Colorectal cancer (CRC) exhibits substantial molecular heterogeneity, necessitating the inference of subtype-specific driver genes and their interactions for drug-target discovery and precision oncology. Prior studies often fail to capture subtle, latent nonlinear regulatory mechanisms (dark causal relationships) driving tumor progression in specific subtypes. Here, we develop an explainable intelligence computational framework, Symbolic Trajectory-Embedded Dark Causal Interaction Inference (STE-DC2I), which combines symbolic trajectory embedding with historical prediction mechanisms to model nonmonotonic oscillatory dependencies between genes. Integrating single-cell transcriptomic and multiomics profiles from malignant epithelial subpopulations, STE-DC2I classifies CRC subtypes, reconstructs developmental trajectories, and uncovers interpretable subtype-specific driver genes with functional relevance. Unlike correlation-based and explicit causal approaches, STE-DC2I captures weak yet biologically critical regulatory signals, outperforming state-of-the-art methods in predicting subtype-specific CRC driver genes. Functional assays in CRC cell lines (in vitro) validated nine predicted driver genes, highlighting their therapeutic potential.This work systematically explores dark causal interactions between genes in CRC subtypes. STE-DC2I offers interpretable insights and a generalizable strategy for CRC drug-target discovery.
Meng Huang, Huijin Hu, Ming Li et al.· Journal of Chemical Informat...· 0 citations
ConspectusThe field of covalent drug discovery has witnessed a remarkable resurgence in recent years, a trend underscored by the approval of more than 125 covalent drugs by the US FDA as of 2025, which demonstrates their immense therapeutic potential. Driven by ever-increasing computational power and vast amounts of data, deep learning (DL) is profoundly transforming numerous fields, from natural language processing to drug discovery. In the development of covalent drugs, in particular, advanced computational methods centered on data-driven approaches and artificial intelligence (AI) exhibit immense potential. The realization of this potential depends on the construction of a synergistic ecosystem. Here, we define this "ecosystem" as an integrated set of components─including (i) curated covalent-relevant databases, (ii) AI/physics-based predictive and scoring models, (iii) interoperable computational workflows spanning site identification, docking/virtual screening, and lead optimization, and (iv) closed-loop feedback that systematically incorporates experimental outcomes to update data resources and refine/validate models. This begins with the systematic collection of past experimental results to build high-quality databases. These databases, in turn, provide the foundation for developing AI-driven computational tools capable of precisely interfacing with and accelerating downstream tasks, such as molecular docking (for generating physically plausible conformations and conducting large-scale virtual screening) and lead optimization. The application of these AI tools not only guides experimental design, but the resulting key data also feed back into and enrich the databases. Furthermore, in the cutting-edge field of covalent drugs, the precise identification of "druggable" covalent sites on target proteins has emerged as another critically important downstream task.In this Account, we describe a computational and AI-driven ecosystem for structure-based covalent drug discovery and highlight our contributions to this field. By explicitly linking databases, models, workflows, and experimental feedback into a single framework, this Account moves beyond a simple inventory of individual tools to instead offer a systematic and panoramic perspective on an integrated ecosystem for covalent drug discovery, driven by data and computational engines including AI. We focus on how this ecosystem systematically addresses the challenges from covalent binding site identification to lead discovery, thereby fundamentally accelerating the development of next-generation covalent therapies. We first articulate the philosophy behind the construction and updating of covalent databases, emphasizing the necessity of high-quality data. Subsequently, we delve into a suite of cutting-edge, AI-driven computational methods, exploring the potential of deep learning in tasks such as molecular docking, covalent binding site prediction, and lead optimization. To bridge the gap between computational theory and experimental validation, we will use the discovery of potent covalent CRM1 inhibitors as a specific case study, detailing how our customized, structure-based virtual screening pipeline was utilized to achieve a seamless workflow from computational prediction to biological validation. This section is intended to offer actionable guidance for experimental researchers seeking to leverage these powerful computational tools. Finally, we highlight the limitations and potential pitfalls of this AI engine─concerns that are equally relevant when developing AI-driven covalent docking algorithms. Building on our group's recent benchmarking of AI docking methods, we objectively evaluate current performance and discuss how transformative advances such as AlphaFold3 may reshape the field.
Shi Li, Hongyan Du, Xujun Zhang et al.· Accounts of Chemical Researc...· 4 citations
The growing domain of liquidity in computing extends its boundaries to include advancements like liquid artificial intelligence (AI). Liquid AI leverages liquid software using isomorphic Internet of Things (IoT) architecture to enhance computation at the edge. This innovation unveils vast opportunities yet also introduces significant challenges, particularly around privacy and trust. We explore the vulnerabilities that might hinder the progression of this technological fusion toward achieving trustworthy AI. Through an intensive examination of the literature, this research highlights the heightened threats to data integrity and stakeholder trust in these evolving ecosystems. Four main challenges: Data collection, Data storage and Access, Data utilization and sharing, and Surveillance and profiling were identified and examined under privacy, and two, Algorithms and decision-making and Security of IoT infrastructure under trust. The concerns are further categorized to highlight their impact on the development of trustworthy AI. The study acknowledges the early state of the field. Consequently, this research navigates through the limited available literature, initiating a pioneering discourse emphasizing fostering a foundation for developing secure and trustworthy Liquid AI environments.
M. Agbese, Niko Mäkitalo, Muhammad Waseem et al.· IoT· 6 citations· ⚡1
AI coding agents increasingly act directly within software environments, yet existing analyses of their failures rely on benchmark trajectories that miss how developers actually experience misalignment. We present an observational study of 20,574 coding-agent sessions from 1,639 repositories across IDE and CLI workflows. We operationalize misalignment as a breakdown made visible through developer pushback, and annotate each episode along four axes: form, cause, cost, and resolution. We identify seven recurring forms, spanning how agents read projects, interpret developer intent, follow rules, bound their actions, implement and execute code, and report progress. 90.50% of episodes impose effort and trust costs rather than irreversible system damage, yet 91.49% of visible resolutions still require explicit user correction. Misalignment patterns also differ across IDE and CLI settings, persist across adjacent sessions, and shift over time: while overall rates decline, constraint violations and inaccurate self-reporting grow in share. Our findings inform the design of training, evaluation, and interfaces for keeping coding agents aligned with real developer workflows.
Ningzhi Tang, Chaoran Chen, Gelei Xu et al.· 0 citations
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Digital video is central to communication, education, and entertainment, but without audio description (AD), blind and low-vision users are excluded. While crowdsourced platforms and vision-language models (VLMs) expand AD production, quality is rarely checked systematically. Existing evaluations rely on NLP metrics and short-clip guidelines, leaving open the question of how to assess long-form AD quality at scale. To address this, we developed a methodological workflow using Item Response Theory to evaluate VLM and human rater proficiency against expert-established ground truth. Evaluations were based on a six-dimensional framework, grounded in professional guidelines and shaped by insights from our accessibility experts and blind consultants. Findings suggest that top-performing VLMs can approximate ground-truth ratings at levels comparable to human raters. However, qualitative analysis reveals that VLM reasoning is less reliable and actionable than that of human respondents. These insights underscore the potential of hybrid evaluation systems that leverage VLMs alongside human oversight, offering a path toward scalable AD quality control.
Lana Do, Gio Jung, Juvenal Francisco Barajas et al.· 0 citations
We present OLIVE, a framework for adapting a foundation model to provide real-time assistance in temporally demanding, high-stakes, and dynamic tasks. We show that passive EEG, fused online with behavioral evidence, can meaningfully extend the number of targets users detect and engage beyond their unaided action bandwidth. OLIVE learns from both explicit behavioral signals (the targets the user shoots down in an XR first-person shooter game) and implicit physiological signals (fixation-locked EEG) to provide timely guidance, continuously adapting a frozen vision-language model's inference on which items are task-relevant by jointly estimating per-source reliability without manual labels or offline training. Through three user studies, including two live deployments of an assistive agent driven by OLIVE in XR, we show that OLIVE Pareto-dominates prior test-time adaptation frameworks, achieving the highest convergence rate at comparable convergence speed. Combining implicit physiological and explicit behavioral signals, the OLIVE agent produces the largest and most reliable within-session improvement to a user's ability to detect and engage targets, largely independent of the individual's skill. When the target switches silently, the agent that uses both behavioral and physiological signals reconverges significantly faster than the behavior-only agent (1.27 times faster on average, p = .008), restoring trustworthy guidance at the moment the task changes, precisely when reliable assistance matters most.
Ziheng Li, Xichen He, Haoyan Chen et al.· 0 citations
Clinical AI often optimizes predictive performance without engaging how clinicians decide where to look and what to write. We present Co-Annotator, which distills expert gaze and dictation into two guidance components: a gaze-aligned Vision Transformer producing fixation-aligned areas of interest (AOIs), and an ontology-bounded vision-language model (VLM) that pre-fills editable biomarker summaries for retinal optical coherence tomography (OCT). We first collect expert gaze and dictations (US1) to train the models, significantly improving diagnostic accuracy and biomarker generation. We then deploy the system with ophthalmology residents: a controlled resident study (US2) confirmed each modality is safe and independently beneficial, with AOI guidance producing lasting perceptual efficiency gains through post-guidance carryover and VLM guidance more than doubling biomarker documentation breadth. In a combined deployment across two academic institutions (US3), providing both modalities simultaneously produced efficiency gains that substantially exceeded either modality alone: correct diagnoses per minute increased by 40% and comment editing time fell by 67%, without compromising diagnostic accuracy. Notably, neither modality improved efficiency during guidance in US2, which makes the in-guidance efficiency gain under combined guidance in US3 the more striking result. Expert-distilled multimodal guidance can remove two distinct clinical workflow bottlenecks at once (visual search overhead and documentation burden) without compromising the diagnostic accuracy clinicians already achieve.
Ziheng "Leo" Li, Benjamin Freeman, Akshay Raman et al.· 0 citations
Privacy protection for live web traffic requires more than detecting private spans. Agent-based privacy protection systems must determine whether an outgoing action complies with the destination site's privacy policy, then apply only the level of rewriting or sanitisation justified by the residual disclosure risk. We present GuardianAgent, a policy-conditioned anonymization framework that couples structured risk assessment with verified adaptive rewriting. GuardianAgent computes risk through AMRSF (Adaptive Multi-factor Risk Scoring Formula), an explicit controller that combines policy-violation likelihood with data sensitivity, recipient transmission, purpose legitimacy, contextual basis, and policy transparency, rather than relying on an LLM to assign risk directly. This risk score determines both the allow/transform/deny decision and the initial anonymization level. For efficiency, GuardianAgent uses an evidential fast path for low-uncertainty policy matches and invokes an LLM slow path only for uncertain cases. For rewriting, it applies a five-level hierarchy driven by a verified adversarial guesser: guesses trigger escalation only when supported by the original text, preventing hallucinated attacker confidence from causing unnecessary over-anonymization. Experiments across three benchmarks spanning legal text (TAB), Reddit posts (SynthPAI), and multi-format synthetic PII records (PII-Masking-300k) show that GuardianAgent achieves the strongest privacy-utility trade-off among published baselines and is the only method to reach more than 0.90 privacy in all three domains, remaining robust under a backbone switch. Action-context stress tests further show that the same outgoing text receives different decisions and anonymization strengths under different recipients, purposes, action bases, and policy-transparency conditions.
Ruiyi Yang, Gayathri Lihinikaduarachchi, Rahat Masood et al.· 0 citations
Large language models can support writing, but existing tools require users to explicitly articulate prompts-particularly burdensome in creative writing, where intentions are often ambiguous. Proactive support that infers users' needs from writing interactions could alleviate this burden, but raises two challenges: determining what support to provide and when to intervene. This work focuses on the former. We hypothesize that Flower and Hayes' cognitive process theory of writing-which characterizes writing through six cognitive processes-offers an interpretable bridge between observable writing behavior and appropriate support types. Through a formative study and literature review, we identify 14 writing support types associated with these cognitive processes, along with characteristic interaction behaviors linked to each process. We then instantiate this framework in AToM CoWriter, which infers support needs from writing interactions and document context. Two within-subjects studies (N = 21) provide initial evidence that this approach improves expressiveness and idea exploration, and that cognitive process inference increases engagement with proactive suggestions. These findings suggest that cognitive processes can provide a promising basis for support selection in proactive writing systems.
Masahiro Yoshida, Atsuya Kobayashi, Kei Tateno et al.· 0 citations
Social media platforms increasingly use AI-based credibility indicators to help users judge misinformation. Unlike individual human-AI decision-making, these indicators are embedded in information spread: users see both an AI prediction and earlier judgments shaped by the same AI, and their own judgments may then enter the public history. Yet how to analytically characterize this process remains under-explored. We therefore introduce a social-learning lens for this setting by extending the classical Bayesian cascade model with the AI indicator as a shared public signal. The resulting Gateway condition compares the evidence from the AI prediction with users' private impressions. Through this view, we show that AI changes what public history means. Crowd agreement may reflect accumulated independent human evidence, or repeated dependence on the same AI prediction. This creates a preservation-correction trade-off: stronger reliance on AI can preserve correct predictions, but can also lock in incorrect ones by blocking corrective private impressions. We calibrate the model using human-subject data on news veracity judgments. Although the AI outperforms human users, the average user weights it below her own impression but above several peer judgments, while individual users vary from discounting the AI to relying on it enough to cascade. Simulations show that over-reliance on a weak AI is especially harmful, and that diversifying AI signals across users can better keep the crowd informative. We conclude with implications for understanding human-AI interaction in information spread and designing misinformation interventions.
Zhuoran Lu, Weilong Wang, Yangyang Yu et al.· 0 citations
As artificial intelligence (AI) is increasingly integrated into social-emotional learning (SEL) initiatives, the need for evidence-based policy has become paramount. We systematically reviewed 65 peer-reviewed papers that examine the intersection of AI and SEL to investigate how these studies articulate policy implications. Our analysis revealed a substantial "policy deficit" in the current AI x SEL literature: nearly three-quarters of the studies did not mention policy implications at all. Using the "WH-question" framework (Who, What, Why, When/Where, and How), we map the policy implications narratives present in the literature and show that they often lack the specificity and actor-oriented guidance required for effective evidence-informed policymaking. We find a significant association between publication venue and policy engagement, suggesting that current academic incentive structures may prioritize technical innovation and pedagogical feasibility over explicit engagement with governance and regulation. This study identifies a "techno-solutionist" trap, where technical potential is foregrounded while the institutional conditions for responsible implementation remain under-specified. We conclude by proposing a shift from "implication-as-afterthought" to "implication-as-methodology" and offer a set of actionable guidelines for researchers, editors, reviewers, and policymakers to bridge the gap between AI innovation and educational governance. Rather than presenting policy as a generic ethical horizon, we argue that AI-SEL studies should systematically specify Who should act, What actions are recommended, Why these actions are needed, When and Where they apply, and How strongly they are framed, thereby strengthening the translation of AI x SEL innovation into educational policy and practice.
Tran Van Cuong, Liu Yihan, Nguyen Van Tuong· 0 citations
Task handover requires communicating enough current state for a successor to resume work, yet the relevant information is often divided between system records and human observations. System records can be precise and timestamped but only partially observe the task, while human reports capture intent and task knowledge that no log contains but are vulnerable to omission and memory error. We present a provenance-aware pipeline that converts task telemetry and human-authored reports into a shared typed task-state representation, aligns and reconciles their facts, detects conflicts, and generates structured handover reports. We evaluate the approach on 13 paired task states collected in a controlled spatial multitask environment, using task-grounded metrics that estimate the state-reconstruction cost a report would spare a hypothetical recipient and the misinformation burden it would impose. Reconciling both sources preserved greater estimated task-state utility than either the user report or telemetry alone. Relative to a direct end-to-end LLM given the same inputs, structured reconciliation maintained comparable estimated utility while incurring substantially less misinformation, and task-aware rendering retained utility more efficiently (per token) than exhaustive rendering. An exploratory content analysis further shows that human reports contain substantial strategic knowledge that lies outside state-focused metrics. These results support provenance-aware state reconciliation as a design pattern for safer AI-assisted handover.
Kayleigh Bishop, Maria P. Stull, Breanne Crockett et al.· 0 citations
