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

"I Didn't Make the Micro Decisions": Measuring, Inducing, and Exposing Goal-Level AI Contributions in Collaboration

As large language models (LLMs) increasingly shape how users form, refine, and extend their goals, attributing contributions in human-AI collaboration becomes critical for users calibrating their own reliance and for evaluators assessing AI-assisted work. Yet existing methods focus on final artifacts, missing the process through which goals themselves are jointly shaped. We introduce a goal-level attribution framework, CoTrace, that decomposes explicit goals into verifiable requirements and traces both direct contributions and indirect influences across dialogue turns. Applying CoTrace to 638 real-world collaboration logs, we find that while models account for only 11-26% of goal-shaping contribution, they contribute substantially more on introducing lower-level concrete requirements, and make various kinds of indirect contributions. Through controlled simulations, we show that interaction design choices significantly affect model goal-shaping behavior. In a user study, exposing participants to goal-level analyses shifts their perceived contributions by nearly 2 points on a 5-point scale, revealing systematic miscalibration in how users understand their own AI-assisted work.

02.
arXiv (CS.CV) 2026-06-17

Reasoning Text-to-Video Retrieval for Operating Room Clips via Action-Driven Digital Twins

Text-to-video retrieval in operating rooms (OR) is an enabling technology for OR safety, as it allows stakeholders to retrieve and inspect recordings of specific events. However, because the most safety-critical events may not follow the common structure, to unlock its full potential text-to-video retrieval must be able to handle implicit queries that require reasoning to identify the right video (e.g., the step right before clipping). However, existing methods rely on global embeddings that cannot reason over such queries. We propose OR3, a text-to-video retrieval method that converts clips into action-driven digital twins (ActDTs), grouping concurrent subject-action-object triplets under non-overlapping temporal intervals. Moreover, rather than cross-modal matching through paired encoders, OR3 performs imagination-based retrieval where an LLM generates hypothetical ActDTs from queries. This enables intra-modal matching via a single encoder trained with ActDT-tailored hard negatives. Finally, evidence-grounded refinement revises imagined ActDTs based on discrepancies with top candidates to capture procedure-specific patterns. We construct a benchmark from MM-OR with 276 implicit queries across four reasoning categories over 386 clips from robotic knee procedures. OR3 achieves 57.6 R@1 and 77.3 R@5, outperforming the strongest baseline. These results demonstrate that OR3 enables fine-grained discrimination between visually similar OR video clips through temporal action reasoning.

03.
arXiv (quant-ph) 2026-06-11

Shadow Engineering of Quantum Processes

arXiv:2606.12035v1 Announce Type: new Abstract: Characterizing quantum processes is essential for hardware benchmarking, error diagnosis, and algorithm verification. While recent work [PRX QUANTUM 4, 040337 (2023)] extended classical shadows from quantum state to quantum process, enabling efficient single-channel $\mathcal{E}$ property prediction, its applicability to composite processes $f(\mathcal{E}_1, \mathcal{E}_2,\cdots, \mathcal{E}_k)$ remains unexplored. We introduce shadow engineering, a framework encoding the classical shadows of processes into sparse transfer matrices to predict $f(\mathcal{E}_1, \mathcal{E}_2,\cdots, \mathcal{E}_k)$ properties with proven polynomial sample complexity, matching single-channel efficiency while exponentially lower than quantum process tomography. Crucially, this approach repurposes existing $\mathcal{E}_m$-shadow data without physical execution of $f(\mathcal{E}_1, \mathcal{E}_2,\cdots, \mathcal{E}_k)$, enabling flexible quantum process characterization with minimal hardware overhead. We demonstrate the framework's effectiveness and practicality on a superconducting quantum processor for typical applications such as error mitigation and Hamiltonian dynamical simulation. This framework unlocks new capabilities for predicting complex quantum behaviors without physical re-execution, with immediate applications in near-term device calibration and quantum simulation.

04.
arXiv (math.PR) 2026-06-15

Lehner's operator norm formulas, semidefinite programming, and spiked matrix models

arXiv:2606.14687v1 Announce Type: new Abstract: Lehner (1999) derived elegant formulas for the operator norm $\|\mathfrak{X}\|$ of operators of the form $\mathfrak{X} = \mathbf{A}_0 \otimes \mathfrak{1} + \sum_{i = 1}^n \mathbf{A}_i \otimes \mathfrak{m}_i$, also easily generalized to the spectral edge $\lambda_{\max}(\mathfrak{X})$, in terms of nonlinear optimization problems over positive definite matrices. Here the $\mathbf{A}_i$ are finite-dimensional Hermitian matrices, the $\mathfrak{m}_i$ are either free semicircular or free Rademacher families of operators, and $\mathfrak{1}$ is the identity operator. We first show that both of Lehner's nonlinear optimizations can be rewritten as linear semidefinite programs (SDPs), even in the Rademacher case where Lehner's optimization is not itself convex. We give the primal and dual forms of these SDPs, derive the complementary slackness relations and consequences thereof, and propose that the SDPs are more stable and accurate than the iterative numerical scheme proposed in Lehner's original work. We then apply the SDPs from the semicircular case to spiked matrix models, studied recently via Lehner's formula by Bandeira, Cipolloni, Schröder, and van Handel (2024). We give a new proof of the Baik–Ben Arous–Péché (BBP) transition they establish in models with isotropic (but possibly correlated) Gaussian noise by constructing feasible variables for the associated primal and dual SDPs. Combining our construction with a sensitivity interpretation of optimal dual variables, we study the fluctuations of leading eigenvectors of such models. We conjecture and give numerical evidence that these fluctuations are Gaussian but anisotropic and non-universal, and that their covariance may be computed in terms of the optimizer of the dual of Lehner's formula, which in turn is approximately the leading eigenmatrix of a completely positive operator associated to the covariance of the noise model.

05.
arXiv (CS.LG) 2026-06-18

ToolChain-CRC: Conformal Risk Control for Agentic AI Under Retrieval and Tool-Use Drift

arXiv:2606.18467v1 Announce Type: cross Abstract: Modern AI agents retrieve documents, call tools, check intermediate information, and then produce a final answer or action. This creates a risk-control problem that is not visible from the final answer alone. A final response may look acceptable even when the retrieval was weak, a tool output was wrong, or an earlier step was unsupported. We propose ToolChain-CRC, a conformal risk-control method for retrieval-augmented and tool-using agents under drift. The method treats each agent run as a full trajectory of actions, observations, and final output. It builds step-level risk scores, combines them into a trajectory risk score, calibrates an accept-or-intervene rule, and adds an anytime alarm that can stop risky runs before the final answer. We prove trajectory-level risk control under exchangeable calibration runs, give a drift-aware extension with auditable constants, and prove an anytime escalation rule through a supermartingale construction. Experiments cover synthetic tool-chain drift, RAG/tool-use stress tests, public SQuAD-derived retrieval tasks, an API-free agentic QA case study, ablations, target-risk sensitivity checks, 20-seed robustness checks, a drift-margin audit, and a live RAG/tool-use agent benchmark. Across these settings, final-answer-only calibration can miss retrieval and tool failures, while trajectory-level calibration keeps accepted-trajectory risk below the target.

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

CellNet – Localizing Cells using Sparse and Noisy Point Annotations

Counting living cells is an important step in many biological research workflows. Our collaborators at the Wellcome Sanger Institute study vital genes in humans via large scale saturation genome editing screening, which requires repeatedly counting cells a great number of times. Computer Vision based automation is crucial for high throughput and resource efficiency. In this work, we develop a regression-based deep learning computer vision algorithm to detect and count cells in phase-contrast microscopy images. To reduce annotation effort, which in practice often becomes a bottleneck, we focus on counting cells only using sparse point annotations, which are fast and easy to acquire. By comparison to state-of-the-art 0-shot methods, we show that regression-based counting is a promising alternative in low data regimes. Through developing methods to automatically count living cells in microscopy images, we contribute to valuable research on the human genome. The code is available at https://github.com/beijn/cellnet.

07.
arXiv (CS.CV) 2026-06-19

Reliability-Aware Prototype Calibration for Frozen Pose-Flow Video Anomaly Detection

Pose-flow video anomaly detectors are attractive for one-class surveillance because they provide likelihood-based rankings for tracked skeleton windows. However, a single likelihood score may hide multimodal normal behavior and be sensitive to pose-observation noise. We study a frozen-detector setting in which the pose-flow backbone, cached skeleton tracks, and evaluation pipeline are fixed. Reliability-Aware Prototype Calibration (RPC) is a post-hoc score calibration method for this setting. It adds a standardized nearest-prototype deviation in the frozen latent space to the standardized flow score, and uses keypoint confidence only to gate this added geometric evidence. Thus, RPC preserves the original density signal while correcting the ranking with empirical normal-mode structure under pose reliability. Across two frozen pose-flow backbones and four datasets, RPC improves frame-level AUROC in all eight backbone-dataset pairs, with gains ranging from 0.34 to 4.49 percentage points and averaging 2.03 points. Ablation and reliability analyses show that prototype deviation is the main corrective signal, while reliability gating is most useful when pose observations are less trustworthy. These results suggest that lightweight post-hoc calibration can strengthen cached pose-flow systems when retraining or reproducing the full pose pipeline is impractical.

08.
bioRxiv (Bioinfo) 2026-06-17

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Transfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systematic tRNAome profiling, we currently lack a simple and robust statistical framework for nanopore tRNA data analyses. Here, we address this gap by developing AMaNITA (Abundance, Modifications, and Nanopore Intensity Toolbox Application), an end-to-end bioinformatic workflow that enables simplified, robust, and scalable analyses of nanopore native tRNA sequencing datasets. AMaNITA streamlines the entire analytical trajectory: from upstream processing (basecalling, mapping, filtering, batch effect correction) to downstream assessment of differential tRNA abundance and modification stoichiometry. The workflow generates an interactive HTML report for data exploration and analysis, allowing the user to download the source data files and resulting plots. AMaNITA can be executed using Singularity from the command line, without requiring installation of dependencies.

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

HiLo-Token: Input-Adaptive High-Low Frequency Token Compression for Efficient Image Editing

Creative image editing tools, such as Photoshop's Remove or Generative Fill buttons, are central to everyday customer use and account for a major share of traffic in Photoshop and Lightroom. However, current generative AI models face significant latency challenges, which become even more pronounced when transitioning from convolution-based U-Nets to Diffusion Transformers (DiTs). In our evaluation on hundreds of representative image editing samples spanning a wide range of mask ratios, the DiT module alone accounts for an average of 73% of the total model latency, even after being distilled from 50 timesteps down to 8 timesteps. To tackle this challenge, we propose $HiLo-Token$, an input-adaptive token compression framework that allocates more token budget to high-frequency, rich-context regions while assigning fewer tokens to low-frequency areas. Specifically, for the editing region specified by the user mask, we retain all tokens within a dilated mask to preserve strong locality and contextual relevance. Outside the editing region, we introduce a simple yet effective high-frequency token selection strategy based on spatial frequency to capture important local details, while using tokens from a 16x downsampled image to represent low-frequency components and preserve the blurry but global structure. Extensive experiments on production-level evaluation data validate the effectiveness of the proposed method, achieving 3.13x, 2.59x, and 1.67x DiT speedups on A100-80GB for image editing tasks across small, medium, and large mask ratio categories with average ratios of 6.38%, 15.92%, and 35.36%, respectively, without any regression in generation quality.

10.
arXiv (CS.AI) 2026-06-17

DRFLOW: A Deep Research Benchmark for Personalized Workflow Prediction

arXiv:2606.18191v1 Announce Type: new Abstract: Deep research (DR) systems are increasingly used for complex information-seeking tasks, but existing works mainly focus on generating reports and summaries. In contrast, many enterprise tasks instead require an agent to identify concrete workflows which is a sequence of action-steps. For example, rather than summarizing budgeting policies, an agent should be able to determine the steps needed to answer a question such as: "How do I request new headcount given a fixed budget?". Therefore, we introduce DRFLOW, a benchmark for evaluating personalized workflows predicted by agents from heterogeneous sources. Each task requires the agent to identify relevant evidence from scattered sources, then use that evidence to predict the correct action-step sequence for the user's task. DRFLOW contains 100 tasks across five domains, with 1,246 reference workflow steps grounded in more than 3,900 sources. We define seven diagnostic metrics covering factual grounding, step recovery, structural ordering, condition resolution, and personalization. We further present DRFLOW-Agent (DRFA), a workflow-oriented reference agent to predict personalized workflow. We show that although DRFA improves over strong baseline agents (upto 10.02% average F1 score), there is substantial room for improvement remains across these workflow metrics, indicating that predicting complete and correct personalized workflows remains a challenging frontier for deep research.

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

LLMZero: Discovering Adaptive Training Strategies for RL Post-Training via LLM Agents

RL post-training strategies are dataset-dependent and reveal a recurring empirical pattern: capacity parameters accumulate monotonically across stages, while regularization parameters predominantly oscillate in response to shifting training dynamics. This distinction matters because fixed schedules commit all parameters to fixed trajectories and therefore cannot express the non-stationary exploration-exploitation tradeoffs that regularization must track; the principle provides actionable design rules for multi-stage training. We discover this through LLMZero, a system where LLM agents search over training trajectories via tree search, diagnosing pathologies at each checkpoint and proposing coordinated multi-parameter transitions. Across 4 diverse GRPO tasks, LLMZero discovers strategies that improve over the base model by 9% to 140% relative and over grid search by 6% to 15% relative, consistently outperforming random search and the skill-based agent. The structural principle transfers across tasks, providing an explanation for why discovered strategies take qualitatively different forms yet share similar parameter dynamics.

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

Physics-Informed Neural Networks and Radial Basis Functions for PDEs with Dirac Delta Sources

arXiv:2606.12735v1 Announce Type: new Abstract: Physics-Informed Neural Networks (PINNs) are a machine learning method for solving forward and inverse Partial Differential Equations (PDEs). When applied to PDEs with Dirac delta functions in the forcing terms, boundary conditions, or initial conditions, PINNs require approximating them with smooth surrogate functions, a practice that can introduce significant modeling errors. In this work, we exploit the interpretation of PINNs as Residual Least Squares (RLS) methods and show that this perspective enables direct treatment of Dirac delta terms by integrating the weak-form equation. Among RLS formulations other than PINN, we focus on the Radial Basis Function (RBF) expansion (also known as a single-layer RBF Network). We show that while integrating out the Dirac delta in PINNs causes residuals to fail to converge to zero, RBF-RLS consistently provides good forward and inverse solutions to transport problems. We explain this finding using the Neural Tangent Kernel (NTK) theory. We test both approaches on linear PDEs that represent groundwater flow and transport in porous media and rivers. We solve inverse problems to fit synthetic data, noisy synthetic data, and real-world measurements.

14.
arXiv (CS.CV) 2026-06-16

Unified Multimodal Model for Brain MRI Imputation and Understanding

Multimodal large language models (MLLMs) hold great potential for medicine, as they inherit knowledge from LLM and allow multiple data modalities to be integrated, analysed and interpreted in natural language. However, the field of medical MLLMs is constrained by non-trivial challenges, notably the scarcity of high-quality training data and the frequent occurrence of missing data in the real-world clinical setting. Here, we propose a novel unified multimodal model, UniBrain, for brain magnetic resonance image (MRI) analysis. To address potential missing brain MRI modalities, we employ a unified training strategy to perform joint imaging modality imputation and brain image understanding. During training, an interleaved and description-enriched data flow is constructed to train the model in an autoregressive manner, enabling medical reasoning with generated multimodal data. A self-alignment strategy is introduced to leverage dense image embeddings to learn fine-grained anatomical features without requiring detailed image captions. Furthermore, we propose a dynamic hidden state mechanism to alleviate the exposure bias during long-context multimodal inference. Extensive experiments on multi-disease brain MRI dataset demonstrate that UniBrain achieves high performance for brain image imputation, understanding, and disease diagnosis under various extents of modality incompleteness.

15.
PLOS Medicine 2026-05-26

Requiring code sharing to strengthen transparency and trust in research

by Helen Lumbard, Lauren Cadwallader, Devin Soper, on behalf of the PLOS Medicine Staff Editors PLOS Medicine has always championed open science and data transparency. Now, recognizing that code is as essential a research artifact as the data it analyzes, we are strengthening our code sharing policy to further ensure reproducibility and trust in the scientific record. Recognizing that code is as essential a research artifact as the data it analyzes, this Editorial outlines how PLOS Medicine is strengthening its code sharing policy to further ensure reproducibility and trust in the scientific record.

16.
arXiv (CS.CV) 2026-06-19

Through the PRISM: Preference Representation in Intermediate States of Video Diffusion Models

Evaluating video generation with clean, pixel-based reward models disconnects evaluation from the noisy diffusion process and incurs massive VAE decoding costs. In this paper, we challenge this paradigm by asking a fundamental question: Can a powerful video generator inherently discriminate preferences directly from noisy latents? To answer this, we introduce PRISM (Preference Representation in Intermediate States of Diffusion Models). PRISM employs a lightweight Query-based Aggregation head with a frozen video diffusion backbone to decode preference signals from noisy latents. Surprisingly, PRISM not only achieves SOTA preference accuracy but also unlocks strong noise-robustness, which enables early-stage Best-of-$N$ sampling. This allows for filtering suboptimal candidates at the very beginning of denoising, drastically reducing computation while boosting video quality. We also reveal a strong positive correlation between a backbone's generative performance and its inherent evaluative power, enabling self-improving video backbones.

17.
arXiv (quant-ph) 2026-06-19

Unleashing Emergent Fermions with Rydberg Atom Simulators

arXiv:2606.19444v1 Announce Type: cross Abstract: Rydberg atom simulators, in both analog and digital modes, have attracted significant recent interest due to their versatile geometric reconfigurability. In this work, leveraging this feature, we propose two complementary approaches, one for each mode, to characterize emergent fermions in critical quantum many-body systems. In the analog mode, we assemble the Rydberg atoms in a "developable" (namely, preserving local couplings) Möbius band geometry to realize antiperiodic boundary conditions, where fermionic states reside. Spectroscopic measurement in this sector then reveals universal energy ratios of the bosonic and fermionic states. In the digital mode, we carry out a fermionic version of Kibble-Zurek ramping with a quantum circuit, directly addressing the fermionic scaling form. Reconfigurability allows an exponential speed-up of this task, with an $O(\log L\log\log L)$ circuit-depth overhead. Our work establishes the Rydberg atom simulator as a uniquely powerful platform to attack the notoriously difficult issue of experimentally probing emergent fermions that are nonlocally defined in a bosonic system.

18.
medRxiv (Medicine) 2026-06-24

Model-based Detection of Spatial Disease Boundaries Using Amortized Bayesian Inference

Disease boundary analysis identifies abrupt changes in health outcomes across geographic boundaries, guiding targeted public health interventions and outbreak surveillance. Current implementations often adopt a Bayesian "wombling" approach and largely rely on Markov Chain Monte Carlo (MCMC) posterior sampling, presenting scalability issues for large-scale disease surveillance. We leverage amortized Bayesian inference (ABI) to accelerate the detection of spatial health disparities between neighboring US counties by embedding neural posterior estimation within a Bayesian areal wombling framework. Exploiting the computational efficiency of ABI, we further introduce the Residual Disparity Elimination Target, a metric for the required reduction in mortality or prevalence for a region to eliminate a significant disparity with its neighbor. We analyze tracheal, bronchus, and lung cancer mortality rates across mainland US counties and achieve results concordant with MCMC analysis while scaling areal wombling to hundreds of outcomes and translating disparity detection into interpretable policy objectives.

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

Structural Kolmogorov-Arnold Convolutions: Learnable Function on the Values or the Filter Shape as Parameter-Efficient Alternative to Per-Edge Convolutional KANs

arXiv:2606.24371v1 Announce Type: cross Abstract: Convolutional Kolmogorov–Arnold Networks (KANs) replace the fixed weights of a convolutional kernel with learnable univariate functions. The dominant formulation attaches one such function to every kernel entry and lets it act on pixel values, expressive but parameter-heavy and prone to overfitting. We argue that the learnable functions are better placed in the structure of the convolution than on each edge, and we organise the design space along a single axis: whether the function acts on the pixel values or on the filter shape. We study three realisations. SV-KAN applies one shared univariate function to the values and leaves the spatial filter free and static, aa classical convolution with a single learnable shared activation. AG-KAN keeps the shared value function but supplies the spatial structure through a content-adaptive Gaussian gate. RF-KAN instead moves the learnable functions onto the filter shape, building each filter from oriented ridge profiles expanded in a localised oscillatory (Morlet) wavelet basis with content-adaptive amplitudes. Under a matched four-layer protocol with in-run references and three seeds, RF-KAN and SV-KAN reach $88.47\pm0.10\%$ and $88.20\pm0.31\%$ on CIFAR-10 and $64.40\pm0.19\%$ and $64.57\pm0.30\%$ on CIFAR-100, at about $0.4$M parameters. At this matched scale the shape model and the simplest value model meet at the top, both above a plain convolution and every per-edge KAN we tested, including the official Gram variant, at roughly a fifth of the parameters. A controlled study attributes the RF-KAN gain to an intrinsically localised oscillatory basis and to content adaptivity, and an ablation that removes the learned shape entirely, leaving only the shared value function, collapses accuracy by over forty points, identifying the learned shape as the load-bearing ingredient at this scale.

20.
Nature (Science) 2026-06-17

The EU needs to back its ambition to end animal testing with cash

作者: 未知作者

The European Union has declared that it wants to stop using animals in chemical safety testing. Its goal will need a timeline and a serious funding commitment. The European Union has declared that it wants to stop using animals in chemical safety testing. Its goal will need a timeline and a serious funding commitment.

21.
arXiv (CS.LG) 2026-06-18

Enhanced Graph Neural Networks using K-Hop Gaussian Diffusion

arXiv:2606.18317v1 Announce Type: new Abstract: Most graph neural network (GNN) cores rely on graph convolutions, typically implemented as message passing between direct (single-hop) neighbors. In many real-world graphs, edges can be noisy or poorly defined, limiting information propagation to local neighborhoods. Existing diffusion kernels, such as Personalized PageRank (PPR) and Heat Kernel, alleviate this issue through global propagation, but still struggle with complex local structures and distant node noise. To address these limitations, we propose a K-Hop Gaussian (KHG) diffusion kernel as a preprocessing module for graph data. KHG introduces multi-hop diffusion with Gaussian weighting for remote nodes, balancing local and global information propagation before applying standard GNNs. Experiments on multiple benchmark datasets demonstrate that KHG significantly outperforms traditional message-passing GNNs, as well as PPR and Heat Kernel diffusion, particularly in noisy or structurally complex graphs.

22.
arXiv (CS.CL) 2026-06-19

TerraMARS: A Domain-Adapted Small-Language-Model Pipeline for Mars Terraforming Literature

Researchers are interested in learning about Mars so that it may eventually become habitable for humans. To achieve this, there is a need for comprehensive knowledge of the planet's atmosphere, hydrology, surface chemistry, radiation environment, and spatial features through the scientific literature. These contain valuable information and meaningful quantitative constraints that can be used in other models and studies, such as habitability assessment and future terraforming studies. We present TerraMARS, an end-to-end information extraction pipeline that combines a domain-adapted Small Language Model to answer Mars terraforming-related questions and convert unstructured Mars science text into machine-readable structured outputs in JavaScript Object Notation (JSON) format. A corpus of open-access papers is collected and processed using a multistage retrieval and chunking framework. Google Gemma 3 1B was adapted to the domain using Quantized Low-Rank Adaptation (QLoRA) fine-tuning on Mars-specific question-answering and information extraction datasets. The resulting pipeline generates both types of output and provides a foundation for integrating knowledge from scientific literature into downstream applications like digital twins and habitability modeling for Mars. The output from this pipeline looks promising, but further improvements are needed to increase extraction accuracy and factual consistency.

23.
arXiv (CS.AI) 2026-06-18

Two-Phase Bilevel Search for the Moving-Target Traveling Salesman Problem with Moving Obstacles

arXiv:2606.18730v1 Announce Type: cross Abstract: The Moving-Target Traveling Salesman Problem (MT-TSP) seeks a minimum cost trajectory for an agent that departs from a static depot, visits a set of moving targets, each within one of their assigned time windows, and returns to the depot. In this article, we study the Moving-Target Traveling Salesman Problem with Moving Obstacles (MT-TSP-MO), a generalization of the MT-TSP where the agent trajectory must avoid moving obstacles. We present a Mixed-Integer Conic Programming (MICP) formulation that can be solved using off-the-shelf solvers, as well as a fast and scalable Two-Phase Bilevel Search (TPBS) algorithm that computes high-quality feasible solutions for the problem. We evaluate our approaches against an existing baseline algorithm on a broad range of problem instances with up to 40 targets and 40 obstacles. The results demonstrate that both the proposed methods significantly outperform the baseline with respect to success rates, solution costs, and computation time.

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

Sparsity, Superposition, and Forgetting: A Mechanistic Study of Representation Retention in Continual Learning

arXiv:2606.20431v1 Announce Type: new Abstract: Continual learning (CL) systems often forget previously acquired knowledge, yet the mechanisms driving forgetting remain hard to isolate in practice because real datasets entangle many factors. We present a controlled, toy-world framework that makes these mechanisms observable and testable. Using a synthetic generator-separator pipeline, we define ground-truth latent features, build tasks with tunable sparsity and overlap, and introduce measurable quantities for representation strength and superposition (directional overlap among features). We then study retention dynamics-the temporal change of representation strength by fitting sparse dynamical relations (via SINDy) between retention, superposition, and exposure history. A complementary task-level analysis based on effective rank characterizes how representational capacity is allocated across tasks. Our controlled experiments yield three takeaways. (1) Superposition tends to increase over time with transient dips at task boundaries, suggesting boundary-specific interference rather than steady drift. (2) Higher feature sparsity induces more superposition yet does not inevitably cause forgetting; when representations remain strong, forgetting can be reduced despite overlap. (3) Task-level effective rank grows with sparsity, indicating broader capacity usage under sparse regimes. Together, these results nuance the common intuition that more superposition leads to more forgetting by showing that overlap interacts with representation strength and capacity allocation. Our toy analysis provides falsifiable hypotheses and diagnostic tools for CL.

25.
bioRxiv (Bioinfo) 2026-06-22

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences

Sex chromosomes are central to many ecological and evolutionary processes. Evidence has accumulated that sex chromosome systems vary extensively in age, turnover and transitions, motivating renewed efforts to study the diversity of sex chromosome systems across the tree of life. However, successful genomic detection of sex chromosomes depends on several factors, including the size and divergence time, background genetic diversity, and the number of sequenced females and males. In addition, technical challenges associated with sequencing and analysing the sex-limited Y/W chromosome remain. Here, we present PhaseWY, an automated Snakemake pipeline that uses whole-genome sequencing data from multiple female and male individuals to identify sex-chromosomal regions and extract the corresponding Y/W sequences. PhaseWY (i) detects sex differences in alignment depth, (ii) applies read-based and statistical haplotype phasing, (iii) identifies sex-linked regions using haplotype clustering, and (iv) subsets autosomal, X/Z- and Y/W-linked variants for downstream analyses. We applied PhaseWY to simulated data to benchmark factors influencing sex-linkage detection and successful extraction of Y/W-linked variants. To demonstrate its practical utility, we further applied PhaseWY to the neo-sex chromosome system in Alauda larks (Alaudidae) and performed a range of downstream analyses demonstrating the scope of applications of the PhaseWY output. We conclude that PhaseWY provides an easy-to-use and reproducible tool for population-genomic analyses in non-model organisms, with particular importance for advancing our understanding of sex-chromosome evolution.