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01.
arXiv (quant-ph) 2026-06-19

Robust Generation of Topological Biphoton Mode via Adiabatic Passage

arXiv:2606.19786v1 Announce Type: new Abstract: Topological waveguide arrays support robust mode propagation in the presence of fabrication imperfections, providing a significant advantage for on-chip quantum information processing. However, this robustness does not fully extend to nonlinear biphoton generation. Structural disorder can enhance the excitation of non-topological biphoton modes during nonlinear interactions, which degrades the quantum properties of the generated state. To overcome this limitation, we propose an adiabatic passage that connects an isolated site to a topological defect array. By initiating the nonlinear process in a strongly isolated regime, nonlinear coupling to unwanted modes is effectively suppressed, thereby preserving the Schmidt number of the generated state. The subsequent adiabatic connection facilitates the high fidelity transfer of the generated biphoton into the topological biphoton mode. Our numerical simulations demonstrate that, unlike conventional topological structures, the adiabatic scheme maintains both high biphoton fidelity and a unit Schmidt number in the presence of waveguide gap disorder. Furthermore, we show that this robustness extends to path entangled NOON states, achieving a near-unity quantum interference visibility. Our approach provides a practical design strategy for disorder-tolerant integrated quantum photonic devices.

02.
arXiv (CS.CL) 2026-06-11

ISE: An Execution-Grounded Recipe for Multi-Turn OS-Agent Trajectories

Training capable OS agents requires data that simultaneously captures structured user intents, multi-turn task delegation, and grounded tool execution–properties absent from existing datasets. We propose ISE (Intent -> Simulate -> Execute), a three-stage synthesis paradigm that addresses these gaps jointly. Stage 1 constructs roughly 50000 structured intents via a 4D framework (Persona x Domain x Task x Complexity); after deduplication the pool contains 43956 unique intents and attains a Vendi Score of 61.57 over the entire pool on mpnet-base-v2 embeddings (cosine kernel, q=1). Stage 2 drives multi-turn user-agent interaction through a role-locked user simulator that grounds each user turn in actual execution outcomes, producing 23132 complete trajectories averaging 8.12 user turns and 68.24 total dialogue turns. Stage 3 runs every tool call inside a live, isolated OS workspace, generating authentic failure-recovery dynamics instead of simulated responses. Fine-tuning on ISETrace improves ClawEval pass@1 from 19.3 to 37.7 using Qwen3-8B on agent tool-use tasks with a standard protocol. This result outperforms zero-shot GPT-4o and the larger Qwen3-32B base model which is four times bigger. An ablation on Stage 2 proves multi-turn simulation brings a large portion of the performance gain. We release all source code and dataset at https://github.com/Valiere01/ISE-Trace.

03.
arXiv (CS.LG) 2026-06-19

On the Variance of Temporal Difference Learning and its Reduction Using Control Variates

arXiv:2606.20357v1 Announce Type: new Abstract: We analyze the variance of temporal difference (TD) learning using the phased setting with tabular representation, and show that one of the mechanisms behind its ability to reduce variance is by effectively aggregating over a larger number of independent trajectories. Based on this insight, we demonstrate that (1) the variance of TD is asymptotically bounded from above by Monte Carlo (MC) estimators, and (2) shorter horizon updates incurs less variance for a fixed number of samples. Beyond TD, we show that Direct Advantage Estimation (DAE), a method for estimating the advantage function, can be seen as a type of regression-adjusted control variate, which achieves a tighter bound on the variance compared to TD in the large-sample limit. Finally, we numerically illustrate the behaviors of these estimators with carefully designed environments.

04.
bioRxiv (Bioinfo) 2026-06-18

segSHAPE: RNA secondary structure prediction from nanopore direct RNA sequencing

RNAs adopt complex structures that regulate key biological processes, making accurate structure prediction essential. Chemical probing coupled with Nanopore direct RNA sequencing (DRS) offers a route to single-molecule structural inference, but current tools are limited by inaccurate signal-to-sequence alignment, which degrades modification-rate estimation and downstream structure prediction. Here we introduce segSHAPE for RNA secondary structure prediction from Nanopore DRS data (both RNA002 and RNA004 chemistries), a probe-agnostic framework that improves signal alignment using prior information of basecalling and per-read signal baseline shift correction, learns position-specific k-mer raw signal parameters, and estimates per-nucleotide modification rates with an unsupervised anomaly detector. On three public RNA002 DRS datasets spanning different chemical probes (AcIm, NAI-N3) and RNAs from 421 to 1552 nt, segSHAPE achieves the highest F1 score and Matthews correlation coefficient (MCC) on all RNAs, exceeding the strongest baseline by 3.4 to 5.8 percentage points in MCC. It additionally captures the ligand-induced conformational change of the thiamine pyrophosphate (TPP) riboswitch RNA directly from RNA002 DRS data using the DEPC probe. On a public RNA004 DRS dataset, segSHAPE improves over the sm-PORE-cupine baseline by 17 ROC-AUC points in modification rate estimation and by 6.7 MCC points in structure prediction. These results establish segSHAPE as a unified, probe-agnostic pipeline for RNA structure prediction from Nanopore DRS data.

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

Output Type Before Quality: A Standards-Derived XAI Admissibility Rubric for Autonomous-Driving Safety

arXiv:2606.05461v2 Announce Type: replace Abstract: Safety standards for ML-based autonomous driving specify the kind of evidence an assurance case must contain (directed cause-and-effect chains, quantified interventional effects, named root-cause variables), yet the XAI literature is organised by output type and technique family (saliency maps, feature attribution, counterfactuals, causal graphs, language traces). SHAP, the most-recommended ADS XAI method, returns a ranked feature list that no implementation effort can convert into a directed chain (Fig.1). We name this mismatch the evidence-type gap. From AMLAS, ISO 26262, ISO21448, ISO/PAS 8800 we derive 19 testable evidentiary criteria across 7 lifecycle stages with representative clause-cited derivations and score six XAI method classes structurally. Causal XAI emerges as structurally required to satisfy the derived criteria at three stages: hazard identification (+62% rubric gap), incident investigation (+50%), and data management (+50%); the verdict set is stable across thresholds T in (0%, 50%]$ and survives a worst-case single-cell flip down to T = 25%. At the remaining four stages, correlational or language-based methods are comparable or sufficient. The rubric identifies structural admissibility (necessary but not sufficient for compliance): an admissible method's specific output content may still be wrong, and validating that fidelity (the edges a fitted SCM produces, the cause a trace names) is the open assurance challenge. A single-VLA proof of concept on 1,996 real-world driving clips (79,840 rows, ten splits) is consistent with each method's observed output type matching its rubric prediction. XAI method selection for ADS safety assurance should be driven by lifecycle-stage evidence demand, not by method popularity.

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

An Evaluation of Data Leakage Risks in Tool-Using LLM Agents in Realistic Scenarios

arXiv:2606.17114v1 Announce Type: cross Abstract: AI agents are increasingly being adopted in enterprise and personal settings with access to emails, databases, documents, and other tools where they can read, update, and disseminate sensitive information. Much of prior research on data leakage risks in agents has focused on adversarial data exfiltration through prompt injections and jailbreaks. However, sensitive information may also be exposed during non-adversarial use, creating leakage risks even when users issue benign requests. We report a joint evaluation by the Singapore AI Safety Institute and the Korea AI Safety Institute examining agent data leakage in 12 realistic, non-adversarial tasks spanning customer support, DevOps, web automation, and enterprise and personal productivity. The evaluation covers five risk types: lack of data awareness, audience awareness, policy compliance, data minimization, and access-boundary awareness. Both institutes tested a common set of scenarios mirroring real-world deployments using independent testing environments and task-specific LLM-judge rubrics. Across the three tested agents, none achieved fully correct and fully safe execution across all scenarios. Successful task completion often coincided with data-handling failures such as accessing unnecessary information or disclosing information to inappropriate recipients, indicating that capability and data-handling safety should be evaluated separately. Qualitative review also revealed claim-action mismatches, simulation-aware behavior, user-simulator role reversal, and interpretation gaps in automated judging. Overall, the results indicate that operational data leakage is a first-order agent-safety concern distinct from adversarial exfiltration and provide a methodology for future evaluations of agent data-handling safety.

07.
arXiv (CS.CV) 2026-06-25

USS: Unified Spatial-Semantic Prompts for Embodied Visual Tracking with Latent Dynamics Learning

Embodied Visual Tracking (EVT) requires an agent to continuously follow a specified target while actively moving through dynamic environments. However, prevailing EVT paradigms predominantly rely on language-based target indication. While language is expressive and convenient, cluttered scenes often contain multiple objects that satisfy the same semantic description, leading to ambiguous target grounding. We therefore propose a paradigm shift, reframing target indication in EVT from text-only specification to unified spatial-semantic prompting. Based on this paradigm, we introduce Unified Spatial-Semantic Prompts for Embodied Visual Tracking with Latent Dynamics Learning, USS, an end-to-end embodied tracking framework that supports text, point, bounding box, and mask prompts within a unified architecture. USS encodes heterogeneous prompts with modality-specific encoders, fuses prompt tokens with visual features through hybrid attention, and decodes compact prompt-conditioned representations into egocentric waypoints. To further improve temporal robustness, USS incorporates a latent world model that predicts future representations through self-supervised alignment. Real-robot experiments demonstrate that explicit spatial target cues yield higher success rates than text-only prompts, particularly in scenarios involving similar distractors and longer-horizon tracking where maintaining instance-level target identity is critical. In the simulation benchmark, USS also achieves state-of-the-art performance among non-MLLM-based methods and competitive results against recent MLLM-based approaches with faster inference speed. Our findings reveal that spatial-semantic prompting provides a more precise and flexible target indication interface for embodied visual tracking. Project site: https://arescheah.github.io/uss-project-page/.

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

Measuring Curriculum Alignment across Topical Coverage, Competency, and Cognitive Depth: A Longitudinal Framework Applied to CS2013 and CS2023

arXiv:2606.19469v1 Announce Type: new Abstract: Undergraduate computer science is governed by international curricular guidelines revised about once a decade, yet programs lack a reliable, reproducible way to measure how completely they cover the current guidelines and how that coverage shifts when the guidelines are restructured. We address this with a human-in-the-loop pipeline that measures a program's coverage of an external body of knowledge, applied longitudinally to one accredited BSc in Computer Science against Computer Science Curricula 2013 (CS2013) and 2023 (CS2023). The pipeline represents the program and each guideline as structured corpora, generates candidate course-to-knowledge-unit matches by semantic retrieval, and confirms them through human judgment under an explicit coverage definition. Of seven benchmarked retrievers, a reciprocal-rank-fusion ensemble was strongest, and a reputed long-context model underperformed a small sentence model, so retriever choice must be measured. Both maps were validated by an independent second rater (Cohen's kappa 0.64 for CS2023, 0.69 for CS2013). The program covers 49.7% of CS2023 and 50.9% of CS2013 knowledge units, near-constant across a decade. Extending the same retrieve-then-confirm design to competency articulation and cognitive depth shows that the program articulates the competency for ~88% of covered units under each guideline, yet delivers it at the recommended depth for 76% of present units under CS2023 against 95% under CS2013, a gap reflecting the newer guideline's raised expectations, not the program. The longitudinal comparison separates persistent structural gaps (parallel and distributed computing, foundations of programming languages, systems fundamentals), uncovered against both guidelines and ABET, from differences that reflect the standard's evolution. The instrument is reusable and available from the authors on request.

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

Tensor-Coord: Algebraic Decomposition of Joint Plan Tensors for Conflict-Free Multi-Agent LLM Planning

arXiv:2606.16478v1 Announce Type: new Abstract: Large language models (LLMs) remain limited in multi-agent planning because independently generated plans can create coordination failures such as spatial collisions, resource contention, and temporal deadlocks. We introduce Tensor-Coord, a multilinear algebra framework that represents the joint plan of N agents as a third-order tensor \(T \in R^{N \times H \times A}\) over agents, timesteps, and actions. Canonical Polyadic (CP) and Tucker decompositions are used to identify latent coordination structure. The minimal epsilon-approximate CP rank R* defines a computable coordination complexity measure, with \(CC(Pi)=(R*-N)/N\). We prove that R*=N is necessary and sufficient for plan independence. The residual \(E=T-T_{R*}\) defines a conflict score over agent pairs, timesteps, and actions, localizing failures without domain-specific rules. Tucker factors provide interpretable agent roles, temporal phases, and action clusters that are converted into natural language constraints for iterative LLM replanning. Experiments on multi-robot delivery tasks across Easy (2 agents, 5x5 grid), Medium (3 agents, 5x5 grid), and Hard (4 agents, 5x5 grid) settings show convergence to conflict-free plans in 100% of 2-agent cases within 1.4 iterations on average, 80% of 3-agent cases within 3.2 iterations, and 60% of 4-agent cases within 4.0 iterations. CP rank scaled approximately linearly as \(R*(N) = 3.9N + 0.5\), supporting its use as a predictor of coordination complexity.

10.
arXiv (CS.AI) 2026-06-12

A Zero-shot Generalized Graph Anomaly Detection Framework via Node Reconstruction

arXiv:2606.12673v1 Announce Type: cross Abstract: Cross-domain graph anomaly detection (GAD) aims to identify abnormal nodes in unseen target graphs, showing strong potential in real-world applications with heterogeneous graph data. However, existing methods often depend on dataset-specific feature semantics and structural patterns, which limits their ability to generalize across different domains. To address this challenge, we propose AlignGAD, a zero-shot generalized graph anomaly detection framework. Our framework is built upon three key components: a Global Unification Module that aligns heterogeneous node features and normalizes graph signals in the spectral domain; a Clustering Module that constructs cluster-aware graph views to capture group-level abnormal patterns; and a Node Discrepancy Scoring Module that measures reconstruction discrepancy and aggregates anomaly evidence from different graph views. Experiments on multiple real-world datasets demonstrate the effectiveness of AlignGAD under the zero-shot GAD setting.

11.
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.

12.
arXiv (CS.AI) 2026-06-24

Prob-BBDM: a Probabilistic Brownian Bridge Diffusion Model for MRI sequence image-to-image translation

arXiv:2606.24313v1 Announce Type: new Abstract: AI-driven image-to-image synthesis is rapidly advancing, with growing applications in medical imaging. Multi-modal image analysis plays a crucial role in optimizing examination quality, yet acquiring multiple imaging modalities in clinical settings remains resource-intensive and time-consuming, especially for 3D imaging. To address this challenge, we propose a novel image-to-image translation model based on Brownian Bridge Diffusion Models (BBDM), which synthesizes magnetic resonance imaging (MRI) sequences from 2D axial slices. Our approach integrates a variational encoder-guided diffusion mechanism, leveraging probabilistic image distributions to enhance synthesis quality. Evaluated on the BraTS 2021 dataset, our Probabilistic-BBDM (Prob-BBDM) achieves superior performance across multiple translation tasks, reaching up to 88.46% SSIM and 26.09 dB PSNR, with consistent improvements over baselines. Notably, our diffusion process requires only 4 steps, making it computationally efficient while maintaining high-quality synthesis. To further validate generalizability, we test Prob-BBDM on an external third-party dataset, demonstrating consistent performance across domains. Additionally, we assess the clinical utility of the synthesized slices by using them as input to a pre-trained segmentation model. Tumor segmentation yields a Dice score of 88.71% and an HD95 of 3.49 mm, confirming that the synthesized slices preserve critical diagnostic information. These results highlight the potential of Prob-BBDM for high-quality, efficient, and generalizable MRI synthesis, offering a promising step toward improved medical image translation.

13.
arXiv (CS.AI) 2026-06-19

Efficient and Sound Probabilistic Verification for AI Agents

arXiv:2606.20510v1 Announce Type: cross Abstract: Securing AI agents that operate in complex digital environments has become a critical need, and runtime monitoring approaches that formulate and enforce policies expressed in a formal language like Datalog offer a promising solution. However, existing approaches are restricted to deterministic policies. In many practical applications of AI agents, there is a need to enforce security policies in the face of ambiguity, leading to probabilistic predicates or state transitions (for example, a declassifier or Personally Identifiable Information (PII) detector that has some failure probability on each invocation). Furthermore, in many such applications, one cannot easily make the independence assumptions necessary to invoke prior work on probabilistic inference in Datalog. We address this by introducing a sound and efficient framework for such verification based on distributionally robust optimization, computing sound upper bounds on the probability of policy violation regardless of possible correlations between predicates. On standard benchmarks for terminal and tool calling agents, we demonstrate that our approach outperforms prior art and improves the security-utility trade-off while ensuring rigorous bounds on the probability of policy violation.

14.
arXiv (CS.LG) 2026-06-12

When to Align, When to Predict: A Phase Diagram for Multimodal Learning

arXiv:2606.11190v2 Announce Type: replace Abstract: Cross-modal alignment (CA) and cross-modal prediction (CP) are the dominant paradigms for multimodal representation learning, yet there is no systematic understanding of when each succeeds, when each fails, and when cross-modal training helps at all – a gap that leaves practitioners, especially in scientific domains like biomedicine or astrophysics, with heterogeneous instruments and multiple levels of organization and measurement, unable to diagnose why standard methods underperform the best single modality. We develop a unified linear framework that addresses both questions. Under a spiked signal-plus-noise model with structured cross-modal nuisance correlation, we derive separation ratios for both objectives that expose complementary failure modes: alignment whitens each modality and fails when nuisance is strongly correlated across views; prediction encodes whatever is cross-predictable through a one-sided whitening, with recovery governed by source-modality quality. The resulting phase diagram partitions multimodal problems into four regimes: Both, CA only, CP only, and Neither. We present a data-driven procedure to locate real-world datasets in this diagram using a small labeled subsample, identifying the preferred objective and prediction direction before any cross-modal training. Experiments on synthetic data, stereo-vision benchmarks, image-caption pairs, and real astrophysical data validate the predictions in the nonlinear regime, including the Neither regime where cross-modal training is actively harmful. Our framework lets practitioners diagnose their multimodal problem and choose the right objective before committing to training. Code to reproduce the results is available at https://github.com/IlayMalinyak/mm_align_vs_pred.

15.
arXiv (CS.AI) 2026-06-19

Exploring Feature Extraction Technique Parameters for Acoustic Gunshot Classification

arXiv:2606.19568v1 Announce Type: cross Abstract: Acoustic gunshot detection is a problem with applications across civilian public safety, military operations, and wildlife conservation, yet the field lacks a rigorous exploration of feature extraction techniques with a focus on generalization to realistic data. The mixed effectiveness of commercial gunshot detection and classification systems indicates an open problem that is not adequately addressed by the current literature. In this paper, we present a systematic investigation of common feature extraction techniques using a dataset of 23,000 gunshot recordings across 85 firearms and 21 calibers. We benchmark three feature extraction techniques with 12 total unique parameter sets using ResNet-18. Our results demonstrate that using the correct feature extraction technique can improve top-1 accuracy by up to 20%, and utilizing the correct parameters for a given feature extraction technique can improve that value by up to 4.7%.

16.
medRxiv (Medicine) 2026-06-11

The impact of pre-stroke statin use on baseline corrected infarct volume and collateral perfusion

Stroke is a leading cause of disability and mortality worldwide, with ischaemic stroke the most prevalent type. Statins, used for cholesterol management, have demonstrated benefits in reducing stroke risk and improving outcomes in preclinical studies. However, the impact of pre-stroke statin use on stroke outcomes remain inconsistent. In this study, we aim to evaluate whether pre-stroke statin use is associated with greater volume of salvaged tissue and improved cerebral collateral perfusion. A retrospective analysis was conducted using data from 281 patients presenting with acute ischemic stroke to the John Hunter Hospital between May 2015 and May 2020. Patients were grouped based on pre-stroke statin use, and clinical variables, including infarct volume and collateral perfusion, were assessed. The primary outcome was salvage volume derived from baseline perfusion lesion volume minus infarct volume at follow-up. Collateral perfusion was measured by the hypoperfusion volume defined by delay time (DT)>6 seconds divided by the hypoperfusion volume defined by DT >2 seconds. Patients on statins at admission were significantly older and had more comorbidities. No significant association was found between pre-stroke statin use and salvage volume or collateral perfusion after adjusting for covariates. Larger initial infarct core was a significant predictor of salvage volume due to larger salvageable tissue volume at baseline. These findings indicate that pre-morbid statin use is not associated with larger salvage volume or improved cerebral collateral perfusion.

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

Data-driven sparse identification of governing PDEs via knockoff filters and multi-criteria trade-offs

arXiv:2605.26631v2 Announce Type: replace-cross Abstract: We propose KO-PDE-IDENT, a data-driven framework for identifying parsimonious partial differential equations (PDEs) with false discovery rate (FDR) control. PDE discovery from noisy observations is often hindered by extreme multicollinearity among candidate terms, which causes typical sparse-regression methods to select spurious terms. To address this problem, KO-PDE-IDENT initially mines a support set of potential candidate terms via model-X knockoff filters with finite-sample FDR control, then refines and ranks the surviving PDE alternatives. The framework integrates three components. First, knockoff feature statistics are constructed by coupling $\ell_{0}$-constrained adaptive best-subset selection with SHapley Additive exPlanations (SHAP), yielding an effective and computationally efficient difference statistic. Second, a recursive feature elimination (RFE) procedure removes terms whose marginal contributions are dispensable and assesses statistical necessity through knockoff-perturbed hypothesis testing. Third, the final model selection is formulated as a multi-criteria decision-making (MCDM) problem, where the optimal governing equation is the alternative that best balances a wide range of criteria such as predictive accuracy, model complexity and coefficient uncertainty. We evaluate KO-PDE-IDENT on five canonical PDEs under severe noise corruption. Empirical results show that our framework can exactly recover the true PDE structure, eliminating false discoveries while retaining all true underlying terms, with low coefficient estimation error.

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

Accelerated Convex Optimization via Hamiltonian Dynamics with Deterministic Integration Time

arXiv:2606.17260v1 Announce Type: cross Abstract: We develop Hamiltonian dynamics-based algorithms for smooth convex optimization that achieve accelerated rates of convergence. By exploiting contraction of averaged Hamiltonian flow trajectories rather than requiring contraction at trajectory endpoints, we show that Hamiltonian dynamics-based optimization methods admit deterministic and accelerated convergence guarantees, extending prior work that is limited to quadratic objectives or holds only in expectation. We analyze an idealized continuous-time algorithm and derive practical discrete-time implementations with optimal first-order complexity, thereby establishing Hamiltonian dynamics as a useful algorithmic primitive for deterministic accelerated convex optimization.

19.
PLOS Computational Biology 2026-06-18

Ten simple rules for turning your qualifying exam into an NIH-style fellowship proposal: A guide for graduate students

by Courtney Peña-Lima, Cameron S. Bader, Brendan K. Ball, Troy C. Dildine, Mekhala V. Dissanayake, Iris van ‘t Erve, Albina Ibrayeva, Amy Nippert, M.K. Quinn, Chelse Spinner, Samuel Thompson, Antonio Tomasso, Crystal M. Botham Qualifying exams, often referred to as “quals” or candidacy exams, are an important milestone in doctoral programs. Although the style of quals varies greatly by program and institution, it is usually a proposal that requires students to develop research ideas as well as their scientific writing skills. Many quals are modeled after funding mechanisms that graduate students can apply to and on a topic that the student will pursue in their dissertation. This paper offers graduate students a step-by-step guide on how to turn their quals into a fellowship-style research proposal, using National Institutes of Health (NIH) mechanisms as a benchmark, as this is the norm within US research institutions. This paper will be most useful for students who have completed or are in the process of completing proposal-based qualifying exams, usually in the second year of a doctoral program.

20.
arXiv (CS.AI) 2026-06-24

Accuracy and Satisfaction in Multi-Turn LLM Dialogues for NFR Assessment

arXiv:2606.24834v1 Announce Type: new Abstract: LLM-based dialogue assistants have become mainstream tools for software developers, yet current evaluation benchmarks focus exclusively on functional correctness. This leaves a critical gap in assessing the quality and accuracy of these conversations when handling Non-Functional Requirements (NFRs), which are inherently vague, context-dependent, and involve many parts of a program. Evaluating how well these systems support collaborative reasoning about NFRs requires methods that go beyond single-turn accuracy to capture both the correctness of the system's outputs and the quality of the multi-turn interaction. In this paper, we investigate the accuracy and quality of multi-turn conversations between developers and an LLM-based agent in the domain of Health Insurance Portability and Accountability Act (HIPAA) regulatory compliance. We hired 49 programmers to interact with GitHub Copilot to assess 148 HIPAA-derived NFRs against the iTrust codebase, a system designed to comply with HIPAA regulations, across three dimensions: requirement satisfaction level, reasoning, and code localization. We find that developers tend to agree with LLM assessments, but accuracy against expert ground truth is low. We model user satisfaction and find that longer system responses and more information-providing turns negatively affect user satisfaction, whereas proactive interactions positively affect it. Our findings provide insights for designing LLM-based dialogue systems that support NFR assessment.

21.
arXiv (math.PR) 2026-06-15

Secondary terms for first moments of Selmer groups of twists of elliptic curves over global function fields

作者:

arXiv:2606.14274v1 Announce Type: cross Abstract: Let $E$ be a non-isotrivial elliptic curve over a global function field $\mathbb{F}_q(t)$ of characteristic coprime to $2$ and $3$. Under some explicit conditions, we determine the secondary terms for the first moments of prime Selmer groups of cyclic prime twist families of $E$ over $\mathbb{F}_q(t)$.

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

DifFRACT: Diffusion Feature Reconstruction and Attribution for Circuit Tracing

Mechanistic interpretability seeks to explain neural network behavior by decomposing model computations into interpretable features and circuits. While transcoder-based circuit tracing has recently enabled detailed causal analyses of large language models, multimodal diffusion transformers for image generation remain comparatively opaque. We still lack tools for understanding how semantic information propagates across denoising steps and how text and image representations interact within double-stream MM-DiT architectures. Existing methods provide only partial insight: attention maps expose a limited view of token interactions, while sparse autoencoders can discover interpretable features but do not directly reveal how these features are transformed and composed through nonlinear MLP layers. In this work, we extend transcoder-based circuit tracing to multimodal diffusion transformers. We train timestep-conditioned transcoders that faithfully approximate the input-output behavior of MLP sublayers in FLUX.1[schnell]. By replacing MLPs with transcoders and linearizing the remaining computation, we obtain exact feature-to-feature attribution and recover compact, interpretable circuits. Empirically, our transcoders match or slightly outperform sparse autoencoders on the sparsity-faithfulness tradeoff. The resulting circuits reveal mechanisms underlying attribute binding and cross-stream semantic propagation, and provide causal explanations for systematic generation errors. Moreover, circuit-guided interventions are substantially more precise and effective than standard SAE-based steering. Our results demonstrate that transcoder-based circuit analysis is feasible for state-of-the-art diffusion transformers and provides a powerful framework for understanding and controlling multimodal generative models. The code is available at https://github.com/Artalmaz31/DifFRACT

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

E-mem: Multi-agent based Episodic Context Reconstruction for LLM Agent Memory

arXiv:2601.21714v5 Announce Type: replace Abstract: The evolution of Large Language Model (LLM) agents towards System~2 reasoning, characterized by deliberative, high-precision problem-solving, requires maintaining rigorous logical integrity over extended horizons. However, prevalent memory preprocessing paradigms suffer from destructive de-contextualization. By compressing complex sequential dependencies into pre-defined structures (e.g., embeddings or graphs), these methods sever the contextual integrity essential for deep reasoning. To address this, we propose E-mem, a framework shifting from Memory Preprocessing to Episodic Context Reconstruction. Inspired by biological engrams, E-mem employs a heterogeneous hierarchical architecture where multiple assistant agents maintain uncompressed memory contexts, while a central master agent orchestrates global planning. Unlike passive retrieval, our mechanism empowers assistants to locally reason within activated segments, extracting context-aware evidence before aggregation. Evaluations on the LoCoMo benchmark demonstrate that E-mem achieves over 54\% F1, surpassing the state-of-the-art GAM by 7.75\%, while reducing token cost by over 70\%.

24.
arXiv (CS.AI) 2026-06-12

CausalMoE: A Billion-Scale Multimodal Foundation Model for Granger Causal Discovery with Pattern-Routed Heterogeneous Experts

arXiv:2606.13024v1 Announce Type: cross Abstract: Granger Causal Discovery (GCD) is fundamental for analyzing temporal dependencies in complex systems. However, existing neural GCD methods predominantly rely on a "one-size-fits-all" paradigm, struggling to capture distribution shifts and dynamic regime changes inherent in real-world time series. This often leads to entangled representations and spurious causal graphs. In this paper, we propose CausalMoE, a billion-scale multimodal Granger causal foundation model that explicitly models patch-level heterogeneity. CausalMoE introduces a Pattern-Routed Mixture of Heterogeneous Experts, which dynamically identifies latent temporal patterns and routes patches to specialized domain experts, effectively decoupling regime-specific mechanisms from shared dynamics. To ensure interpretable graph recovery, we design a Causality-Aware Self-Attention mechanism operating across variables, yielding sparse Granger causal graphs via proximal optimization. Furthermore, CausalMoE is the first to integrate LLMs and VLMs to align numerical signals with textual and visual priors, regularizing causal estimation in complex scenarios. Extensive experiments demonstrate that CausalMoE establishes a new state-of-the-art on fully supervised benchmarks, while effectively generalizing to few-shot settings where traditional methods fail.

25.
medRxiv (Medicine) 2026-06-15

CDH13 is associated with cellular viability after exposure to ionizing radiation using genome-wide screening

Background: It is well known that genetic variants contribute to cellular sensitivity to chemotherapeutic agents and ionizing radiation (IR). The aim of this study was to identify single nucleotide polymorphisms (SNPs) and genes associated with the spectrum of normal cellular sensitivity of lymphoblastoid cell lines (LCLs) towards ionizing radiation and mitomycin C (MMC). Methods: In a first step, we determined the viability of LCLs established from male participants of the Berlin Aging Study II (BASE-II) aged >=62 years following treatments with increasing doses of IR (n=137 cell lines) or MMC (n=140 cell lines) using the alamarBlue assay. Results from intra-experimental triplicates and three independent experiments for each cell line and treatment were used to calculate the area under the curves (AUCs) representing the specific sensitivity to IR and MMC of each LCL. The data from these experiments were subsequently used as outcomes in genome-wide association studies (GWASs). In addition, we calculated polygenic risk scores (PGS) from UK Biobank GWAS results for four cancer-related phenotypes and assessed the extent to which the variance in the IR and MMC sensitivity is explained by these PGS. Results: The GWAS analyses revealed one variant, rs74728080, located in CDH13 on chromosome 16, to show genome-wide significant (p < 5 x 10-8, beta = 2.81) association with cellular viability after treatment with IR. In the GWAS on MMC sensitivity the most interesting signal was elicited by SNP rs113978558 in an intron of the PLD5 gene on chromosome 1 (p = 9.232 x 10-8; beta = 1.44). Several other SNPs with statistically suggestive (i.e., p < 1 x 10-5) evidence of association with IR or MMC sensitivity were identified. PGSs calculations from GWAS of four cancer-related traits in UKB explained ~5% and ~3% of phenotypic variance in IR- and MMC-induced cell viability, respectively. Conclusion: The genome-wide significant association of rs74728080 with IR sensitivity and the location of this variant in CDH13 is interesting and functionally highly plausible given its known involvement in oxidative-stress response and function as tumor suppressor. Taken together, our novel data suggest that CDH13 may be genuinely involved in regulating cellular IR sensitivity.