Large language model agents have shown promise in bioinformatics, but most existing systems focus primarily on producing final answers, treating planning, tool use, and code execution as transient interactions. This design is poorly suited to long-horizon bioinformatics tasks, where conclusions must remain connected to the data, computations, and intermediate evidence that support them. We introduce \textbf{Bioinfoysis}, a multi-agent harness that represents each request as a persistent, artifact-grounded analysis run. Bioinfoysis combines global planning with step-wise, evidence-driven replanning: the planner maintains an executable checklist and revises pending steps using structured handoffs returned after each worker execution. These handoffs bind intermediate results to their responsible agent, checklist step, and plan generation, preventing stale evidence from being silently reused after replanning. A controlled runtime validates generated scripts, tables, and figures before they are used in downstream analysis or reporting, while role-specific context, persistent memory, and governed bioinformatics skills support reliable execution over long analysis trajectories. We evaluate Bioinfoysis on BixBench and two question-answering tracks of LAB-Bench 2. On BixBench, Bioinfoysis achieves state-of-the-art accuracy of 82.4\%. Across four underlying language models, Bioinfoysis increases average accuracy from 27.81\% to 64.13\% on SeqQA2 and from 3.13\% to 31.25\% on DbQA2. These results demonstrate that reliable bioinformatics automation depends not only on model capability, but also on the harness that governs planning, execution, memory, and evidence flow. We hope that the emergence of Bioinfoysis will play a driving and leading role in the development of the bioinformatics community. Our demo website can be seen in https://report.bioinfoysis.com/.
Qing-Yang Shao, Xin Zhang, Zhou-Yang Yuan et al.· 0 citations
Retail supply chain operations rely on coupled decision modules that must adapt as requirements evolve. LLMs offer a natural-language interface for this task, but existing methods primarily focus on individual optimization models. Extending them to heterogeneous decision pipelines is challenging because a requirement may admit multiple intervention paths with different downstream effects. We formulate requirement-driven adaptation as the joint selection of an intervention route and an admissible module-level change, and propose a graph-constrained agentic framework in which domain agents expose admissible reformulation interfaces and a central processor searches over bounded intervention paths. Candidates are validated and compared using downstream KPIs. In collaboration with a large retail partner, we evaluate 100 warehouse requirements elicited from practitioner interviews, with GPT, Qwen, and DeepSeek as base LLMs. Relative to direct LLM reformulation, our framework improves correctness and end-to-end success across all three models, raising end-to-end success from 72--76% to 79--83%.
Lei Zheng, Liping Yang, Zihao Li et al.· 0 citations
Knowledge graphs describe reality in crisp assertions, while the systems now consuming them, foundation models and autonomous agents, reason natively in probabilities. We argue that this mismatch is why the integration of language models and knowledge graphs remains a data-feeding pipeline rather than a unified reasoning architecture. We envision Semantic Bayesian World Models (SBWMs): a Web that describes the world not as a database of facts but as a shared, evolving fabric of beliefs over knowledge graphs, where ontological axioms constrain priors, observations update beliefs by Bayesian conditioning, and actions intervene upon the world. We work through what an agent gains from such a model: a home-security agent deciding whether the figure at the gate is a courier or a burglar, an actuarial estimate aggregated by entailment rather than by string frequency, a planning task that language models reliably fail, and the estimation of quantities that no document has ever stated. We then set out what the community must build to make them possible: belief annotation over RDF~1.2, probabilistic entailment regimes, semantic calibration layers, and protocols by which agents that have never met can exchange, and disagree over, calibrated beliefs.
Collaborative perception enhances environment understanding through multi-agent information sharing, but its performance in real-world scenarios is constrained by heterogeneous sensor modalities and model architectures. Recent protocol-based two-stage methods alleviate this problem by mapping heterogeneous features into a shared protocol space; however, independently trained modality-specific converters often generate modality-specific pseudo-protocol distributions, leading to semantic inconsistency and error accumulation, which is particularly pronounced in scenarios with large modality discrepancies. To address this issue, we propose CauseCollab, a causal unified and modality-agnostic network. CauseCollab formulates representation learning in the protocol space from a causal perspective, explicitly disentangling semantic factors from modality-specific statistical confounders via causal metric learning. Meanwhile, CauseCollab adopts context-guided Unified Converter for heterogeneous modalities to ensure cross-modal semantic consistency. In addition, integrating new modalities only requires training adapters with minimal parameters. Extensive experiments on the OPV2V and DAIR-V2X datasets demonstrate that CauseCollab achieves state-of-the-art performance, with more significant gains in scenarios involving large modality gaps.
Weize Li, Yang Li, Quan Yuan et al.· 0 citations
Reach audiences
Advertise in front of researchers, engineers, and readers.
Scalable Vector Graphics (SVG) generation is attracting increasing attention as generative models improve in expressiveness and controllability. Progress, however, is held back by the lack of domain-specific evaluation protocols: current practice relies on metrics designed for natural images, most notably CLIPScore, which was never trained on vector graphics and aligns only partially with human judgment. We introduce \textbf{\ours}, a human-aligned evaluation framework for text-to-SVG generation. Through controlled caption and image perturbations, we first show that CLIP-based scores barely react to the errors SVG generators actually make, such as wrong colors, counts, and spatial relations, and that off-the-shelf Vision-Language Model (VLM) judges, while more sensitive, respond unevenly across error types and SVG styles. We then introduce a human-annotated dataset for \textit{Semantic Alignment}, measuring how faithfully a generated SVG reflects its caption. Building on it, we develop two complementary evaluators: CLIP scorers adapted to vector graphics and then aligned to human preferences, for fast large-scale evaluation, and a VLM judge trained with supervised fine-tuning and reward-shaped reinforcement learning, for more expressive and interpretable assessment. Using both, we benchmark major open-source, commercial, and optimization-based SVG generators on an independent caption set.
Marco Cipriano, Leonardo Zini, Alexandra Schild et al.· 0 citations
Federated learning is increasingly presented as a privacy-preserving advance: personal data remain on the device, and only model updates are shared. It borrows the vocabulary of the federated social web, yet inverts its logic, distributing computation while the resulting model stays with whoever convened the training. We argue that federation is not in itself a remedy for extractive AI, because outcomes depend on who governs the data and the model and who has agency over the practices that shape them. We describe three layers at which a creative community can hold its work: storage, circulation, and learning. Examining artist-governed trusts, cooperatives, and consent infrastructures, we show that creator governance is established at storage and circulation but stops at learning: contributors can consent to training, yet have little say over the resulting model or its federation. We map the research space this opens, pairing technical open problems with the human questions from which they unfold. We propose four design principles for a creative data commons that governs models and their federation, not only datasets: govern the model, not only the corpus; make the terms legible at the moment of contribution; design for refusal as a first-class state; and decide stewardship in the open and account for it.
Phoenix Perry, George Simms, Elizabeth Wilson et al.· 0 citations
Long-term human-AI interaction is difficult because the information that guides inference is updated implicitly by the model and is not directly inspectable or controllable by the user. We introduce the TRANSparent Framework for Interactive, Verifiable, Editable Representation (Transfiver), an architecture for human-AI co-inference through a shared editable state. Its central idea is that interaction-specific information is maintained in a single persistent state $(S_t)$ that both the model and the human update.
Transfiver distinguishes two modes of state evolution. In an implicit stream update, the model interprets ongoing interaction and decides whether new information revises an existing state item or creates a new one. In an explicit directed edit, a human inspects and modifies an addressed item. Both act on the same underlying state, so a human correction changes the state that subsequent computation reads, rather than adding another instruction or separate record.
The architecture separates shared parameters $(\theta)$, learned before ordinary use, from the persistent state $(S_t)$, which evolves during deployment without parameter retraining. Extending Transfiver to rich natural-language, relational, and large-scale shared states remains open.
AI agents increasingly gather evidence, invoke tools, apply constraints, and produce decisions that people or software may commit to action. A final output alone cannot show which evidence, tool state, rule, authorization, or action path produced it. We present DNative-Twin, a graph-native digital twin that records a committed agentic decision as a typed trajectory and re-executes its decision mechanism under declared conditions. The graph links the state observed by the agent, the path it followed, and the authority behind the resulting action. The twin synchronizes this information, replays the mechanism in isolation, and compares it under controlled changes. We instantiate the framework in enterprise decision processes using three public process logs and controlled replay suites. The experiments identify a specific failure: graph structure localizes represented changes but cannot determine the consequence of an unobserved tool state. In a three-condition controlled experiment with 300 injected instances, unresolved-divergence recall increased from 0 to 0.667 when replay-contract state was added and to 1.0 when verification results were also available; the held-out set contained no critical-class instance. Across 500--5,000 BPI 2020 cases, median end-to-end time increased from 0.794 to 8.889 seconds on the reported platform. These results separate the roles of graph structure, replay context, and verification evidence in reviewing a decision mechanism.
Junjie Pang, Zhenzhen Xie, Haoke Han et al.· 0 citations
World models have progressed from compact latent dynamics to generative, controllable, and interactive simulators of embodied environments. However, high predictive likelihood and visual fidelity do not necessarily ensure that a model preserves the evidence required for safe decision-making. This perspective identifies three structural mismatches in current world modeling: likelihood versus risk, prediction versus intervention, and finite-horizon prediction versus accumulated consequences. We propose the Risk-Informed World Model (RIWM) as a decision-centric research direction for safety-critical embodied systems. RIWM organizes world modeling around consequences, intervention, epistemic uncertainty, and recoverability, and integrates four interdependent capabilities: decision-relevant representation, counterfactual reasoning, safety-critical episodic memory, and runtime safety assurance. It distinguishes physical, social, and operational consequences while using epistemic uncertainty to qualify the evidence supporting action. We further discuss open challenges in identifying consequential futures, validating counterfactual reasoning, maintaining revisable safety memories, translating learned consequences into executable constraints, and determining when evidence is sufficient to act. This perspective argues that future world models should move beyond predicting likely futures toward identifying which futures matter, revising judgments through experience, and recognizing when to act, revise, sense, defer, or abstain.
Kailang Ma, Heye Huang, Inhi Kim et al.· 0 citations
As large language models (LLMs) become increasingly capable, the long-term value of AI systems depends not only on solving individual requests, but also on transforming experience and accumulated knowledge into durable, reusable competence. We introduce SimSkill, a self-evolving agent built around the Simulation of Urban MObility (SUMO) traffic simulator. SimSkill identifies capability gaps, generates and solves environment-grounded tasks, verifies solutions through an action--critic loop, and consolidates experience into episodic, procedural, and semantic memory without updating the backbone model. Through autonomous exploration, it builds a reusable library spanning the traffic-simulation workflow. We evaluate SimSkill on two held-out benchmarks with three backbone LLMs and independent artifact-based verification. SimSkill improves verified completion by up to 25 percentage points, while ablations show complementary contributions from procedural and semantic memory. Its benefits remain backbone- and budget-dependent: memory does not improve every model or uniformly reduce inference cost. More broadly, SimSkill illustrates a design paradigm in which natural language preserves and composes computational capabilities, while executable tools and code provide precise and reproducible execution. All code and experimental data are publicly available at https://github.com/qiliuchn/SimSkill-V1.
Large language model agents can plan, invoke tools, and modify external states, yet most systems still take an explicit user instruction as a fixed starting point. Proactive service moves the decision upstream: an agent must infer service opportunities from incomplete environmental and user signals, choose among remaining silent, asking, assisting, and acting, and account for interruption, misunderstanding, overreach, and privacy costs. This survey gives an operational definition centered on initiative and formulates the problem as a partially observable sequential decision process constrained by authorization and risk. The formulation represents timing, content, and delivery within one structured action, while making explicit the option value of waiting, the decision value of questions, and feedback-induced state changes. On this basis, we organize existing methods along one decision pipeline (state and need estimation, intervention gating, action construction, and feedback adaptation) and describe prescribed, predictive, model based, and return optimizing mechanisms as nonexclusive policy-construction components. We further normalize decision units and three-axis evidence descriptors across streaming dialogue, screen, video, software-engineering, and human-agent collaboration resources, and formalize metrics for triggering, timing, calibration, user burden, safety, and policy value. The synthesis shows why offline classification performance alone does not predict deployment benefit and why long-term memory is not a defining condition of proactivity. Reliable proactive service instead requires calibrated incremental intervention value, verifiable authorization, recoverable execution, and counterfactual evidence.
Yan Tang, Tingyu Cao, Yuanbo Tang et al.· 0 citations
Data centers are increasingly optimized by artificial intelligence and, at the same time, increasingly loaded by it. The literature treats these as two unrelated problems: control studies model workload as an exogenous arrival process, while sustainability studies model infrastructure as a fixed multiplier. We screen roughly 194 papers retrieved through a documented protocol, code 63 of them, and report what the coding shows. Of 28 primary control-oriented studies, 18 are validated in simulation alone and 5 reach physical hardware or a production facility; none account for water withdrawal, and none account for embodied carbon. Reported savings intervals across four technique families overlap almost completely, which means the field cannot presently rank its own methods. Ten recurring gaps are scored for consequence and tractability, and we set out CLEAR-DC, a framework coupling a control-policy branch to a workload-demand branch through an explicit elasticity term, reads out net rather than direct benefit, and emits a schema-conformant record covering energy, carbon, water, embodied share and validation venue. The framework is an architectural and methodological proposal, not a trained system; the contribution we defend empirically is the corpus analysis and the reporting schema derived from it. Coding sheet, derived statistics and all result artifacts: https://github.com/Kimalice/AI-for-Energy-Optimization-in-Data-Centers-Closing-the-Optimizer-Load-Loop
Mohammed Basharath Ullah, Summaiya Unnisa Begum, Mohammed Nadeem Ullah· 0 citations
