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01.
arXiv (CS.CV) 2026-06-24

MATCH: Flow Matching for Multi-View Anomaly Detection

Detecting anomalies in industrial objects is an important topic for increasing production efficiency. More complex objects often require the analysis of several view points, which has led to the field of multi-view anomaly detection. We present MATCH, the first multi-view anomaly detection method based on Flow Matching (FM). With the ODE formulation of Flow Matching, we can estimate likelihoods and thereby derive an anomaly score to detect anomalies in multi-view image data at object, image, and pixel-level. The architectural flexibility of FM models allows us to efficiently transform features of different spatial sizes to the normal distribution. We evaluate thoroughly on the already established Real-IAD data set and are also the first to provide a comprehensive evaluation of popular anomaly detection methods for the MANTA-Tiny data set. MATCH achieves state-of-the-art performance in both anomaly detection and segmentation, all while running on consumer-level hardware. By omitting the costly divergence term needed for likelihood estimation, we ensure that MATCH is usable in real-time production scenarios. Lastly, several ablation studies are conducted to validate the methodological choices.

02.
arXiv (CS.AI) 2026-06-18

Dynamic In-Group Persona Generation for Enhancing Human-AI Rapport

arXiv:2606.18256v1 Announce Type: cross Abstract: LLM-based chatbots are increasingly applied in interpersonal domains such as counseling and peer support, where establishing human-AI rapport is crucial yet remains challenging. In this work, we introduce a novel approach for conditioning LLMs with in-group personas, which (i) first identifies a user's primary concern and brief personal context (e.g., a computer science undergraduate worried about future career prospects), and (ii) generates a synthetic in-group persona that shares a similar primary concern while differing in background and narrative details, such as age or profession (e.g., a junior researcher at an AI startup). Furthermore, we conduct a human-subject study to systematically evaluate the effectiveness of in-group persona agents in enhancing human-AI rapport. We compare our approach against two baseline conditions: a conventional agent without persona conditioning and an agent exhibiting minimal self-disclosure (e.g., "I've felt that too"). Results from post-task questionnaires assessing rapport and user experience indicate that the in-group persona agent significantly improves perceived rapport and personal relevance compared to the baselines, and also yields more positive user experience-most notably higher engagement.

03.
arXiv (CS.LG) 2026-06-17

Sign-Rank, Index, and List Replicability: Connections and Separations

arXiv:2606.18236v1 Announce Type: new Abstract: In learning theory, the sign rank of a binary concept class captures the smallest dimension in which it can be represented by points and halfspaces. Despite tremendous interest, lower bounds on sign rank are notoriously difficult to come by. Two recent approaches to the problem establish lower bounds on sign rank by measures that are easier to analyze: the $\mathbb{Z}_2$-index and the list replicability number. We order these measures, showing that the $\mathbb{Z}_2$-index is upper-bounded by a linear function of the list replicability number. As a main consequence, we obtain a strong separation between sign rank and $\mathbb{Z}_2$-index, thereby resolving a question of Frick, Hosseini, and Vasileuski. This motivates a thorough study of list replicability, the stronger of the two lower-bounding measures. We establish upper bounds on the list replicability number by two combinatorial measures: height and minimum star number. We also prove a fundamental composition result, showing that the product of two concept classes has list replicability number bounded by the sum of the list replicability numbers of the two classes.

04.
arXiv (CS.CL) 2026-06-17

E2Vec: Feature Embedding with Temporal Information for Analyzing Student Actions in E-Book Systems

Digital textbook (e-book) systems record student interactions with textbooks as a sequence of events called EventStream data. In the past, researchers extracted meaningful features from EventStream, and utilized them as inputs for downstream tasks such as grade prediction and modeling of student behavior. Previous research evaluated models that mainly used statistical-based features derived from EventStream logs, such as the number of operation types or access frequencies. While these features are useful for providing certain insights, they lack temporal information that captures fine-grained differences in learning behaviors among different students. This study proposes E2Vec, a novel feature representation method based on word embeddings. The proposed method regards operation logs and their time intervals for each student as a string sequence of characters and generates a student vector of learning activity features that incorporates time information. We applied fastText to generate an embedding vector for each of 305 students in a dataset from two years of computer science courses. Then, we investigated the effectiveness of E2Vec in an at-risk detection task, demonstrating potential for generalizability and performance.

05.
arXiv (CS.CV) 2026-06-15

Morphology-Aware Sample Assignment: Overcoming IoU Insensitivity for Surface Defect Detection

Intersection-over-Union (IoU), as a pivotal metric for evaluating the spatial alignment between candidate proposals and ground-truth annotations, directly determines the quality of positive sample sets and the training efficacy of visual detection models. Through theoretical modeling and analysis, we uncover a non-sensitive region on the IoU response curve, within which samples yield nearly identical IoU scores despite distinct geometric overlaps. To overcome this limitation, we introduce a set of morphological similarity metrics covering area, shape, and aspect ratio, to refine the positive sample assignment process, thereby ensuring more discriminative and reliable matching. A supplementary matching score is derived via mean-based aggregation of these multidimensional similarities, compensating for the intrinsic limitation of IoU in representing structural correspondence. Theoretically, incorporating morphological similarity reshapes the response distribution of the matching function, yielding both effective directional gradients and polygon-like iso-response contours, which tightly confine high-response regions around each ground-truth instance and substantially enhance the precision of positive sample selection. Experiments based on the YOLOv9 framework demonstrate consistent performance gains on both NEUDET and GC10- DET datasets. Notably, the proposed approach is fully plug-and-play and incurs zero additional inference overhead, thereby ensuring deployment efficiency for industrial visual inspection.

06.
arXiv (quant-ph) 2026-06-19

Smooth time-dependent control of dipolar Bose-Einstein condensates

arXiv:2606.20507v1 Announce Type: cross Abstract: We consider protocols for control of dipolar Bose-Einstein condensates where the critical role is played by the long-range anisotropic interatomic magnetic dipole-dipole interaction. The phase diagram of such a condensate has been explored theoretically and experimentally with certain values of the interatomic scattering length corresponding to superfluid and supersolid phases, where supersolidity appears as a modulation in the ground state density. Preparation of this modulated ground state is challenging, since excitations appear as a result of a finite-time evolution required to produce qualitative changes in the wavefunction density. To solve this problem we consider the time-dependent control of a dipolar Bose-Einstein condensate using shortcuts to adiabaticity techniques, concentrating on design of the time-dependent scattering length, a parameter of the system easily tunable by contemporary experiments. The first technique is the variational approach based on the Euler-Lagrange equations for a separable ansatz describing the evolution of the superfluid state. Secondly, we study the transition from superfluid to supersolid using a direct optimization protocol. We discuss the fidelity of the developed protocols in terms of the evolution time.

07.
arXiv (CS.AI) 2026-06-12

EpiBench: Verifiable Evaluation of AI Agents on Epigenomics Analysis

arXiv:2606.13602v1 Announce Type: new Abstract: We introduce EpiBench, a verifiable benchmark for short-horizon epigenomics analysis. EpiBench evaluates whether agents can make well-defined analysis decisions from realistic workflow states and return deterministically gradable answers. The benchmark includes 106 evaluations across CUT\&Tag/CUT\&RUN, ATAC-seq, ChIP-seq, and DNA methylation workflows. Across 5,088 valid trajectories from 16 model-harness pairs, no system passed a majority of attempts: GPT-5.5 / Pi led at 45.0\% (143/318 attempts; 95\% confidence interval (CI), 36.3–53.7), followed by GPT-5.5 / OpenAI Codex at 39.9\% (127/318 attempts; 95\% CI, 31.6–48.3). Claude Opus 4.8 Max / Pi and GPT-5.4 / Pi each passed 39.0\% (124/318 attempts; 95\% CI, 30.2–47.8 and 31.0–47.0, respectively). Performance varies across assay types, and many failed runs still contain parts of the correct answer. Agents often found the right files and computed useful intermediate results, but failed when the task required deeper, assay-specific scientific judgment.

08.
arXiv (CS.AI) 2026-06-17

Cluster-Aware Dual-Level Test Specification Generation for Large-Scale Automotive Software Requirements

arXiv:2606.17197v1 Announce Type: cross Abstract: Generating test specifications that satisfy Automotive SPICE SWE.6 requirements becomes increasingly challenging and time-consuming as projects scale to thousands of requirements. Because this manual process often consumes weeks of engineering effort, automation becomes a critical necessity. However, standard Large Language Model (LLM) approaches struggle at scale: processing requirements individually discards vital inter-requirement dependencies, while feeding entire corpora at once exceeds context-window limits, leading to incomplete integration coverage and redundant test cases. This paper presents a novel "Cluster-then-Summarize" pipeline that addresses these limitations through three-stages. Requirements are embedded using sentence transformers and grouped using UMAP dimensionality reduction followed by HDBSCAN density-based clustering. This grouping utilizes an automatic minimum cluster size selection driven by a quality criterion combining normalized Silhouette and Calinski-Harabasz scores. A multi-level map-reduce summarization algorithm then distills each cluster into concise, domain-conformant descriptions while preserving quantitative thresholds and safety integrity levels. The pipeline exploits the derived cluster topology to generate test specifications at two levels: individual requirement verification and cluster-level integration tests that verify cross-requirement feature behavior. A nearby-cluster context mechanism provides bounded cross-feature awareness during each LLM call, and Retrieval-Augmented Generation grounds all outputs in ISO 26262 and ASPICE standards. Evaluation on automotive requirement datasets of varying scale demonstrates that the cluster-aware approach improves integration test coverage and maintains summarization fidelity compared to baseline methods while scaling efficiently to thousands of requirements.

09.
arXiv (CS.CV) 2026-06-15

MVAD: A Benchmark Dataset for Multimodal AI-Generated Video-Audio Detection

The rapid advancement of AI-generated multimodal video-audio content has raised significant concerns regarding information security and content authenticity. Existing synthetic video datasets predominantly focus on the visual modality alone, while the few incorporating audio are largely confined to facial deepfakes–a limitation that fails to address the expanding landscape of general multimodal AI-generated content and substantially impedes the development of trustworthy detection systems. To bridge this critical gap, we introduce the Multimodal Video-Audio Dataset (MVAD), the first comprehensive dataset specifically designed for detecting AI-generated multimodal video-audio content. Our dataset exhibits three key characteristics: (1) genuine multimodality with samples generated according to three realistic video-audio forgery patterns; (2) high perceptual quality achieved through diverse state-of-the-art generative models; and (3) comprehensive diversity spanning realistic and anime visual styles, four content categories (humans, animals, objects, and scenes), and four video-audio multimodal data types. Our dataset will be available at https://github.com/HuMengXue0104/MVAD.

10.
bioRxiv (Bioinfo) 2026-06-18

novelBGC: An interactive dual-score framework for biosynthetic gene cluster novelty assessment and candidate prioritisation

Genome mining now yields tens of thousands of putative biosynthetic gene clusters (BGCs) per project, yet, separating genuinely novel candidates from rediscoveries of known compounds remains the rate-limiting step before experimental validation. Single-axis prioritisation tools, antiSMASH similarity, BiG-FAM GCF distance, and self-resistance-enzyme (SRE) filters such as ARTS, each surface a different facet of evidence, yet their isolated use systematically over-ranks rediscovery-prone BGCs and overlooks genuinely orphan clusters. We present novelBGC, a web-hosted framework that converts these disparate outputs into two deliberately non-inverse continuous metrics per BGC, a Novelty (N) and a Reference Similarity (RS) score which together define a 2D decision plane that resolves rediscoveries, divergent family members, contig-edge artefacts, and uncharted chemistry with interactive visualisations, with all component weights user-tuneable at submission. Retrospective validation across three independent experimental datasets demonstrates the utility of the framework for candidate prioritization. Within the first 186-BGC SRE-guided cloning study, every confirmed bioactive product fell within the low-to-mid N band whereas 55 high-N (N [≥] 0.50) BGCs were never selected. Moreover, in the other two studies, it correctly prioritised the fully orphan lariocidin BGC of Paenibacillus sp. M2 and the divergent within-family indanopyrrole-A idp BGC of Streptomyces sp. CNX-425. Together, these case studies demonstrate that the joint (N, RS) space facilitates prioritization decisions that are difficult to achieve using any single criterion alone. from identical input data. novelBGC requires no command-line expertise, no local tool installation, and no manual integration of intermediate output formats, addressing a well-documented accessibility barrier for wet-laboratory researchers engaging with genome-mining workflows. novelBGC is freely available at https://project.iith.ac.in/sharmaglab/novelbgc/.

11.
arXiv (CS.LG) 2026-06-19

Statistical Properties of Training & Generalization

arXiv:2606.20299v1 Announce Type: cross Abstract: Deep learning has managed to evade numerous intuitions from classical statistics to achieve unprecedented performance on a number of real-world tasks. In this article, we investigate the key features and surprises of deep learning from a physics-informed perspective, taking care to point out and justify where possible the many choices inherent in constructing a deep learning model. In particular, we review the phenomenon of neural scaling laws and discuss their interplay with the constraints and inductive biases which may be present when applying machine learning to problems in physics.

12.
arXiv (quant-ph) 2026-06-24

Interaction-Enhanced Ergotropy in Phase-Driven Andreev Bound State Quantum Batteries

arXiv:2606.24456v1 Announce Type: new Abstract: We investigate a phase-driven quantum battery composed of two interacting Andreev bound state (ABS) units, providing a minimal superconducting platform for coherent energy storage. By analyzing the ergotropy dynamics under a superconducting phase ramp, we show that the interplay between avoided-crossing excitation and interaction-induced hybridization strongly modifies the charging process. In the high-transparency regime relevant for graphene SNS junctions, the interaction enhances the stored extractable work and generates pronounced oscillatory charging dynamics associated with coherent redistribution between coupled ABS sectors. The phase-resolved evolution further reveals optimal charging windows during the Josephson cycle, indicating the possibility of phase-programmable energy extraction through partial-cycle operation. Overall, our results identify interaction-assisted avoided-crossing dynamics as a microscopic mechanism for controllable energy storage in superconducting quantum batteries.

13.
arXiv (CS.AI) 2026-06-16

Revisiting Chebyshev Polynomial and Anisotropic RBF Models for Tabular Regression

arXiv:2602.22422v2 Announce Type: replace-cross Abstract: Smooth-basis models such as Chebyshev polynomial regressors and radial basis function (RBF) networks are well established in numerical analysis. Their continuously differentiable prediction surfaces suit surrogate optimisation, sensitivity analysis, and other settings where the response varies gradually with inputs. Despite these properties, smooth models seldom appear in tabular regression, where tree ensembles dominate. We ask whether they can compete, benchmarking models across 55 regression datasets organised by application domain. We develop an anisotropic RBF network with data-driven centre placement and gradient-based width optimisation, a ridge-regularised Chebyshev polynomial regressor, and a smooth-tree hybrid (Chebyshev model tree); all three are released as scikit-learn-compatible packages. We benchmark these against tree ensembles, a pre-trained transformer, and standard baselines, evaluating accuracy alongside generalisation behaviour. The transformer ranks first on accuracy across a majority of datasets, but its GPU dependence, inference latency, and dataset-size limits constrain deployment in the CPU-based settings common across applied science and industry. Among CPU-viable models, smooth models and tree ensembles are statistically tied on accuracy, but the former tend to exhibit tighter generalisation gaps. We recommend routinely including smooth-basis models in the candidate pool, particularly when downstream use benefits from tighter generalisation and gradually varying predictions.

15.
medRxiv (Medicine) 2026-06-15

Validating Field-Feasible Measures of Recent Khat Use: A Diagnostic Accuracy Study Comparing Amphetamine Immunoassay and Assisted Self-Report Against HPLC in an Ethiopian Male Cohort

Background: Khat (Catha edulis) is a widely consumed natural amphetamine-analog used across East Africa and the Arabian Peninsula. Accurate field-feasible measurement of recent khat use is a prerequisite for large-scale epidemiological research; yet no validated alternatives to laboratory reference methods have been identified in the scientific literature. This nested validation study evaluated the diagnostic accuracy of two point-of-care measures, a commercial amphetamine immunoassay and a Timeline Followback (TLFB) Assisted Self-Report (ASR), against high-performance liquid chromatography (HPLC) quantification of urinary norephedrine (NE), while additionally assessing agreement between the two field measures. Methods: A prospective, random sub-sample of 119 male participants aged 18-40 years from the Gilgel Gibe Field Research Center (GGFRC) longitudinal cohort, Ethiopia (validation timepoint T2, 2015), was used. Three index-reference comparisons were conducted: (1) amphetamine immunoassay (nal von minden, Drug-Screen AMP test, 300 ng/mL cutoff) vs. HPLC; (2) binary ASR (past-week use) vs. HPLC; and (3) binary ASR vs. immunoassay. Sensitivity (positive percent agreement, PPA), specificity (negative percent agreement, NPA), positive predictive value (PPV), negative predictive value (NPV), overall accuracy (overall percent agreement, OPA), and Cohen's kappa were calculated with 95% confidence intervals. Pre-specified secondary analyses applied three pharmacokinetically-informed recall windows (0-2, 3-5, and 6-7 days prior to interview) to ASR. Results: Against HPLC (77 positive, 42 negative), the immunoassay showed perfect specificity (1.0 [0.916-1.0]) and PPV (1.0 [0.91-1.0]) but low sensitivity (0.52 [0.40-0.64]), NPV (0.53 [0.42-0.65]), overall accuracy (0.69 [0.60-0.77]), and weak kappa (0.43 [0.34-0.52]). Binary ASR showed high sensitivity (0.96 [0.89-0.99]), specificity of 0.60 [0.433-0.74], PPV (0.81 [0.72-0.89]), NPV (0.89 [0.72-0.98]), with overall accuracy 0.83 [0.75-0.89] and moderate kappa (0.60 [0.51,0.69]). Restricting ASR to use within 0-2 days improved specificity to 0.69 [0.52-0.84], PPV to 0.86 [0.77-0.93], overall accuracy to 0.87 [0.79-0.93], and kappa to 0.69 [0.61-0.78] (moderate), while sensitivity (0.96 [0.89-0.99]) and NPV (0.89 [0.72-0.98]) remained stable. Against the immunoassay, ASR achieved high PPA of (1.0 [0.91-1.0]), NPA of 0.35 [0.25-0.47], OPA of 0.57 [0.48-0.66], and minimal kappa (0.27 [0.19-0.35]). Conclusions: Time-stratified ASR (0-2 days) is a valid, scalable alternative to biological testing for recent khat use in resource-limited settings. The immunoassay's 300 ng/mL cutoff functions as a marker of heavy or recent high-dose khat use rather than any-use detection. Its perfect specificity and PPV make it valuable as a confirmatory test for substantial exposure, while its lower sensitivity reflects calibration to amphetamine rather than to khat-derived cathinone metabolite. Keywords: khat; Catha edulis; diagnostic accuracy; STARD; self-report; immunoassay; HPLC; Ethiopia; substance use measurement

16.
arXiv (CS.LG) 2026-06-15

LoMC: Localized Multidirectional Correction for Refusal Suppression in Routed Foundation Models

arXiv:2606.13709v1 Announce Type: cross Abstract: We study controlled post-training refusal suppression in routed MoE and hybrid-MoE foundation models, aiming to increase non-refusal target-response behavior while preserving general capability under a compact intervention footprint. Existing broad direction-based edits can perturb general-purpose computation, whereas support-only expert edits often lack sufficient capacity to correct heterogeneous refusal representations. To address this limitation, we introduce Localized Multidirectional Correction (LoMC), a support-gated intervention framework that follows a support-then-correction execution order: it first identifies a compact edit support, then aggregates prototype correction directions into layer-wise correction directions, and finally applies rank-one layer-wise correction only within the selected support. By using the edit support as a structural gating constraint, LoMC increases correction capacity without expanding the intervention scope. Experiments on text-only and multimodal safety benchmarks across four routed backbones show that LoMC substantially improves non-refusal target-response behavior while maintaining general capability under a compact intervention footprint.

17.
medRxiv (Medicine) 2026-06-22

Virtual Responsive Neurostimulation Implantation: From Intracranial Connectivity to Optimized Lead Placement

Responsive neurostimulation (RNS) is an implanted device that delivers direct brain stimulation for drug-resistant focal epilepsy. Individual responses are highly variable, and no validated framework exists to predict outcome or guide lead placement before implantation. We hypothesized that this variability is partly explained by lead placement in relation to patterns of functional connectivity in brain networks. Fourty-nine patients with drug-resistant focal epilepsy who underwent pre-implantation intracranial EEG (iEEG) and RNS implantation across three independent epilepsy centers were retrospectively studied. We developed a composite functional connectivity score, based on simple Spearman correlation, combining the standard deviation and kurtosis of interictal iEEG connectivity distributions to predict the response outcome in a training cohort (HUP, n=18) and validated in two independent cohorts (NYU, n=17; UCSF, n=14). We accounted for a spatial mismatch between iEEG and RNS electrodes with a distance-based correction. The score was extended to generate patient-specific 3D maps of predicted RNS efficacy across 200 simulated, or virtual RNS, lead configurations. Accuracy of the score in predicting clinical outcome was 72% at the group level, 61% at the individual patient level, and, after distance-based optimization, 100% in patients with RNS electrodes placed close to location of iEEG electrodes. Applied to the validation cohort, the same score reached 68% accuracy (71% balanced accuracy, 55% sensitivity, 88% specificity). The spatial combination of the scores at different SEEG contacts localization gives a spatial score for each patient. Responders showed significantly higher spatial scores than non-responders, supporting that actual RNS lead placement in responders was located in map-identified favorable regions. Interictal iEEG functional connectivity predicts individual RNS response across independent epilepsy centers, and patient-specific 3D maps derived from this biomarker could prospectively guide lead implantation toward favorable network regions, opening a promising avenue toward network-informed RNS surgical planning.

18.
arXiv (CS.AI) 2026-06-18

Engagement Intensity as a Learner-Modeling Signal for Adaptive AI Ethics Instruction

arXiv:2606.18548v1 Announce Type: cross Abstract: Adaptive AI ethics instruction in graduate research training benefits from intake measures that reflect differences in prior LLM experience. Prior coursework or workshop attendance is an obvious candidate, but it is not clear whether it is associated with pre-instruction ratings on key AI perception items. We compare three candidate intake features, self-reported usage frequency, self-rated LLM familiarity, and prior AI education, across five baseline perception outcomes in 93 bioscience graduate and postdoctoral trainees enrolled in a required research ethics course. Usage frequency shows Holm-corrected associations with all five outcomes, self-rated familiarity with three, and prior AI education with none. A threshold-like pattern at the lower end of the scale is most visible for training interest and accuracy trust rather than appearing as a uniform gradient across all five outcomes. In a short intake survey, reported LLM use is more consistently associated with these perceptions than prior coursework or workshops, with self-rated familiarity serving as a secondary indicator. These results suggest that simple pre-instruction behavioral signals can inform lightweight intake profiling for adaptive AI ethics education.

19.
arXiv (CS.CV) 2026-06-19

iSAGE: A Human-in-the-Loop Framework for Remote Sensing Semantic Segmentation via Sparse Point Supervision

Semantic segmentation in remote sensing requires costly pixel-level annotations, and nearly every problem demands a new dataset since models rarely transfer across sensors, platforms, or geographies. Existing human-in-the-loop frameworks expand sparse clicks into dense supervision via auxiliary machinery (pseudo-labels, propagation, CRFs, foundation-model prompts, auxiliary heads), all operating on the model's predictive distribution. A confidently wrong pixel is indistinguishable from a confidently correct one in that distribution by construction, so no rule reading it can separate the two; the distinguishing signal is external to the model. This paper hypothesizes that expert clicks targeting confident model errors, not arbitrary pixels, suffice to match dense supervision, with no expansion machinery. iSAGE (Iterative Sparse Annotation Guided by Expert) realizes this hypothesis on an integrated open-source platform, where an error-weighted loss amplifies the gradient at each click and the annotation record itself is the dataset, extensible, correctable, and auditable. Experiments use a minimum-effort regime: at most one labeled pixel per class per frame. On BsB Aerial, iSAGE recovers 97.2% of dense supervision (74.79% mIoU on 0.040% of pixels) with contrasting class dynamics: amorphous classes (permeable areas) saturate from the seed, while small classes (cars) require late-iteration effort. On ISPRS Vaihingen (external benchmark), iSAGE reaches 76.78% mIoU with 0.011% of pixels, matching the dense baseline (76.65%) and exceeding all published methods. Under the same pipeline, four output-reading mechanisms (oracle entropy across budgets 1–100x, pseudo-labels across thresholds 0.90–0.99, CRF-based propagation, uniform random) plateau 7.4 to 14.5 pp below iSAGE. Across 31 surveyed methods, iSAGE is the only iterative human-in-the-loop framework operating without auxiliary machinery.

21.
bioRxiv (Bioinfo) 2026-06-21

Machine learning evaluation of gene expression-based ALS subtypes across brain and blood tissues

The clinical and molecular heterogeneity observed in amyotrophic lateral sclerosis (ALS) presents a challenge for diagnosis, prognosis, and treatment. RNA sequencing of post-mortem brain samples from ALS patients has identified several subtypes with distinct molecular signatures. We sought to evaluate these subtypes across diverse tissues and datasets and assess the feasibility of supervised machine learning models for sample classification. Unsupervised clustering and pathway analysis were performed to confirm the presence of ALS subtypes in motor cortex samples. Three machine learning strategies were then used to create models based on post-mortem motor cortex expression data of 112 people with ALS from the London Neurodegenerative Diseases Brain Bank. These models were subsequently improved through feature selection and evaluated in independent cohorts from motor cortex (n = 257, NYGC ALS Consortium) and blood (n = 96, Macquarie University Neurodegenerative Disease Biobank) samples. Multi-class linear discriminant analysis (LDA) models were then used for subtype classification. Clustering of ALS post-mortem motor cortex samples confirmed the presence of three subtypes: neuroinflammation (ALS-Neu), extracellular matrix organisation and muscle contraction (ALS-OxA), and synaptic and neuropeptide signalling (ALS-SNs). Among all machine learning strategies, random forests produced the most accurate and stable models for binary classification (~93% accuracy across the three subtypes). After feature selection, random forest models were able to classify samples from an independent post-mortem motor cortex cohort in their respective subtypes (AUC of ~0.98 across the three subtypes). When these models were evaluated in blood using LDA, we found consistent clustering patterns, with samples aligning in the same subtype regions of the post-mortem motor cortex samples, with ALS-SNs being the subtype in which samples were classified with the highest confidence (LDA class probability ~86%). Moreover, classification for this subtype improved when blood samples were collected closer to death. Our findings support the presence of three gene expression-based ALS subtypes in motor cortex samples and the utility of machine learning strategies for subtype classification. We also observed that the subtypes identified in the brain partially match those in the blood, with samples from the late stages of the disease more likely to be correctly predicted into the ALS-SNs cluster. This suggests a longitudinal effect in subtype identification that requires further investigation.

22.
arXiv (CS.AI) 2026-06-16

Early Diagnosis of Wasted Computation in Multi-Agent LLM Systems via Failure-Aware Observability

arXiv:2606.01365v2 Announce Type: replace Abstract: Failure-aware observability diagnoses wasted computation in multi-agent LLM systems before final-answer evaluation can explain what went wrong. We propose a trace-based framework for a three-agent architecture – orchestrator, search agent, and execution agent – that converts structured events into online signals for loops, budget pressure, low information gain, and tool instability, then adds offline semantic grounding metrics and selective LLM-as-judge evaluation. On 165 GAIA validation traces under identical caps, 98 runs produce usable final answers and 67 fail or stop without one. Among warned failed runs, 58.1% of tokens are spent after the first warning on average, indicating substantial opportunity for intervention. A 10-task Level-2 pilot uses warnings to diversify search or require evidence, reducing post-warning token fraction from 0.638 in the baseline to 0.304. The results support a layered design: cheap online signals help the orchestrator redirect or halt redundant behavior, while deeper semantic checks identify whether completed answers are grounded enough to trust.

23.
arXiv (CS.CV) 2026-06-16

No One Knows the State of the Art in Geospatial Foundation Models

Geospatial foundation models (GFMs) have been proposed as generalizable backbones for disaster response, land-cover mapping, food-security monitoring, and other high-stakes Earth-observation tasks. Yet the published work about these models does not give reviewers or users enough information to tell which model fits a given task. We argue that nobody knows what the current state of the art is in geospatial foundation models. The methods may be useful, but the GFM literature does not standardize evaluations, training and testing protocols, released weights, or pretraining controls well enough for anyone to compare or rank them. In a 152-paper audit, we find 46 cross-paper disagreements of at least 10 points for the same model, benchmark, and protocol; 94/126 papers with extractable pretraining data use a configuration no other paper uses; and 39% of GFM papers release no model weights. This lack of community standards can be solved. We propose six concrete expectations: named-license weight release, shared core evaluations, copied-versus-rerun baseline annotations, variance reporting, one shared evaluation harness, and data-vs-architecture-vs-algorithm controls. These gaps are a coordination failure, not a fault of any individual lab; the authors of this paper, like many others in the GFM community, have contributed to them. Rather than just critiquing the community, we aim to provide concrete steps toward a shared understanding of how to innovate GFMs.

24.
arXiv (CS.AI) 2026-06-24

GUI vs. CLI: Execution Bottlenecks in Screen-Only and Skill-Mediated Computer-Use Agents

arXiv:2606.24551v1 Announce Type: new Abstract: Computer-use agents can execute software tasks through either graphical interfaces or programmatic command interfaces, but existing evaluations confound interaction modality with differences in tasks, initial states, verifiers, and permitted actions. We introduce a matched execution-layer benchmark of 440 desktop tasks across 18 applications and 12 workflow categories, where screen-only GUI agents and skill-mediated CLI agents receive identical goals, states, and final-state verifiers while being restricted to modality-native actions. In this controlled setting, the strongest GUI agent reaches a 59.1% full pass rate, outperforming the strongest original-skill CLI agent at 48.2%; however, verifier-guided skill augmentation raises CLI success to 69.3%, showing that much of the CLI deficit comes from incomplete skill coverage rather than model capability alone. These results suggest that GUI and CLI expose different execution bottlenecks: GUI agents are limited by reliable grounded interaction over long-horizon workflows, whereas CLI agents are limited by the coverage and scalability of their skill interfaces.

25.
PLOS Computational Biology 2026-06-08

Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings

by Julia Pilarski, Tanja Stadler, Sophie Seidel Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters – cell division, differentiation, and death rates – from this tracking data remains challenging and needs to be systematically evaluated. We perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvements as the recorder capacity increases. We observe more accurate phylogenetic reconstruction from sequential compared to random recordings, but no substantial improvement in phylodynamic inference when using the additional information contained in the order of edits. Overall, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division when appropriate models are used. However, we detect biases in the inferred rates of cell division and death under phylodynamic model misspecification, i.e., when fitting classic memoryless birth-death processes to synchronous cell divisions. Moreover, for scenarios when cells differentiate into distinct types, we demonstrate that Bayesian phylodynamic analysis of sparse end-point measurements can resolve these cell differentiation trajectories by lineage and time. Under prototypical dynamics, we recover cell type-specific division and death rates, and cell type transition rates in over 80% of simulations. Overall, this simulation study explores how much information on cellular development can be extracted from state-of-the-art genetic lineage tracing data using phylogenetic and phylodynamic methodology.