating TRM into policy optimization leads to significant gains in both answer correctness and usefulness.
DepthLM: Metric Depth From Vision Language Models
Venue: arXiv cs.CV 2025
Year: 2025

Vision language models (VLMs) can flexibly address various vision tasks through text interactions. Although successful in semantic understanding, state-of-the-art VLMs including GPT-5 still struggle in understanding 3D from 2D inputs. On the other hand, expert pure vision models achieve super-human accuracy in metric depth estimation, a key 3D understanding task. However, they require task-specific architectures and losses. Such difference motivates us to ask: Can VLMs reach expert-level accuracy without architecture or loss change? We take per-pixel metric depth estimation as the representative task and show that the answer is yes! Surprisingly, comprehensive analysis shows that text-based supervised-finetuning with sparse labels is sufficient for VLMs to unlock strong 3D understanding, no dense prediction head or complex regression/regularization loss is needed. The bottleneck for VLMs lies actually in pixel reference and cross-dataset camera ambiguity, which we address through visual prompting and intrinsic-conditioned augmentation. With much smaller models, our method DepthLM surpasses the accuracy of most advanced VLMs by over 2x, making VLMs for the first time comparable with pure vision models. Interestingly, without explicit enforcement during training, VLMs trained with DepthLM naturally avoids over-smoothing, having much fewer flying points at boundary regions than pure vision models. The simplicity of DepthLM also enables a single VLM to cover various 3D tasks beyond metric depth. Our code and model will be released at the link below.
Rethinking Parameter Sharing for LLM Fine-Tuning with Multiple LoRAs
Venue: arXiv cs.LG 2025
Year: 2025

Large language models are often adapted using parameter-efficient techniques such as Low-Rank Adaptation (LoRA), formulated as $y = W_0x + BAx$, where $W_0$ is the pre-trained parameters and $x$ is the input to the adapted layer. While multi-adapter extensions often employ multiple LoRAs, prior studies suggest that the inner $A$ matrices are highly similar during training and thus suitable for sharing. We revisit this phenomenon and find that this similarity is largely attributable to the identical initialization rather than shared knowledge, with $B$ playing a more critical role in knowledge encoding and transfer. Motivated by these insights, we propose \textbf{ALoRA}, an asymmetric multi-LoRA design with multiple $A$ matrices and a single shared $B$ in multi-task fine-tuning, and \textbf{Fed-ALoRA}, which shares $B$ across clients in federated fine-tuning under both homogeneous and heterogeneous settings, through a novel matrix decomposition strategy to accommodate heterogeneous ranks across clients. Experiments on commonsense reasoning, math reasoning, multi-task NLP dataset, and federated NLP dataset demonstrate that our methods achieve more balanced performance across tasks with comparable or superior average accuracy relative to existing multi-LoRA approaches. Codes are available at https://github.com/OptMN-Lab/ALoRA.