arXiv:2503.05860v3 Announce Type: replace-cross Abstract: Benchmarks are essential for unified evaluation and reproducibility. The rapid rise of Artificial Intelligence for Software Engineering (AI4SE) has produced numerous benchmarks for tasks such as code generation and bug repair. However, this proliferation has led to major challenges: (1) fragmented knowledge across tasks, (2) difficulty in selecting contextually relevant benchmarks, (3) lack of standardization in benchmark creation, and (4) flaws that limit utility. Addressing these requires a dual approach: systematically mapping existing benchmarks for informed selection and defining unified guidelines for robust, adaptable benchmark development. We conduct a review of 247 studies, identifying 273 AI4SE benchmarks since 2014. We categorize them, analyze limitations, and expose gaps in current practices. Building on these insights, we introduce BenchScout, an extensible semantic search tool for locating suitable benchmarks. BenchScout employs automated clustering with contextual embeddings of benchmark-related studies, followed by dimensionality reduction. In a user study with 22 participants, BenchScout achieved usability, effectiveness, and intuitiveness scores of 4.5, 4.0, and 4.1 out of 5. To improve benchmarking standards, we propose BenchFrame, a unified framework for enhancing benchmark quality. Applying BenchFrame to HumanEval yielded HumanEvalNext, featuring corrected errors, improved language conversion, higher test coverage, and greater difficulty. Evaluating 10 state-of-the-art code models on HumanEval, HumanEvalPlus, and HumanEvalNext revealed average pass-at-1 drops of 31.22% and 19.94%, respectively, underscoring the need for continuous benchmark refinement. We further examine BenchFrame's scalability through an agentic pipeline and confirm its generalizability on the MBPP dataset. All review data, user study materials, and enhanced benchmarks are publicly released.

Background: Computer perception (CP) technologies hold significant promise for advancing precision mental health care systems, given their ability to leverage algorithmic analysis of continuous, passive sensing data from wearables and smartphones (eg, behavioral activity, geolocation, vocal features, and ambient environmental data) to infer clinically meaningful behavioral and physiological states. However, successful implementation critically depends on cultivating well-founded stakeholder trust. Objective: This study aims to investigate, across adolescents, caregivers, clinicians, and developers, the contingencies under which CP technologies are deemed trustworthy in health care. Methods: We conducted 80 semistructured interviews with a purposive sample of adolescents (n=20) diagnosed with autism, Tourette syndrome, anxiety, obsessive-compulsive disorder, or attention-deficit/hyperactivity disorder and their caregivers (n=20); practicing clinicians across psychiatry, psychology, and pediatrics (n=20); and CP system developers (n=20). Interview transcripts were coded by 2 independent coders and analyzed using multistage, inductive thematic content analysis to identify prominent themes. Results: Across stakeholder groups, 5 core criteria emerged as prerequisites for trust in CP outputs: (1) epistemic alignment—consistency between system outputs, personal experience, and existing diagnostic frameworks; (2) demonstrable rigor—training on representative data and validation in real-world contexts; (3) explainability—transparent communication of input variables, thresholds, and decision logic; (4) sensitivity to complexity—the capacity to accommodate heterogeneity and comorbidity in symptom expression; and (5) a nonsubstitutive role—technologies must augment, rather than supplant, clinical judgment. A novel and cautionary finding was that epistemic alignment—whether outputs affirmed participants’ preexisting beliefs, diagnostic expectations, or internal states—was a dominant factor in determining whether the tool was perceived as trustworthy. Participants also expressed relational trust, placing confidence in CP systems based on endorsements from respected peers, academic institutions, or regulatory agencies. However, both trust strategies raise significant concerns: confirmation bias may lead users to overvalue outputs that align with their assumptions, while surrogate trust may be misapplied in the absence of robust performance validation. Conclusions: This study advances empirical understanding of how trust is formed and calibrated around artificial intelligence–based CP technologies. While trust is commonly framed as a function of technical performance, our findings show that it is deeply shaped by cognitive heuristics, social relationships, and alignment with entrenched epistemologies. These dynamics can facilitate intuitive verification but may also constrain the transformative potential of CP systems by reinforcing existing beliefs. To address this, we recommend a dual strategy: (1) embedding CP tools within institutional frameworks that uphold rigorous validation, ethical oversight, and transparent design; and (2) providing clinicians with training and interface designs that support critical appraisal and minimize susceptibility to cognitive bias. Recalibrating trust to reflect actual system capacities—rather than familiarity or endorsement—is essential for ethically sound and clinically meaningful integration of CP technologies.

npj Digital Medicine, Published online: 13 December 2025; doi:10.1038/s41746-025-02157-1

Legal implications of AI standard of care integration on patients’ informed consent: lessons from surgery

arXiv:2512.10058v1 Announce Type: new Abstract: While much research in artificial intelligence (AI) has focused on scaling capabilities, the accelerating pace of development makes countervailing work on producing harmless, "aligned" systems increasingly urgent. Yet research on alignment has diverged along two largely parallel tracks: safety--centered on scaled intelligence, deceptive or scheming behaviors, and existential risk--and ethics--focused on present harms, the reproduction of social bias, and flaws in production pipelines. Although both communities warn of insufficient investment in alignment, they disagree on what alignment means or ought to mean. As a result, their efforts have evolved in relative isolation, shaped by distinct methodologies, institutional homes, and disciplinary genealogies. We present a large-scale, quantitative study showing the structural split between AI safety and AI ethics. Using a bibliometric and co-authorship network analysis of 6,442 papers from twelve major ML and NLP conferences (2020-2025), we find that over 80% of collaborations occur within either the safety or ethics communities, and cross-field connectivity is highly concentrated: roughly 5% of papers account for more than 85% of bridging links. Removing a small number of these brokers sharply increases segregation, indicating that cross-disciplinary exchange depends on a handful of actors rather than broad, distributed collaboration. These results show that the safety-ethics divide is not only conceptual but institutional, with implications for research agendas, policy, and venues. We argue that integrating technical safety work with normative ethics--via shared benchmarks, cross-institutional venues, and mixed-method methodologies--is essential for building AI systems that are both robust and just.

arXiv:2512.09934v1 Announce Type: cross Abstract: The growing presence of IoT devices in academic environments has increased operational complexity and exposed security weaknesses, especially in academic institutions without unified policies for registration, monitoring, and incident response involving IoT. This work presents IoTEdu, an integrated platform that combines access control, incident detection, and automatic blocking of IoT devices. The solution was evaluated in a controlled environment with simulated attacks, achieving an average time of 28.6 seconds between detection and blocking. The results show a reduction in manual intervention, standardization of responses, and unification of the processes of registration, monitoring, and incident response.

arXiv:2512.10098v1 Announce Type: cross Abstract: Accurate and interpretable image-based diagnosis remains a fundamental challenge in medical AI, particularly un- der domain shifts and rare-class conditions. Deep learning mod- els often struggle with real-world distribution changes, exhibit bias against infrequent pathologies, and lack the transparency required for deployment in safety-critical clinical environments. We introduce MedXAI (An Explainable Framework for Med- ical Imaging Classification), a unified expert knowledge based framework that integrates deep vision models with clinician- derived expert knowledge to improve generalization, reduce rare- class bias, and provide human-understandable explanations by localizing the relevant diagnostic features rather than relying on technical post-hoc methods (e.g., Saliency Maps, LIME). We evaluate MedXAI across heterogeneous modalities on two challenging tasks: (i) Seizure Onset Zone localization from resting-state fMRI, and (ii) Diabetic Retinopathy grading. Ex periments on ten multicenter datasets show consistent gains, including a 3% improvement in cross-domain generalization and a 10% improvmnet in F1 score of rare class, substantially outperforming strong deep learning baselines. Ablations confirm that the symbolic components act as effective clinical priors and regularizers, improving robustness under distribution shift. MedXAI delivers clinically aligned explanations while achieving superior in-domain and cross-domain performance, particularly for rare diseases in multimodal medical AI.

MiTEs are myeloid-targeted immunocytokine prodrugs that block TREM2+ tumor-associated macrophages while activating cytotoxic lymphocytes via TME-specific IL-2 activity, eliciting strong anti-tumor efficacy in preclinical models with minimal systemic toxicity.

npj Digital Medicine, Published online: 10 December 2025; doi:10.1038/s41746-025-02119-7

Potential for Algorithmic Bias in Clinical Decision Instrument Development

arXiv:2512.08026v1 Announce Type: new Abstract: Screening patients for clinical trial eligibility remains a manual, time-consuming, and resource-intensive process. We present a secure, scalable proof-of-concept system for Artificial Intelligence (AI)-augmented patient-trial matching that addresses key implementation challenges: integrating heterogeneous electronic health record (EHR) data, facilitating expert review, and maintaining rigorous security standards. Leveraging open-source, reasoning-enabled large language models (LLMs), the system moves beyond binary classification to generate structured eligibility assessments with interpretable reasoning chains that support human-in-the-loop review. This decision support tool represents eligibility as a dynamic state rather than a fixed determination, identifying matches when available and offering actionable recommendations that could render a patient eligible in the future. The system aims to reduce coordinator burden, intelligently broaden the set of trials considered for each patient and guarantee comprehensive auditability of all AI-generated outputs.

arXiv:2512.08674v1 Announce Type: new Abstract: Multimodal clinical reasoning in the field of gastrointestinal (GI) oncology necessitates the integrated interpretation of endoscopic imagery, radiological data, and biochemical markers. Despite the evident potential exhibited by Multimodal Large Language Models (MLLMs), they frequently encounter challenges such as context dilution and hallucination when confronted with intricate, heterogeneous medical histories. In order to address these limitations, a hierarchical Multi-Agent Framework is proposed, which emulates the collaborative workflow of a human Multidisciplinary Team (MDT). The system attained a composite expert evaluation score of 4.60/5.00, thereby demonstrating a substantial improvement over the monolithic baseline. It is noteworthy that the agent-based architecture yielded the most substantial enhancements in reasoning logic and medical accuracy. The findings indicate that mimetic, agent-based collaboration provides a scalable, interpretable, and clinically robust paradigm for automated decision support in oncology.

arXiv:2512.08815v1 Announce Type: new Abstract: Neurons, as eukaryotic cells, have powerful internal computation capabilities. One neuron can have many distinct states, and brains can use this capability. Processes of neuron growth and maintenance use chemical signalling between cell bodies and synapses, ferrying chemical messengers over microtubules and actin fibres within cells. These processes are computations which, while slower than neural electrical signalling, could allow any neuron to change its state over intervals of seconds or minutes. Based on its state, a single neuron can selectively de-activate some of its synapses, sculpting a dynamic neural net from the static neural connections of the brain. Without this dynamic selection, the static neural networks in brains are too amorphous and dilute to do the computations of neural cognitive models. The use of multi-state neurons in animal brains is illustrated in hierarchical Bayesian object recognition. Multi-state neurons may support a design which is more efficient than two-state neurons, and scales better as object complexity increases. Brains could have evolved to use multi-state neurons. Multi-state neurons could be used in artificial neural networks, to use a kind of non-Hebbian learning which is faster and more focused and controllable than traditional neural net learning. This possibility has not yet been explored in computational models.

arXiv:2512.08715v1 Announce Type: cross Abstract: The performance of algorithms, methods, and models tends to depend heavily on the distribution of cases on which they are applied, this distribution being specific to the applicative domain. After performing an evaluation in several domains, it is highly informative to compute a (weighted) mean performance and, as shown in this paper, to scrutinize what happens during this averaging. To achieve this goal, we adopt a probabilistic framework and consider a performance as a probability measure (e.g., a normalized confusion matrix for a classification task). It appears that the corresponding weighted mean is known to be the summarization, and that only some remarkable scores assign to the summarized performance a value equal to a weighted arithmetic mean of the values assigned to the domain-specific performances. These scores include the family of ranking scores, a continuum parameterized by user preferences, and that the weights to consider in the arithmetic mean depend on the user preferences. Based on this, we rigorously define four domains, named easiest, most difficult, preponderant, and bottleneck domains, as functions of user preferences. After establishing the theory in a general setting, regardless of the task, we develop new visual tools for two-class classification.

arXiv:2501.06039v2 Announce Type: replace-cross Abstract: Spatial proteomics technologies have transformed our understanding of complex tissue architecture in cancer but present unique challenges for computational analysis. Each study uses a different marker panel and protocol, and most methods are tailored to single cohorts, which limits knowledge transfer and robust biomarker discovery. Here we present Virtual Tissues (VirTues), a general-purpose foundation model for spatial proteomics that learns marker-aware, multi-scale representations of proteins, cells, niches and tissues directly from multiplex imaging data. From a single pretrained backbone, VirTues supports marker reconstruction, cell typing and niche annotation, spatial biomarker discovery, and patient stratification, including zero-shot annotation across heterogeneous panels and datasets. In triple-negative breast cancer, VirTues-derived biomarkers predict anti-PD-L1 chemo-immunotherapy response and stratify disease-free survival in an independent cohort, outperforming state-of-the-art biomarkers derived from the same datasets and current clinical stratification schemes.

Nature, Published online: 10 December 2025; doi:10.1038/s41586-025-09792-4

High-depth sequencing of non-cancerous tissue from patients with metastatic cancer reveals single-base mutational signatures of alcohol, smoking and cancer treatments, and reveals how exogenous factors, including cancer therapies, affect somatic cell evolution.

Nature Cancer, Published online: 10 December 2025; doi:10.1038/s43018-025-01071-5

Foundation models hold transformative promise for oncology, yet their clinical implementation remains limited, largely owing to their current model design as narrow specialists optimized for static tasks, whereas clinical oncology requires generalist systems capable of integrating multimodal data, capturing disease evolution over time and considering patient perspectives. Design along these requirements is essential to integrating foundation models as trusted partners in cancer care.

Nature, Published online: 10 December 2025; doi:10.1038/d41586-025-03943-3

A growing body of research suggests tumours rely on proteins and genes that are unique to the nervous system to persist in the body.

arXiv:2512.05994v1 Announce Type: cross Abstract: With the rapid advancement of conversational and diffusion-based AI, there is a growing adoption of AI in educational services, ranging from grading and assessment tools to personalized learning systems that provide targeted support for students. However, this adaptability has yet to fully extend to the domain of children's speech, where existing models often fail due to their reliance on datasets designed for clear, articulate adult speech. Children, particularly those in early developmental stages or with speech and language pathologies, present unique challenges that current AI models and datasets are ill-equipped to handle. To address this, we introduce KidSpeak, a multi-task speech-enhanced Foundation Model capable of both generative and discriminative tasks specifically tailored to children's speech patterns. Our framework employs a two-stage training process that incorporates phonetic knowledge into the speech encoder, achieving an average accuracy of 87% across four separate tasks. Furthermore, recognizing the limitations of scalable human annotation and existing speech alignment tools, we propose the Flexible and Automatic Speech Aligner (FASA) and leverage the method to construct high quality datasets for training and evaluation. This novel alignment tool significantly improves the quality of aligned children's speech from noisy data, enhancing data quality by 13.6x compared to human annotations, as demonstrated on the CHILDES dataset. To the best of our knowledge, KidSpeak and FASA represent the first comprehensive solution designed for speech and language therapy in children, offering both a multi-purpose speech LLM and a robust alignment tool.

As digital health technologies become increasingly integrated into health care systems worldwide, there is growing recognition that their full potential can be realized only when development is rooted in patient engagement (PE). Despite its proven value in clinical research and health care delivery, PE remains insufficiently embedded in digital health design and implementation. This perspective paper explores the current state of PE in digital health through findings from the Stakeholder Expectations Matrix program developed by Patient Focused Medicines Development. Drawing from 37 in-depth interviews across 6 key stakeholder groups, complemented by insights gathered during a multisession cocreation track at the Patient Engagement Open Forum, this paper highlights differing perspectives on digital health, the barriers to meaningful engagement, and the fragmented nature of data governance and technology adoption. Findings point not only to significant gaps in shared understanding, infrastructure, and policy but also to clear opportunities for collaboration, including early recommendations for building a more inclusive and patient-centered digital health ecosystem, one that supports sustainable innovation, trust, and systemwide impact.