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01.
arXiv (CS.CL) 2026-06-11

Goal-Autopilot: A Verifiable Anti-Fabrication Firewall for Unattended Long-Horizon Agents

Authors:

Long-horizon LLM agents are not trusted to run unattended: with no human watching, they confidently report success they never verified. We treat honesty – bounding what an agent may claim at termination – as a first-class metric for unattended autonomy, distinct from capability. We present Autopilot, an execution model that makes silent fabricated success structurally impossible rather than merely rarer. Autopilot externalizes all working state into a durable, gated finite-state machine that a scheduler advances one stateless tick at a time; a hard floor forbids any terminal "done" claim whose falsifiable gate did not actually execute and pass. We prove a No-False-Success theorem – under gate soundness, floor enforcement, and plan coverage, termination implies the goal holds – whose only trust points are empirically measurable, and show the worst case degrades to an honest stall, never a fabricated success. Because each tick rehydrates only the state machine, per-step context cost is constant in the horizon. Across a 3,150-cell paired corpus (70 tasks $\times$ 3 systems $\times$ 3 models $\times$ 5 seeds, including 50 SWE-bench Lite tasks across 11 OSS repos), Autopilot fabricates on 0.95% of cells [95% CI 0.38–1.62] while Reflexion and StateFlow baselines fabricate on 8.10% [6.48–9.81] and 25.05% [22.48–27.62] respectively. The headline contrast lives in the hard regime: on SWE-bench Lite, the firewall reduces fabrication from 33.7% (StateFlow) to 0.67%, a paired difference of $-33.07$ pp [95% CI $-36.53, -29.73$]. The mechanism is the gate, not the model: all ten Autopilot fabrications come from the strongest model, while two weaker mid-tier models never fabricate across 700 paired cells. The firewall trades coverage for honesty by design – an honest stall is recoverable; a confident wrong output shipped downstream is not.

02.
arXiv (CS.LG) 2026-06-15

Provably Safe, Yet Scalable Reinforcement Learning

arXiv:2606.14536v1 Announce Type: new Abstract: Safe reinforcement learning (RL) aims to learn policies that optimize rewards while satisfying constraints. Predominant approaches rely on soft-constrained policy optimization, which has achieved empirical success but does not provide formal safety guarantees for the learned policy. In contrast, methods with strict guarantees typically rely on explicit certificate functions, whose construction requires the direct synthesis and verification of control-invariant sets, a process that scales poorly with state dimension and often yields overly conservative behavior. In this paper, we present the Provably Safe, yet Scalable RL (PS2-RL) framework, a novel two-phase architecture for learning provably safe policies in a scalable manner, designed to overcome the key bottlenecks of prior methods. Rather than explicitly computing invariant sets, PS2-RL leverages a learned backup policy to forward-integrate the system dynamics, generating an implicit control-invariant set online. In the first phase, the backup policy is trained with our proposed safe-arrival value function, which characterizes the optimal backup policy for invariant-set construction. In the second phase, an RL policy is trained end-to-end through a differentiable projection layer that strictly enforces the safety guarantees induced by the learned backup policy. By maximizing the volume of the implicit control-invariant set in the first phase, the resulting PS2 policy from the second phase is performant and scalable, while maintaining provable safety. Crucially, PS2-RL imposes no restrictions on the underlying RL algorithm and can be plugged into any existing training pipeline. We establish theoretical guarantees for the proposed framework and evaluate it on robotic control tasks with state dimensions up to 10, a regime in which prior provably safe RL methods struggle or become impractical.

03.
arXiv (CS.CL) 2026-06-24

Faithful by Construction: Claim-Anchored Attribution for Multi-Document Summarization

Authors:

End-to-end large language models (LLMs) produce fluent multi-document summaries but remain prone to hallucination, and the attributions they offer are typically coarse (whole documents or passages) and generated post hoc, leaving each summary statement hard to verify. We revisit the modular Extract–Select–Rewrite paradigm and recast its intermediate representation as the unit of attribution. We present CAMS, a Claim-Anchored Multi-document Summarization framework that (i) extracts atomic claims with token-level provenance from every source document, (ii) clusters equivalent claims across documents while flagging inter-source conflicts, (iii) selects a support-aware and salient subset, and (iv) rewrites the selection into a summary in which every sentence is anchored to a support-checked claim that links back to one or more source spans. Because content is localized before it is realized, the pipeline is attribution-oriented by construction and faithfulness-oriented by construction: it structurally preserves fine-grained, multi-source traceability while using support-aware selection, constrained rewriting, and verification to encourage, rather than guarantee, factual faithfulness. We evaluate quality, faithfulness, and localization on MultiNews, analyze conflict handling on DiverseSumm, and test zero-shot transfer on WCEP, using a two-regime protocol that separates reference-free citation quality from gold-aligned localization accuracy, and we add an evaluator-decoupled audit that tests citation precision with a support model never used for selection or verification. CAMS matches strong end-to-end and span-attribution baselines on summary quality while substantially improving faithfulness and citation precision, lifting multi-source attribution accuracy by roughly two-thirds, and exposing a controllable faithfulness–coverage trade-off that end-to-end models leave implicit.

04.
arXiv (CS.LG) 2026-06-24

A Comparative Study of Bayesian Contextual Bandits for Real-Time Warehouse Sorter Optimization

arXiv:2606.23977v1 Announce Type: new Abstract: Efficient sorter diversion control of automated material handling systems (MHS) is critical for optimizing operational efficiency in large-scale warehouse environments. In this study, we use an inbound receiving sorter at a high-volume e-commerce warehouse as our primary use case, where the sorter diversion system relies on cost functions with static weight configurations that fail to adapt to highly dynamic system contexts, such as volume mode, congestion level, equipment physical status, and upstream/downstream dependencies. To address this real-time sorter diversion optimization challenge, we conducted a comparative study of three candidate hybrid machine learning frameworks: Linear Regression with Gradient Descent Optimization (LR+GDO), XGBoost with Bayesian Optimization (XGB+BO), and Bayesian Contextual Bandits (BCB). Model training and evaluation were enabled by leveraging a high-fidelity physics-aware emulator to overcome the cold-start problem and allow a safe transition from offline to online learning. We performed comprehensive evaluations including reward model predictive accuracy, contextual sensitivity, action distribution, and projected reward uplift. Our results demonstrate that while tree-based reward models offer slightly better predictive power, the BCB framework achieved overall higher performance with 2.03% reward uplift over the heuristic baseline. Furthermore, BCB exhibits several superior characteristics, such as its decisive time-optimal policy backed by Bang-Bang control theory, continuous online learning capability, strategic balance between exploration and exploitation, and significantly shorter inference latency. These results demonstrate the potential of the BCB framework for real-time control optimization in large-scale warehouse environments, motivating further investigation toward operational deployment.

05.
Nature (Science) 2026-06-22

Cancer cells adopt unprecedented strategies to produce a molecule that protects them from iron-dependent death

The finding that spermine molecules in cells bind to iron to prevent it unleashing ferroptosis, a type of cell death, opens up strategies for treating tissue damage and cancer. The finding that spermine molecules in cells bind to iron to prevent it unleashing ferroptosis, a type of cell death, opens up strategies for treating tissue damage and cancer.

06.
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.

07.
arXiv (CS.AI) 2026-06-17

An AI Security Agent for Banking: Multi-Vector Fraud and AML Detection Across Retail and Corporate Accounts

arXiv:2606.17555v1 Announce Type: cross Abstract: Banks simultaneously face signature-based fraud (card-not-present attacks, account takeover, ATM cloning) and behavioural financial crime (structuring, layering, mule networks, business email compromise) – two threat families with fundamentally different detection requirements. Static rule engines that reliably catch brute-force and high-velocity events are structurally blind to business-email-compromise (BEC) payment redirection, session hijacking, and money-laundering layering, which are engineered to appear indistinguishable from legitimate activity at the individual transaction or session level. This paper presents an AI security agent for retail and corporate banking that addresses this gap through a three-component fusion architecture operating on two parallel event streams: a transaction stream (card fraud, ACH/wire fraud, AML categories) and a session stream (account takeover, session hijacking, SIM-swap, insider abuse). Each stream combines an LSTM sequence model capturing per-account behavioural history, a statistical velocity/threshold monitor, and a graph/network module capturing account-counterparty relationship patterns (fan-in, fan-out, pass-through ratio) for money-laundering detection. Experiments on a synthetic event log of 237,669 transactions and 113,508 sessions across 13 threat categories and 3,470 simulated accounts demonstrate overall F1 of 0.787 (transaction stream) and 0.867 (session stream) for the proposed model, versus 0.562/0.733 for a rule-based baseline and 0.655/0.713 for an LSTM-only baseline. The agent includes a customer-facing transaction-verification chatbot (96.6% identity verification accuracy, 86.8% mass-reset attack detection) and an analyst case-summary assistant (99.3% action-recommendation F1), with Critical-tier automated response latency under 0.43 ms at the 95th percentile.

08.
arXiv (CS.AI) 2026-06-19

AutoPass: Evidence-Guided LLM Agents for Compiler Performance Tuning

arXiv:2606.20373v1 Announce Type: cross Abstract: Large Language Models (LLMs) show promise for code compilation tasks, but applying them to runtime performance tuning is difficult due to complex microarchitectural effects and noisy runtime measurements. We present AutoPass, a multi-agent framework for compiler performance tuning that uses compiler and runtime evidence to guide LLM-generated optimization decisions. Rather than treating the compiler as a black box like prior auto-tuning schemes, AutoPass opens up the compiler to the LLM, enabling it to query compiler-internal optimization states and analyze the intermediate representation to orchestrate compiler options. The search process iteratively refines optimization configurations using measured runtime feedback to diagnose regressions and guide latency-improving edits. AutoPass operates in an inference-only, training-free setting and requires no offline training or task-specific fine-tuning, making it readily applicable to new benchmarks and platforms. We implement AutoPass on the LLVM compiler and evaluate it on server-grade x86-64 and embedded ARM64 systems. AutoPass outperforms expert-tuned heuristics and classical autotuning methods, achieving geometric-mean speedups of 1.043x and 1.117x over LLVM -O3 on x86-64 and ARM64, respectively.

09.
arXiv (CS.CV) 2026-06-19

DiffMath: Symbol- and Graph-Aware Latent Diffusion Transformer for Handwritten Mathematical Expression Generation

Handwritten Mathematical Expression Generation (HMEG) is challenging due to the complex two-dimensional layouts and long-range structural dependencies of mathematical expressions. Existing methods typically rely on explicit spatial supervision, such as symbol-level bounding boxes, which incurs high annotation costs and limits scalability. In this work, we propose DiffMath, a symbol- and graph-aware latent diffusion framework that leverages the hierarchical structure inherent in LaTeX as a structural prior, eliminating the need for positional supervision. First, we design a Relational Abstract Syntax Tree (RelAST), a generation-oriented representation that distills MathML trees into compact triplet sequences [S, R, D], where each token directly encodes a symbol identity, spatial relation, or nesting depth. Second, we introduce MathVAE, which learns structure-preserving latent representations through symbol-aware and relation-aware perceptual regularization, ensuring that the latent space captures both character semantics and spatial topology. Third, MathDiT performs conditional denoising in this structured latent space, further guided by a global symbol-count prior via Adaptive Layer Normalization (AdaLN) to improve structural coherence. Experiments show that DiffMath produces structurally consistent handwritten expressions, achieves superior performance over existing methods, and improves the accuracy of downstream OCR models through synthetic data augmentation.

10.
arXiv (math.PR) 2026-06-16

An Algebraic Matrix Spencer Theorem

arXiv:2606.16005v1 Announce Type: new Abstract: We develop an algebraic approach to matrix discrepancy based on the representation theory of finite-dimensional C$^*$-algebras. As an application, we resolve a substantial structured special case of the Matrix Spencer conjecture. In particular, we show that for every family of contractions $A_1,\ldots,A_n$ that are contained in a finite-dimensional $C^*$-algebra $\mathcal A$ with $dim_{\mathbb C} (\mathcal A) \lesssim n$, there exists signs $x\in\{\pm1\}^n$ such that $\|\sum_{i=1}^n x_i A_i\| \le O(\sqrt n)$. As a noteworthy special case, our main result also resolves the Group Spencer conjecture of (Bandeira'24). We furthermore prove that Matrix Spencer continues to hold for low-rank perturbations of matrix families coming from an $C^*$-algebra of small dimension.

11.
arXiv (CS.CV) 2026-06-24

MorVess: Morphology-Aware Pulmonary Vessel Segmentation Network

Accurate pulmonary vessel segmentation remains challenging due to the sparse, tortuous, and multi-scale nature of vascular structures, where small branches are easily lost and topology integrity is difficult to preserve under voxel-wise supervision. Existing deep segmentation models primarily optimize binary masks, lacking explicit geometric constraints, thus struggling to recover continuous tubular morphology and fine vascular connectivity. In this study, we introduce MorVess, a morphology-aware segmentation framework that integrates differentiable geometric priors with large-scale foundation model adaptation to achieve fine-grained vascular parsing. MorVess jointly predicts vessel masks, distance maps, and thickness maps, providing explicit supervision for vascular boundaries, centerline consistency, and smooth diameter transitions. A lightweight 2.5D adapter bridges 3D spatial context and 2D SAM representations, while a global-local fusion block aggregates multi-level semantics and geometric cues for high-fidelity topology reconstruction. Across two challenging pulmonary CT benchmarks, MorVess delivers superior Dice, clDice, and HD95 scores, substantially improving small-vessel recovery and global connectivity. These results demonstrate that embedding geometric intelligence into pretrained vision models offers a principled and scalable pathway toward precise vessel analysis and clinically reliable structural quantification. Our source code is available at https://github.com/MaoFuyou/MorVess.

12.
arXiv (CS.LG) 2026-06-16

False Sense of Safety in Selective Signal Classification: Auditing Bound Tightness and Exchangeability for Risk Control

arXiv:2606.15153v1 Announce Type: new Abstract: Selective prediction with distribution-free risk control promises that, with confidence 1-delta over the calibration draw, the error rate of accepted inputs stays below a user budget alpha. We audit this promise on signal-domain detectors – machine anomalous-sound detection (ASD) and AI-generated-image forensics – for four calibration rules: uncertified empirical thresholding (NAIVE) and certified Hoeffding, Clopper-Pearson (CP), and betting (WSR) upper confidence bounds. We report three findings. (i) NAIVE thresholding, common in practice, exceeds its declared budget in 49-73% of synthetic trials (n=200 calibration points) and in up to 68% of real-data splits: a false sense of safety rather than a broken theorem, since the rule never had a certificate. (ii) Tightness matters: CP and WSR certify substantial coverage where Hoeffding certifies none, with zero observed budget overruns under exchangeable splits. (iii) Under grouped deployment (unseen machine types or generators), certified rules overrun in 9-30% of trials – far above delta – showing the failure lies in the broken exchangeability premise, not in the bounds; a conservative per-group threshold restores validity at a severe coverage cost.

13.
arXiv (quant-ph) 2026-06-24

Cornell Interaction in the Two-body Pauli-Schrödinger-type Equation Framework: The Symplectic Quantum Mechanics Formalism

arXiv:2507.20045v3 Announce Type: replace Abstract: We investigate the quantum behavior of a quark-antiquark bound system under the influence of a magnetic field within the symplectic formulation of quantum mechanics. Employing a perturbative approach, we obtain the ground and first excited states of the system described by the Cornell potential, which incorporates both confining and non-confining interactions. After performing a Levi-Civita mapping in phase space, we solve the time-independent symplectic Pauli-Schrödinger-type equation and determine the corresponding Wigner function. Special attention is given to the observation of the confinement of the quark-antiquark, that is revealed in the phase space structure. Due to the presence of spin in the Hamiltonian, the results reveal that the magnetic field enhances the non-classicality of the Wigner function, signaling stronger quantum interference and a departure from classical behavior. The experimental mass spectra is used to estimate the intensity of the external field, leading to a value that is in order of the transiet magnetic field measured in non-central heavy-ion collisions at RHIC and LHC.

14.
arXiv (CS.CV) 2026-06-11

Plan-and-Verify Video Reward Reasoning with Spatio-Temporal Scene Graph Grounding

Reward models for text-to-video (T2V) generation guide post-training but often fail at fine-grained semantic alignment. We trace this to two structural weaknesses in existing reasoning-based reward models: they do not systematically verify every condition described in the prompt, and the visual evidence supporting each judgment remains implicit in their free-form reasoning. We propose SG-PVR, a video reward model that addresses these limitations through plan-and-verify reasoning grounded in spatio-temporal scene graphs. The verification plan decomposes the prompt into atomic claims, ensuring every requirement is checked. The spatio-temporal scene graph, encoding entities, attributes, and temporally-grounded relations, is extracted from the video and maintained as a persistent structured visual reference throughout reasoning. Each claim is verified against both the video and the scene graph, anchoring judgments in explicit visual evidence. SG-PVR achieves strong performance on semantic alignment, including fine-grained temporal semantics. As a test-time reranker, it further enhances compositional alignment in T2V generation.

15.
arXiv (CS.AI) 2026-06-17

Breaking the Code: Security Assessment of AI Code Agents Through Systematic Jailbreaking Attacks

arXiv:2510.01359v2 Announce Type: replace-cross Abstract: Code-capable large language model (LLM) agents are embedded in software engineering workflows where they can read, write, and execute code, raising "jailbreak" stakes beyond text-only settings. Prior evaluations emphasize refusal or harmful-text detection, leaving open whether agents compile and run malicious programs. We present JAWS-Bench (Jailbreaks Across WorkSpaces), a benchmark spanning three escalating workspace regimes mirroring attacker capability: empty (JAWS-0), single-file (JAWS-1), and multi-file (JAWS-M). We pair this with a hierarchical, executable-aware Judge Framework that tests (i) compliance, (ii) attack success, (iii) syntactic correctness, and (iv) runtime executability, to measure deployable harm. Across seven LLM backends from five families, prompt-only attacks in JAWS-0 achieve 61% compliance; 58% are harmful, 52% parse, and 27% run end-to-end. In JAWS-1, compliance reaches ~100% for stronger models with a mean ASR (Attack Success Rate) ~71%; JAWS-M raises mean ASR to ~75%, with 32% runnable attack code. Wrapping an LLM in an agent increases ASR by 1.6$\times$, by overturning initial refusals during planning and tool use. Similar trends hold for OpenHands, SWE-Agent, and OpenAI Codex, suggesting our JAWS-Bench is agent-agnostic. Category analyses identify which attack classes are most vulnerable and deployable, motivating execution-aware defenses and refusal-preserving agent designs.

17.
arXiv (CS.CL) 2026-06-11

Measuring language complexity from hierarchical reuse of recurring patterns

We introduce the ladderpath index as a measure of language complexity grounded in algorithmic information theory. It counts the minimum steps needed to reconstruct a sequence through hierarchical reuse of repeated substructures, capturing an exactly computable but constrained form of algorithmic compressibility related to, but distinct from, Kolmogorov complexity. We apply the ladderpath approach to 21 parallel corpora from the Parallel Universal Dependencies dataset. The ladderpath index is approximately invariant across the languages, and varies much less than the corpus length. This is more pronounced when all corpora are mapped to a unified binary representation, providing evidence for the equi-complexity hypothesis from a representation-independent perspective. We also observe trade-offs between character inventory size and corpus length, and between vocabulary-level and corpus-level reconstruction complexity, supporting the trade-off hypothesis that total complexity is conserved and redistributed across linguistic levels. The reusable substructures identified by the ladderpath approach, without any linguistic input, overlap with words and morphological components attested in the natural vocabulary. The hierarchical reuse captured by the ladderpath approach parallels the chunking mechanisms proposed in cognitive science, where the human cognitive system compresses linguistic input into nested, reusable units under shared memory and processing constraints. This connection between cognitive chunking and the ladderpath approach provides a new interpretation for the equi-complexity and trade-off hypotheses, grounding both in the shared cognitive architecture that underlies language processing across human languages.

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

Transfer Learning for FHIR Questionnaire Terminology Binding

Electronic prior authorization workflows require FHIR Questionnaire items to carry LOINC codes, yet most items in the HL7 Da Vinci CDS-Library lack these bindings. We treat this as a retrieval problem: given a Questionnaire item's text, find the correct LOINC code in a pool of 97,314 active codes. We compare six methods (TF-IDF, frozen MiniLM, BioBERT, BioLORD, contrastively fine-tuned MiniLM, and a TF-IDF+GPT reranker) on a 54-item evaluation set spanning three query styles (natural question, medium, and terse). No single method wins on every metric. BioLORD, a frozen encoder pre-trained on biomedical ontology definitions, has the best top-rank accuracy (R@1 = 0.185, MRR = 0.246) despite seeing no task-specific data, while a contrastive fine-tune on raw LHC-Forms pairs takes R@5 (0.389) and R@10 (0.426). A distribution-shift ablation shows why the fine-tune in our main table is not the strongest one: adding GPT-generated paraphrases to the raw pairs drops R@5 from 0.389 to 0.296, so the augmented union underperforms raw-only training on every metric except R@1. Performance peaks at 5k training pairs. Error analysis on BioLORD's R@1 failures shows that wrong-specificity and ambiguous-text cases together account for 59% of errors.

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

Reasoning as Attractor Dynamics: Latent Memory Retrieval via Gibbs-Weighted Energy Minimization

arXiv:2606.24543v1 Announce Type: new Abstract: Large Language Models (LLMs) are traditionally viewed as autoregressive generators. However, from the perspective of collective computation, they function as high-dimensional Dense Associative Memories that store complex reasoning patterns as latent attractors. In this work, we investigate the energy landscape of mathematical reasoning. We posit that correct reasoning chains correspond to deep, wide attractor basins ("flat minima") in the model's output distribution, whereas hallucinations manifest as sharp, unstable local minima. To exploit this geometry, we introduce a retrieval mechanism based on a Gibbs measure of the trajectory's spectral entropy. By sampling multiple reasoning paths and weighting them by their inverse energy ($P \propto e^{-\beta E}$), we approximate the equilibrium distribution of the associative memory, effectively ``relaxing'' the system into a robust solution. Empirically, this physics-inspired mechanism improves Microsoft Phi-3.5 performance on GSM8K by 5.38\% (84.7\% $\to$ 90.1\%), demonstrating that inference is better modeled as a dynamic settling process into an attractor basin rather than greedy next-token prediction.

20.
PLOS Medicine 2026-06-23

Multi-omics biomarkers of endothelial dysregulation preceding chronic lung allograft dysfunction: A prospective cohort study

Authors:

by Giulia Iacono, Christina Begka, Bailey Cardwell, Carmel Daunt, Roxanne Chatzis, Celine Pattaroni, Alana Butler, Matthew Macowan, Bronwyn Levvey, Gregory I. Snell, Glen P. Westall, Benjamin J. Marsland Background Long-term survival of lung transplant recipients remains limited by chronic lung allograft dysfunction (CLAD). CLAD is only diagnosed following a persistent and substantial decline in lung function, after which irreversible damage to the lungs has occurred, limiting opportunities to effectively intervene at an early stage. There is a critical need for earlier detection prior to its clinical manifestation. The immunological drivers of CLAD remain unclear, limiting the development of predictive biomarkers and new therapies. Methods and findings In this hypothesis-generating, prospective cohort study, we profiled the microbial, metabolic, lipidomic, and gene expression dynamics of longitudinally collected broncho-alveolar lavages (BALs) from 56 CLAD-free lung transplant recipients up to 30 months post-transplant, and compared BALs from 13 CLAD-free patients to BALs from 13 patients who developed CLAD. In CLAD-free patients, the first 6 months post-transplant were hallmarked by diminished microbial diversity and increased abundance of Staphylococcus and Candida, coupled with upregulated innate and adaptive immune responses, and elevated nitric oxide metabolism (FDR 

21.
arXiv (CS.LG) 2026-06-19

Weibull Weight-Scale Parameter Evolution under AdamW Training Dynamics

Authors:

arXiv:2606.19367v1 Announce Type: new Abstract: Building on a two-parameter Weibull framework for diagnosing transformer weight distributions, we study why the Weibull weight-scale parameter $\lambda$ grows, overshoots, and then relaxes during AdamW training. We derive a leading-order three-force decomposition of the squared weight norm from the AdamW update: an alignment force measuring the correlation between weights and the adaptive update direction, an injection force from adaptive step magnitude, and a decay force from decoupled weight decay. On self-trained Pythia-70M models with ground-truth optimizer moments, alignment dominates the rise phase, contributing 88-94% of the absolute force budget across four random seeds and remaining robust to super-weight removal. Near saturation, alignment and decay approach balance, explaining the transition from weight-scale growth to relaxation. These force dynamics directly govern the squared-norm component underlying $\lambda(t)$; the remaining RMS-to-Weibull reconstruction offset is measurable and decomposes into bridge and integration components, totaling approximately 5-6% in densely sampled regions. To extend the analysis to real models where optimizer moments are unavailable, we introduce a spline displacement method that recovers the alignment force from sparse checkpoints with approximately 92-94% accuracy, about twice the naive two-point baseline. We further observe that the peak value of $\lambda(t)$ varies with training-data coherence in our experiments, suggesting a data-dependent component of weight-scale growth that we leave to a controlled follow-up study. Code and data are available at https://github.com/tiexinding/NPM-Weibull-public.

22.
arXiv (CS.LG) 2026-06-18

KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Prediction

arXiv:2506.13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery. While recent deep learning approaches have demonstrated promising results, they often rely solely on structural features of proteins and ligands, overlooking their valuable biochemical knowledge associated with binding affinity. To address this limitation, we propose KEPLA, a novel deep learning framework that explicitly integrates prior knowledge from Gene Ontology and ligand properties to enhance prediction performance. KEPLA takes protein sequences and ligand molecular graphs as input and optimizes two complementary objectives: (1) aligning global representations with knowledge graph relations to capture domain-specific biochemical insights, and (2) leveraging cross attention between local representations to construct fine-grained joint embeddings for prediction. Experiments on two benchmark datasets across both in-domain and cross-domain scenarios demonstrate that KEPLA consistently outperforms state-of-the-art baselines. Furthermore, interpretability analyses based on knowledge graph relations and cross attention maps provide valuable insights into the underlying predictive mechanisms.

23.
bioRxiv (Bioinfo) 2026-06-16

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

Performance bottlenecks in widely used genomics and bioinformatics software present a substantial and growing burden as biological datasets continue to increase in size and number. Relieving these bottlenecks relies largely on expert manual optimization and therefore remains difficult to scale. Here we present AutoZyme, an agentic framework for scientific software optimization. Given a target function, AutoZyme builds benchmarks, identifies bottlenecks, and iteratively tests code changes, retaining only those that improve runtime while preserving output. We evaluated AutoZyme on 45 functions, improving runtime without substantial memory increases in over 95% of cases considered. Across 38 functions from Seurat, Scanpy and related packages in genomics and bioinformatics, AutoZyme reduced runtime by a median of 8.52-fold, with the largest reductions exceeding 676-fold. The optimized functions are distributed through AutoZyme-Library as drop-in replacements for existing analysis pipelines. We also release AutoZyme as a reusable framework for optimizing additional user-specified packages and functions.

24.
arXiv (CS.LG) 2026-06-16

p-PSO: A Penalized Particle Swarm Optimization Technique for Finding D-Optimal Designs with Mixed Factors in Generalized Linear Models

arXiv:2606.15962v1 Announce Type: cross Abstract: Finding D-optimal designs for generalized linear models (GLMs) is challenging due to the dependence of the Fisher information matrix on unknown parameters and the lack of closed-form solutions, particularly when input factors include both discrete and continuous variables. Although classical algorithms and recent metaheuristic approaches have offered partial solutions, there remains a need for robust and computationally efficient methods. In this paper, we propose a penalized Particle Swarm Optimization (PSO) approach, named $p$-PSO. Here we introduce a new, general-purpose penalty formulation for constrained optimization and demonstrate its effectiveness in optimal design problems. The formulation is algorithm-agnostic and applicable to a broad class of black-box optimization methods. Results show that the method is highly efficient, with its primary contribution being a penalty formulation that enables the direct use of an off-the-shelf PSO algorithm and extends naturally to more general constrained optimization tasks.

25.
arXiv (CS.LG) 2026-06-17

Conformalized Quantum DeepONet Ensembles for Scalable Operator Learning with Distribution-Free Uncertainty

arXiv:2605.00330v2 Announce Type: replace Abstract: Operator learning enables fast surrogate modeling of high-dimensional dynamical systems, but existing approaches face two fundamental limitations: quadratic inference complexity and unreliable uncertainty quantification in safety-critical settings. We propose Conformalized Quantum DeepONet Ensembles, a framework that addresses both challenges simultaneously. By leveraging Quantum Orthogonal Neural Networks (QOrthoNNs), we reduce operator inference complexity from O(n^2) to O(n), enabling scalable evaluation over fine discretizations. To provide rigorous uncertainty quantification, we combine ensemble-based epistemic modeling with adaptive conformal prediction, yielding distribution-free coverage guarantees. A key challenge in ensembling is that naive parallelism scales hardware resources linearly with the number of models. We resolve this by using Superposed Parameterized Quantum Circuits (SPQCs), which compress multiple ensemble members into a single circuit and enable simultaneous multi-model execution. Experiments on synthetic partial differential equations and real-world power system dynamics demonstrate that our approach achieves accurate predictions while maintaining calibrated uncertainty under realistic quantum noise. These results establish a practical pathway toward scalable, uncertainty-aware operator learning in quantum machine learning.