Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

01.
arXiv (CS.LG) 2026-06-15

Machine Learning for Biomedical Raman Spectroscopy: From Spectral Acquisition to Clinical Translation

arXiv:2606.14169v1 Announce Type: new Abstract: Raman spectroscopy provides label-free, chemically specific characterization of biological systems and has become an important tool for cancer diagnosis, molecular subtyping, microbiological identification, and intraoperative decision support. Biomedical Raman spectra are, however, high-dimensional, noisy, and affected by fluorescence background, acquisition variability, and biological heterogeneity, making robust computational analysis essential. This review examines the role of machine learning across the biomedical Raman spectroscopy pipeline, from preprocessing and signal correction to unsupervised structure discovery, supervised diagnosis and molecular stratification, representation and transfer learning, explainability, biomarker discovery, and multimodal integration with imaging, pathology, and molecular profiling. Emphasis is placed on the use of machine learning not only for diagnostic classification, but also for biologically interpretable and clinically actionable analysis. We also discuss the main barriers to clinical translation, including limited dataset sizes, inter-instrument variability, inconsistent preprocessing, insufficient external validation, reproducibility concerns, and limited sharing of software, data, and metadata. We argue that progress will require methodological advances together with standardization, robust validation, explainability, and deployment-ready analytical frameworks. By integrating methodological, biomedical, and translational perspectives, this review outlines key directions for developing reliable and clinically deployable Raman-AI systems.

02.
arXiv (CS.CL) 2026-06-19

Apparent Psychological Profiles of Large Language Models are Largely a Measurement Artifact

Psychological instruments designed for humans are increasingly used to assign large language models (LLMs) stable psychological profiles that affect their usability, safety assessment, and use as proxies for human participants in research. Using a formal psychometric framework, we show that these profiles are largely a measurement artifact. Administering a battery of personality and risk-preference instruments spanning self-reports and behavioral tasks to 56 instruction-tuned LLMs alongside large human reference samples, we report four findings. First, differences between models are driven not by the traits an instrument targets but by a directional response bias, a tendency to respond toward one end of the scale, or one labeled option, regardless of item content; a variance decomposition attributes 81-90% of between-model variation to this bias, against 9-16% in humans. Second, the bias declines with model capability but is not eliminated by it. Third, because bias rather than trait drives responding, an instrument's apparent reliability is almost entirely predicted by its response orthogonality, a term we coin for the proportion of items for which trait and bias point in opposite directions. Fourth, the profile a model appears to have shifts with the items used and can be manufactured through item selection. These results demonstrate that the apparent psychological profiles of LLMs are artifacts of the instrument used to measure them, not properties of the models themselves. As instruments borrowed from human psychology are rarely fully orthogonal and may inherently lack validity for LLMs, we call for dedicated assessments centered on response orthogonality.

03.
medRxiv (Medicine) 2026-06-10

Prediction of immunotherapy response using live tumor fragments from routine clinical biopsies

Functional ex vivo assays using live tumor tissues have demonstrated strong predictive accuracy for response to immune checkpoint inhibitors (ICIs) but are not scalable, requiring manual processing of large resections collected at academic centers. Here, an ex vivo live tumor fragment (LTF) platform was developed using standard-of-care biopsies from 228 patients with suspected malignancy collected across prospective, multicenter observational trials and biobanks. Hierarchical clustering of ICI-mediated changes in cytokine production identified two groups: responders and nonresponders. A binary classifier (elive index) using 8 cytokines achieved an AUC of 0.99 for cluster prediction. elive index correctly predicted clinical benefit in 93% (26/28) of patients (P = 3.2x10-5) and accurately identified 83% (10/12) of objective responders. Critically, elive responders were identified among biomarker-negative patients, highlighting the platform as a scalable approach that complements existing companion diagnostics and expands the population of patients identified to benefit from ICI therapy.

04.
arXiv (CS.LG) 2026-06-15

Deep Learning and Elicitability for McKean-Vlasov FBSDEs With Common Noise

arXiv:2512.14967v2 Announce Type: replace Abstract: We present a novel numerical method for solving McKean–Vlasov forward–backward stochastic differential equations (MV–FBSDEs) with common noise, combining Picard iterations, elicitability and deep learning. The key innovation involves elicitability to derive a pathwise loss function, enabling efficient training of neural networks to approximate both the backward process and the conditional expectations arising from common noise, without requiring computationally expensive nested Monte Carlo simulations. The mean-field interaction term is parameterized via a recurrent neural network trained to minimize an elicitable score, while the backward process is approximated through a hybrid feedforward and recurrent network representing the decoupling field. We validate the algorithm on a systemic-risk inter-bank borrowing and lending model, where analytical solutions exist, demonstrating accurate recovery of the true solution. We further extend the model to quantile-mediated interactions, showcasing the flexibility of the elicitability framework beyond conditional means or moments. Finally, we apply the method to a non-stationary Aiyagari–Bewley–Huggett economic growth model with endogenous interest rates, illustrating its applicability to complex mean-field games without closed-form solutions.

05.
arXiv (CS.AI) 2026-06-16

AgentLeak: A Benchmark for Internal-Channel Privacy Leakage in Multi-Agent LLM Systems

arXiv:2602.11510v3 Announce Type: replace Abstract: Multi-agent Large Language Model (LLM) systems create privacy risks that current output-only benchmarks cannot measure. When agents coordinate on tasks, sensitive data may pass through inter-agent messages, shared memory, and tool arguments, all pathways that final-output audits typically do not inspect. We introduce AgentLeak, a benchmark for evaluating internal-channel privacy leakage in multi-agent LLM systems. AgentLeak instruments seven privacy-relevant communication pathways and provides a large-scale empirical evaluation focused on final outputs, inter-agent messages, and shared memory. Across 1,000 scenarios spanning healthcare, finance, legal, and corporate domains, five production LLMs (GPT-4o, GPT-4o-mini, Claude 3.5 Sonnet, Mistral Large, and Llama 3.3 70B), and 4,979 validated execution traces, we find that multi-agent configurations reduce final-output leakage (C1: 27.2% vs 43.2% in single-agent mode) compared with single-agent baselines but introduce internal channels that raise total system exposure to 68.9% (aggregated across C1, C2, C5). Inter-agent messages (C2) leak at 68.8%, compared with 27.2% for final outputs (C1), meaning that output-only audits miss 41.7% of violations. Across all five models and four domains, the pattern C2 $\geq$ C1 holds consistently. These results suggest, within the evaluated coordinator-worker setting, that privacy risk in multi-agent systems is strongly shaped by architectural coordination channels rather than final-output behavior alone: it arises from internal channels that remain invisible to standard output-level defenses.

06.
arXiv (CS.CV) 2026-06-11

MB-Loc: Multi-planar Bird's-eye-view Localization in outdoor LiDAR scenes

Global LiDAR localization is a fundamental task for autonomous navigation systems. Recent methods perform Scene Coordinate Regression (SCR) and achieve superior accuracy over Absolute Pose Regression (APR) solutions by predicting dense 3D world coordinates. However, SCR approaches introduce two major bottlenecks: severe computational inefficiency from processing raw 3D geometries and significant performance degradation under varying sensor viewpoints. To address these limitations, we present MB-Loc, a lightweight and viewpoint-robust SCR framework. Instead of relying on heavy 3D convolutions, we project the input LiDAR scan into a 2.5D Multi-planar Bird's-Eye View (BEV) representation. By slicing the point-cloud along the Z-axis and mapping signed depths into discrete 2D planes, MB-Loc retains essential 3D geometric structures while exploiting the computational tractability of standard 2D CNNs. To handle the inherent sparsity of outdoor LiDAR, we introduce a KL-regularized latent bottleneck that explicitly models spatial uncertainty without injecting stochastic noise. Finally, to ensure rotation robustness, we apply 3D spatial augmentations prior to planar projection, forcing the network to implicitly learn viewpoint-invariant features. We perform extensive experiments on the publicly available NCLT dataset and demonstrate that our proposed method outperforms the current state-of-the-art. Operating at real-time inference speeds, MB-Loc significantly outperforms traditional 3D-SCR architectures in computational efficiency.

07.
arXiv (CS.AI) 2026-06-11

Sovereign Assurance Boundary: Certificate-Bound Admission for Agentic Infrastructure

arXiv:2606.11632v1 Announce Type: cross Abstract: Agentic infrastructure introduces a critical control-plane authorization problem: non-deterministic reasoning systems can propose high-stakes mutations to production resources, yet existing security mechanisms – such as identity and access management (IAM), policy engines, consensus protocols, and audit logs – either enforce static, context-unaware permissions or merely record actions post-execution. This paper introduces the Sovereign Assurance Boundary (SAB), a certificate-bound runtime admission layer for autonomous execution authority. SAB intercepts agent proposals at an assurance airlock, compiles them into typed execution contracts $C$, and binds these contracts to cryptographic evidence digests $H(E)$ and policy versions. The contracts are then routed through consequence-aware certification paths. Upon successful admission, the system emits a signed Sovereign Assurance Certificate ($\Omega$) that is strictly scoped to a specific execution identity, revocation epoch, and validity window. Finally, a sovereign execution broker verifies $\Omega$ and performs fresh pre-execution revocation and drift checks before invoking infrastructure APIs. We detail the airlock-broker architecture, formalize its admission and revocation invariants, and report preliminary feasibility measurements from a Go prototype evaluated over 2,500 admission attempts. Ultimately, this broker-enforced model prevents autonomous reasoning from directly mutating state, transforming delegated execution authority into a cryptographically verifiable, evidence-bound, revocable, and replayable runtime artifact.

08.
arXiv (CS.CV) 2026-06-15

ZipSplat: Fewer Gaussians, Better Splats

Feed-forward 3D Gaussian Splatting methods reconstruct a scene from posed or pose-free images in a single forward pass, yet current approaches predict one Gaussian per input pixel, tying the representation budget to camera resolution rather than scene complexity. A flat wall and a richly textured object thus produce equally many Gaussians despite very different geometric needs. We propose ZipSplat, a token-based feed-forward model that decouples Gaussian placement from the pixel grid. A multi-view backbone extracts dense visual tokens, and k-means clustering compresses them into a compact set of scene tokens. Cross- and self-attention refine these tokens, and a lightweight MLP decodes each into a group of Gaussians with unconstrained 3D positions. Because clustering is applied at inference, a single trained model spans the quality-efficiency curve without retraining. ZipSplat operates without ground-truth poses or intrinsics, yet sets a new state of the art on DL3DV and RealEstate10K with ${\sim}6{\times}$ fewer Gaussians than pixel-aligned methods, surpassing the best pose-free baseline by 2.1dB and 1.2dB PSNR, respectively. It further generalizes zero-shot to Mip-NeRF360 and ScanNet++, outperforming all comparable baselines. Our project page is at https://veichta.com/zipsplat.

09.
arXiv (CS.CV) 2026-06-16

Uncertainty Quality of VGGT: An Analysis on the DTU Benchmark Dataset

Visual Geometry Grounded Transformer (VGGT) has already attracted a great deal of attention in a short period of time, not least due to the Best Paper Award at CVPR-2025. Similar to DUSt3R and MASt3R, VGGT aims to bring about a paradigm shift by replacing established methods like bundle adjustment and feature matching with a simple, unified, feed-forward neural network that predicts camera poses, depth maps, and dense 3D structure directly from multiple images of a scene in a few seconds. A key aspect is its ability to process an arbitrary number of views consistently in a single forward pass without any post-processing or iterative optimization. For photogrammetry, this opens new possibilities for real-time, scalable, and accessible 3D reconstruction. In this context, not only high reconstruction accuracy but also high-quality uncertainty estimates are crucial, as they foster trust and enable robust quality assurance. This paper therefore investigates the quality of VGGT's uncertainty predictions. The analysis identifies an effective confidence threshold for filtering VGGT's raw output and demonstrates that enhancing uncertainty quality holds strong potential for improving the accuracy of its 3D reconstructions.

10.
arXiv (CS.AI) 2026-06-18

QSignAI: Quantum-Randomness-Seeded Identity Signatures at the Intersection of AI for Science and Science for AI

arXiv:2605.27729v2 Announce Type: cross Abstract: The 2024-2025 Nobel and Turing awards recognised AI and quantum science simultaneously. Yet no deployed system has brought these streams together for the public. This paper presents QSignAI, a production-deployed platform demonstrating a bidirectional AI-quantum relationship in a real-time event participation system. We address three questions: can quantum-randomness generation via a two-source extractor be embedded in an AI-driven social platform with acceptable latency; can an AI bot make quantum phenomena perceptually legible to general audiences; and does the combined system work in practice? A conversational bot routes each participant's first message through a quantum pipeline comprising a Toeplitz two-source extractor over independent single-qubit Hadamard measurements on SV1 and DM1 simulators, plus a 2-qubit Bell state, producing a unique quantum-randomness-seeded identity signature per participant. The first two questions are answered through system architecture and qualitative deployment evidence from live events; the third through successful production deployment. The current deployment uses cloud quantum simulators; physical QPU randomness is the near-term extension. Measurable benchmarks are identified as priority future work.

11.
arXiv (CS.LG) 2026-06-18

A Cross-Model VLM-Judge Protocol for Single-Image 3D Mesh Quality (and Why Cheap Proxies Fall Short)

arXiv:2606.18451v1 Announce Type: new Abstract: Single-image-to-3D generators are improving quickly, but there is no agreed, human-free way to tell whether one generated mesh is better than another. Practitioners commonly rely on cheap automatic proxies (render-space CLIP similarity and mesh geometry-validity statistics), yet how well these track perceived quality is unestablished. We make two contributions. First, we propose and validate a reproducible VLM-judge evaluation protocol: a fixed 24-view headless render rig, two independent vision-language judge families, and a mandatory position-bias correction that queries both presentation orders and keeps only order-consistent verdicts. The two judge families agree substantially with each other (Cohen's kappa = 0.66), well above the chance-agreement floor. Second, using this protocol as the reference, we show the cheap proxies do not substitute for it. Geometry validity is only a weak signal on average (because, as we show, it is bimodal) and stays below our pre-registered target, while render-CLIP is at chance. A learned Bradley-Terry head collapses onto a single manifoldness statistic (giving render-CLIP a negative weight) and matches geometry-only exactly, so learning the feature weights buys nothing. The proxy is also bimodal: it is significantly above chance on contrasts with visible geometric defects but at chance on ambiguous contrasts, consistent with geometry validity tracking the judge only when the defect is visually salient. We therefore recommend the VLM-judge protocol as a reliable, reproducible evaluator under the conditions tested (two feed-forward generators on Google Scanned Objects, with a face-drop degradation regime) and advise against geometry/CLIP proxies as optimization targets.

12.
arXiv (CS.AI) 2026-06-19

CareTransition-Audit: A Benchmark to Audit Discharge Summaries for Efficient Care Transitions

arXiv:2604.05435v2 Announce Type: replace Abstract: Incomplete or inconsistent discharge documentation drives care fragmentation and avoidable readmissions. Despite its critical role in patient safety, auditing discharge summaries relies on manual review and does not scale. We propose an automated framework for auditing discharge summaries using large language models (LLMs). Our approach operationalizes the DISCHARGED framework into a checklist of 46 questions. Using 50 summaries from the MIMIC-IV database, with clinician ground-truth labels, we benchmark 11 LLMs. Model-assessed mean documentation completeness ranges from 54.9% to 74.2%, and the best-performing models achieve a Cohen's kappa values around 0.5 against clinician labels, indicating moderate agreement. All models struggle to identify ambiguous documentation (Unclear), highlighting a key gap in current automated auditing. This work provides a clinician-validated benchmark and zero-shot baselines for systematic quality improvement in clinical documentation.

13.
arXiv (CS.AI) 2026-06-15

FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

arXiv:2602.22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice. While novel architectures constantly claim state-of-the-art performance, inconsistent metadata conditioning and entangled preprocessing pipelines hinder fair architectural comparisons. Besides, existing evaluations are often restricted to curated datasets, failing to capture the heterogeneity and cross-domain shifts of real-world metabolomics. Furthermore, current benchmarks lack difficulty-aware diagnostics and leave blind to how models behave under specific compute or data constraints. To address this, we present FlexMS, a modular public-data benchmark framework that standardizes MS/MS prediction across public resources while keeping molecular encoders, metadata conditioning, predictor heads, and downstream retrieval under one protocol. FlexMS establishes a fair evaluation playground which significantly lowers the barrier for integrating new predictive tools. Rather than solely optimizing for average scores, FlexMS augments aggregate accuracy with difficulty-aware diagnostics, providing actionable guidance on model selection across different compute constraints, data scales, and downstream retrieval objectives. Ultimately, FlexMS provides the community with a reproducible standard to identify which algorithmic conclusions are stable and which operating points are most viable in practice.

14.
bioRxiv (Bioinfo) 2026-06-18

Calculation of sequence space coverage in a mutagenesis library

Directed evolution requires screening of large mutagenesis libraries, but accurate calculation of library sizes needed to discover functional variants remains challenging. Existing models provide baseline estimates, yet current computational approaches for finding the best variants scale poorly with library complexity. Here, we introduce a scalable algorithmic framework to compute exact discovery probabilities in saturation mutagenesis libraries with no requirement for explicit sequence enumeration. By aggregating variants into a composition log–sum distribution and applying log-space convolution across randomisation blocks, it is possible to extend this to massive sequence spaces and mixed codon schemes. By inverting these calculations, absolute mathematical ceilings for experimental design are established. Ultimately, this framework provides a rapid, quantitative tool to balance the statistical coverage-diversity trade-off within the limitations of laboratory screening. Finally, this is implemented as an open-source web application (SSCC) that allows researchers to construct heterogeneous library designs and compute required sampling depths, coverage probabilities, and absolute randomisation limits.

15.
arXiv (CS.CL) 2026-06-12

DSAEval: Evaluating Data Science Agents on a Wide Range of Real-World Data Science Problems

Recent LLM-based data agents aim to automate data science tasks ranging from data analysis to deep learning. However, the open-ended nature of real-world data science problems, which often span multiple taxonomies and lack standard answers, poses a significant challenge for evaluation. To address this, we introduce DSAEval, a benchmark comprising 641 real-world data science problems grounded in 285 diverse datasets, covering both structured and unstructured data (e.g., image and text). DSAEval incorporates three distinctive features: (1) Multimodal Environment Perception, which enables agents to interpret observations from multiple modalities, including text and vision; (2) Multi-Query Interactions, which mirror the iterative and cumulative nature of real-world data science projects; and (3) Multi-Dimensional Evaluation, which provides a holistic assessment across reasoning, code, and results. We systematically evaluate 13 recent advanced agentic LLMs using DSAEval. Our results show that Claude-Sonnet-4.5 achieves the strongest overall performance, MiMo-V2-Pro and GPT-5.2 lead in duration and step efficiency, respectively, and MiMo-V2-Flash is the most cost-effective. We further demonstrate that multimodal perception consistently improves performance on vision-related tasks, with gains ranging from 2.04\% to 11.30\%. Overall, while current data science agents perform well on structured data and routine data analysis workflows, substantial challenges remain in unstructured domains. Finally, we offer critical insights and outline future research directions.

16.
arXiv (CS.AI) 2026-06-18

TxBench-PP: Analyzing AI Agent Performance on Small-Molecule Preclinical Pharmacology

arXiv:2606.19245v1 Announce Type: new Abstract: Artificial intelligence (AI) agents promise to accelerate drug discovery by compressing interpretation and decision-making loops, but practical deployment requires trusted evaluation on realistic program decisions. We introduce TherapeuticsBench Preclinical Pharmacology (TxBench-PP), a verifiable benchmark for small-molecule preclinical pharmacology and the first focused slice of a broader TherapeuticsBench effort across drug-discovery stages and therapeutic modalities. TxBench-PP tests whether agents can recover accurate conclusions from real-world assay data rather than memorized facts from literature. The benchmark contains 100 evaluations indexed by program stage, assay type, and task structure, spanning mechanism-of-action (MoA) and pharmacodynamic (PD) reasoning, compound-target engagement, causal target validation, developability and safety, and translational efficacy. Agents receive realistic workflow snapshots, inspect files in a coding environment, and return structured answers graded deterministically. Across 16 model-harness configurations, comprising 11 models and 4,800 trajectories, no system reliably recovered preclinical pharmacology decisions. The strongest configuration, Claude Opus 4.8 / Pi, passed 59.3\% of endpoint attempts (178/300; 95\% CI, 51.1-67.6), followed by GPT-5.5 / Pi at 55.3\% (166/300; 47.0-63.6).

17.
arXiv (CS.AI) 2026-06-18

An In-depth Study of LLM Contributions to the Bin Packing Problem

arXiv:2510.27353v2 Announce Type: replace Abstract: Recent studies have suggested that Large Language Models (LLMs) could provide interesting ideas contributing to mathematical discovery. This claim was motivated by reports that LLM-based genetic algorithms produced heuristics offering new insights into the online bin packing problem under uniform and Weibull distributions. In this work, we reassess this claim through a detailed analysis of the heuristics produced by LLMs, examining both their behavior and interpretability. Despite being human-readable, these heuristics remain largely opaque even to domain experts. Building on this analysis, we propose a new class of algorithms tailored to these specific bin packing instances. The derived algorithms are significantly simpler, more efficient, more interpretable, and more generalizable, suggesting that the considered instances are themselves relatively simple. We then discuss the limitations of the claim regarding LLMs' contribution to this problem, which appears to rest on the mistaken assumption that the instances had previously been studied. Our findings instead emphasize the need for rigorous validation and contextualization when assessing the scientific value of LLM-generated outputs.

18.
arXiv (CS.CL) 2026-06-12

Two Wrongs, No Right: Auditing Social-Desirability Bias in LLM Annotators for Computational Social Science

作者:

LLM annotators are increasingly used in computational social science (CSS), but it is unclear whether their alignment-shaped errors preserve the empirical conclusions a researcher would report. We audit three open-source 7B instruction-tuned models (Zephyr, Mistral-Instruct, Qwen2.5-Instruct) across six TweetEval tasks under four prompt conditions (72 cells) and find that social-desirability failures do not run in a single direction. Zephyr exhibits leniency bias, systematically under-applying harmful labels (offensive language: false benign rate 0.729, false alarm rate 0.031). Mistral and Qwen exhibit overcorrection, over-applying the same labels (Mistral hate-speech FAR = 0.604). All three models exhibit neutrality bias on abortion stance, underestimating opposition prevalence by 24 to 40 percentage points and inflating the neutral label. None of the four prompting interventions we test (neutral, safety framing, depersonalized, chain-of-thought) corrects these failures across models; safety framing can worsen stance distortion. Strikingly, Zephyr's hate-speech prevalence estimate matches the gold rate exactly while its class-conditional errors are large in both directions, an accidental cancellation that misleads aggregate validation. We translate these patterns into a three-part taxonomy with diagnostic FBR/FAR signatures and a lightweight gold-sample validation protocol. The headline for trustworthy CSS: a model that looks calibrated on aggregate metrics can still flip the substantive empirical conclusion a researcher would report.

19.
arXiv (CS.CL) 2026-06-12

SkillChain: Closing the Loop on Skill Evolution for Image-Based E-Commerce AI Assistants

Image-based AI assistants are now deployed at production scale on e-commerce platforms, where a single uploaded image can trigger fundamentally different user intents: product search, style recommendation, visual encyclopedia, or utility tool calls, each demanding its own response format, tool invocation, and domain knowledge. Without per-intent behavioral constraints, LLM-based systems conflate these heterogeneous modes and fall short of domain quality standards, while the breadth and dynamism of the intent space render manual engineering infeasible. To address this, we present SkillChain, which closes the production feedback loop on Skill evolution, automating the lifecycle of Skills through three stages: Skill Creator for bootstrapping from task specs and trajectories, Route Optimizer for routing alignment, and Body Refiner for iterative Skill Body refinement via dual-path LLM-Judge evaluation. Deployed on a production-scale e-commerce image assistant, SkillChain substantially improves aggregate response quality, with the strongest gains on structural compliance and content quality; a one-week online A/B experiment further confirms significant gains in user engagement, content consumption, and long-term retention.

20.
arXiv (CS.CV) 2026-06-18

AMALIA-VL: A Native European Portuguese Open-Source Vision and Language Model

Large Vision and Language Models (LVLMs) have advanced rapidly, yet European Portuguese (pt-PT) remains systematically underserved by existing open-source multimodal models, which either conflate it with Brazilian Portuguese or severely under-represent it in their training data mixes. We introduce AMALIA-VL, the first open-source instruction-tuned LVLM built natively for pt-PT, pairing a high-resolution vision encoder with dynamic image tiling and a fully open pt-PT-optimized language model via a learned connector. We contribute with a purposefully designed three-stage training process - vision-language alignment, general visual instruction tuning, and preference optimization - together with a pt-PT-centric multimodal data mix combining curated and translated public datasets with novel datasets that address the near-total absence of European Portuguese multimodal resources. Our evaluation shows that AMALIA-VL establishes a strong baseline for open-source pt-PT LVLMs.We will release model weights, training data, and construction pipelines along with machine-translated pt-PT evaluation benchmarks to help democratize pt-PT LVLM development.

21.
arXiv (CS.LG) 2026-06-12

Revisiting Neural Processes via Fourier Transform and Volterra Series

arXiv:2606.01172v2 Announce Type: replace Abstract: Modeling unknown latent functions from finite, irregularly sampled measurements is a recurring challenge across science and engineering. Neural processes (NPs), a family of probabilistic functional models, are promising solutions – especially when endowed with domain-specific symmetries like translation equivariance, which improve sample efficiency and generalization. Yet existing translation-equivariant NPs face two limitations: (i) they stack generic components with non-linearities, obscuring the induced function class and limiting interpretability; and (ii) convolutional designs rely on kernels with local receptive fields and require dense uniform input grids, while attention-based methods avoid these issues but scale quadratically with the number of observations. We address both with two contributions. First, using the Volterra expansion, we characterize continuous translation-equivariant operators as sums of higher-order convolutions, yielding analytical transparency while admitting efficient approximation by first-order convolutions. Second, we introduce set Fourier convolutions (SFConvs), a frequency-domain parameterization that operates directly on irregularly sampled points, achieves approximately global receptive fields, and scales linearly in the number of observations. Building on these ideas, we propose two conditional NPs (CNPs): SFConvCNPs, which stack SFConv blocks with non-linearities, and SFVConvCNPs, which integrate the Volterra formulation. Experiments on synthetic and real-world datasets demonstrate our methods' efficacy against state-of-the-art baselines.

22.
bioRxiv (Bioinfo) 2026-06-17

In silico characterization of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes

Background/aim: Antimicrobial resistance in methicillin-resistant Staphylococcus aureus (MRSA) requires precision non-antibiotic therapeutics, yet phage lytic efficacy is poorly predicted by phenotypic assays, as shown by paradoxical biofilm responses. This study characterized the genomic architecture of lytic S. aureus bacteriophages, focusing on the conservation of the lysis module and the variability of host-recognition modules, to provide a rational basis for phage candidate selection. Materials and methods: Twenty-two complete S. aureus phage genomes were retrieved from NCBI GenBank. Genomic features were extracted with custom Biopython scripts. Lysis (endolysin, holin) and host-recognition (tail fiber/receptor-binding protein) modules were annotated and validated by InterPro domain analysis, with disrupted endolysins resolved by tBLASTn. Phylogeny was reconstructed from large terminase subunit (TerL) sequences using maximum likelihood. Results: Genome size spanned three classes, from 17.5 to 148.6 kb. The LysK-type endolysin (CHAP, Amidase, SH3b) was highly conserved, whereas tail fiber/RBP genes were detected in only 14 of 22 phages. Domain analysis reclassified two proteins annotated as endolysins as virion-associated peptidoglycan hydrolases, and identified two independent mechanisms, HNH endonuclease insertion and intron splitting, that interrupt lysis-module genes and confound automated annotation. Maximum likelihood analysis recovered a strongly supported, highly conserved core clade with EW and SA13 as divergent lineages. Conclusion: Lysis modules are conserved whereas host-recognition modules are variable, indicating that host recognition rather than the lytic enzyme is the principal determinant of host range and the more rational target for phage selection and engineering.

23.
Nature (Science) 2026-06-17

Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago

Plague is among the most devastating diseases in human history1. However, early strains of the plague-causing bacterium Yersinia pestis lacked virulence factors that are required for the bubonic form until around 3,800 years ago2,3. Consequently, the morbidity and mortality of early plague strains remain unclear. Here we describe early plague strains that are associated with two phases of outbreaks among mid-Holocene hunter-gatherers near Lake Baikal in southeast Siberia, beginning from about 5,500 years ago. These outbreaks occur across four hunter-gatherer cemeteries, with a 39% detection rate for plague infection. By reconstructing kinship pedigrees, we show that small familial groups were affected, consistent with human-to-human spread of disease, and that the first outbreak occurred within a single generation. The infections appear to have resulted in acute mortality, especially among children (aged 8 to 11 years). We further note functional differences, including in the ypm superantigen locus, which is also present in present day Yersinia pseudotuberculosis. The new strains diverge ancestrally to known Y. pestis and constrain the timing of its emergence, indicating that this happened before approximately 5,700 years ago. These findings show that plague outbreaks happened earlier than previously thought and were indeed lethal. We contend that the occurrence of outbreaks among mid-Holocene hunter-gatherer communities well outside the sphere of Late Neolithic Europe challenges the notion that higher population densities and lifestyle changes during the Neolithic agricultural transition were prerequisites for plague epidemics. Analyses of ancient DNA from hunter-gatherers near Lake Baikal in southeast Siberia around 5,500 years ago indicate that highly virulent Yersinia pestis emerged earlier than previously estimated, far from the next known cases of infection in Late Neolithic Europe.

24.
arXiv (CS.CV) 2026-06-19

CoMo: Learning Continuous Latent Motion from Internet Videos for Scalable Robot Learning

Unsupervised learning of latent motion from Internet videos is crucial for robot learning. Existing discrete methods generally mitigate the shortcut learning caused by extracting excessive static backgrounds through vector quantization with a small codebook size. However, they suffer from information loss and struggle to capture more complex and fine-grained dynamics. Moreover, there is an inherent gap between the distribution of discrete latent motion and continuous robot action, which hinders the joint learning of a unified policy. We propose CoMo, which aims to learn more precise continuous latent motion from internet-scale videos. CoMo employs an early temporal difference (Td) mechanism to increase the shortcut learning difficulty and explicitly enhance motion cues. Additionally, to ensure latent motion better captures meaningful foregrounds, we further propose a temporal contrastive learning (Tcl) scheme. Specifically, positive pairs are constructed with a small future frame temporal offset, while negative pairs are formed by directly reversing the temporal direction. The proposed Td and Tcl work synergistically and effectively ensure that the latent motion focuses better on the foreground and reinforces motion cues. Critically, CoMo exhibits strong zeroshot generalization, enabling it to generate effective pseudo action labels for unseen videos. Extensive simulated and real-world experiments show that policies co-trained with CoMo pseudo action labels achieve superior performance with both diffusion and auto-regressive architectures.

25.
bioRxiv (Bioinfo) 2026-06-19

HTS-Oracle v2: Prospective AI-Guided Discovery and Experimental Validation of Small Molecule Modulators Across Multiple Targets

High-throughput screening (HTS) remains the cornerstone of early-phase small molecule discovery yet consistently underperforms against immunotherapy targets, yielding validated hit rates below 0.1%. Here we introduce HTS-Oracle v2, which features rigorous cross-validation that ensures honest performance estimates. HTS-Oracle v2 was trained and validated across four clinically significant immune checkpoint targets (CD28, ICOS, LAG-3, and TIGIT) achieving ROC-AUC values of 0.968, 0.969, 0.875, 0.928 respectively under rigorous cross-validation. For prospective experimental validation, HTS-Oracle v2 was applied to an 8,960-compound Enamine Protein Mimetic Library, selecting only 25 compounds per target for experimental testing using temperature-related intensity change (TRIC) technology, a 99.7% reduction in screening burden. HTS-Oracle v2 identified 4, 5, 4, and 6 validated binders from 25 prospectively selected compounds per target, corresponding to validated hit rates of 16%, 20%, 16%, and 24%, respectively. Notably, 67-80% of all experimentally confirmed hits across the full 8,960-compound library were captured within just 25 model-selected compounds per target. For CD28, this represents a 28-fold improvement over HTS-Oracle v1 (239x versus 8.4x), establishing HTS-Oracle v2 as an efficient platform for AI-guided prospective hit discovery across immunotherapy targets.