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01.
arXiv (CS.AI) 2026-06-16

Multi-Sensor Fusion for UAV Classification Based on Feature Maps of Image and Radar Data

arXiv:2410.16089v2 Announce Type: replace Abstract: The unique cost, flexibility, speed, and efficiency of modern UAVs make them an attractive choice in many applications in contemporary society. This, however, causes an ever-increasing number of reported malicious or accidental incidents, rendering the need for the development of UAV detection and classification mechanisms essential. We propose a methodology for developing a system that fuses already processed multi-sensor data into a new Deep Neural Network to increase its classification accuracy towards UAV detection. The DNN model fuses high-level features extracted from individual object detection and classification models associated with thermal, optronic, and radar data. Additionally, emphasis is given to the model's Convolutional Neural Network (CNN) based architecture that combines the features of the three sensor modalities by stacking the extracted image features of the thermal and optronic sensor achieving higher classification accuracy than each sensor alone.

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

Guava: An Effective and Universal Harness for Embodied Manipulation

arXiv:2606.18363v1 Announce Type: cross Abstract: Language models trained on large-scale vision-language data have demonstrated strong potential for embodied agents. Harnessing models through embodied tools use offers a promising alternative to end-to-end vision-language-action systems by combining high-level reasoning with external modules for perception, planning, and control. However, it remains unclear what makes an effective harness for embodied manipulation, and to what extent such a harness can unlock embodied capabilities in a wide range of reasoning models. In this work, we present Guava, a harness framework for embodied tool use developed through systematic exploration of the design space of agent workflows, action spaces, and observation spaces. Our study identifies three key ingredients for effective embodied agents: iterative perception-reasoning-action loops, semantic action abstractions, and multimodal observations. To understand whether these design principles are universal even to small models, we develop an end-to-end training pipeline that distills embodied manipulation capabilities into a 4B open-source model using fewer than 2K trajectories collected entirely in simulation. Experimental results in both simulation and real-world environments show performance comparable to frontier proprietary models while exhibiting strong generalization to unseen objects, novel instructions, and long-horizon tasks. Results suggest that a well-designed harness can serve as a scalable, model-agnostic interface for embodied manipulation, enabling strong emergent embodied capabilities in compact open-source models with minimal training data.

03.
arXiv (CS.CL) 2026-06-11

GraphInfer-Bench: Benchmarking LLM's Inference Capability on Graphs

Graph analysis underlies many applications whose answers cannot be looked up in a single record or retrieved along a path: laundering rings, drug repurposing, user preference, and scientific theme are all inferred from a node together with its neighbourhood. We introduce GraphInfer-Bench, a benchmark for whether LLMs can perform this graph inference: producing an open-ended answer that no single node supports and no path retrieves. Existing graph-QA protocols cannot test this capability: algorithm simulation, node classification, single-node description, KG-QA, and GraphRAG all admit answers retrievable from one node or along a path. GraphInfer-Bench defines five tasks along Description (what a region is) and Comparison (how regions differ), each constructed so the ground truth lives in no single node. The release contains 42,000 samples across six real-world graphs, produced automatically and screened by a four-layer quality-control protocol. We evaluate four method families against the same tasks: graph-token alignment models, zero-shot frontier closed-source LLMs, Graph2Text supervised fine-tuning, and plain GNNs as a structural reference. No method family closes the gap. Graph-token alignment partially handles description tasks (relational, theme) but collapses on comparison tasks. Frontier LLMs lead on outlier detection and community partition among LLM-based methods but lag on masked-node prediction. Graph2Text SFT is the strongest LLM-based method on the description side yet falls behind frontier LLMs on comparison. Across every task, plain GNNs match or beat the strongest LLM-based row, with the largest margin on community detection. GraphInfer-Bench surfaces graph inference as an open capability gap rather than a property of any one architecture.

04.
arXiv (math.PR) 2026-06-11

Second-order PACF asymptotics and discrimination between fractional Gaussian noise and $\operatorname{FARIMA}(0,d,0)$

Authors:

arXiv:2605.31416v2 Announce Type: replace-cross Abstract: Fractional Gaussian noise and $\operatorname{FARIMA}(0,d,0)$ have the same long-memory pole $|\theta|^{-2d}$ and hence the same leading PACF law $\alpha(n)\sim d/n$. We show that this agreement breaks at the first non-universal order. For $0

05.
arXiv (quant-ph) 2026-06-19

Applications of quantum annealing to magnetic dipole hyperfine structure constants: First results beyond energies for atoms

arXiv:2606.20166v1 Announce Type: new Abstract: We report the first results of the magnetic dipole hyperfine structure (HFS) constants of neutral $\mathrm{Li}$, Li-like $\mathrm{Be}$, neutral $\mathrm{Na}$, and Na-like $\mathrm{Mg}$ using a modified version of the Quantum Annealer Eigensolver (QAE) algorithm on D-Wave's quantum hardware. The results are benchmarked against relativistic configuration interaction with multiconfiguration Dirac Hartree-Fock (MCDHF) calculations using the General-purpose Relativistic Atomic Structure Package (GRASP), and simulated annealing. In our modified QAE, a zooming-and-sigma-annealing approach with a floating-point encoding scheme is adopted to estimate the ground-state eigenvalue and eigenvector of the relativistic Dirac-Coulomb Hamiltonian matrices ($H_{\mathrm{DC}}$) constructed from 11 or fewer configuration state functions (CSFs). For calculations with extended correlation orbital sets, we applied a CSF truncation scheme, retaining only CSFs (up to 12) that make significant contributions to the ground-state wavefunction. Our modified QAE precision is kept limited to three decimal places (up to 10 qubits). Hardware demonstrations on the D-Wave quantum processing unit (QPU) yielded results that were completely consistent with GRASP (at the chosen precision) in determining the magnetic dipole HFS constants, with accuracy varying across systems and $H_{\mathrm{DC}}$ matrix dimensions.

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

Integrated Marketing Attribution: A Bayesian Framework for Privacy-Safe Granular Measurement Anchored in MMM

arXiv:2606.16878v1 Announce Type: new Abstract: Retail marketing measurement increasingly requires granular campaign-level insights without relying on user-level tracking. However, the two dominant approaches, Marketing Mix Modeling (MMM) and Multi-Touch Attribution (MTA), often produce fragmented insights. MMM is privacy-safe and robust for channel-level planning but is too coarse for campaign optimization, while MTA provides granular attribution but has become less reliable under increasing privacy restrictions. We propose Integrated Marketing Attribution (IMA), a unified framework that combines MMM with channel specific Bayesian attribution models to derive campaign-level effects from aggregated data. By leveraging MMM-informed priors, IMA delivers granular, privacy-safe attribution while preserving consistency with MMM.

07.
bioRxiv (Bioinfo) 2026-06-11

DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

Summary: Nanopore direct RNA sequencing (DRS) enables simultaneous quantification of transcript abundance and RNA modifications from native RNA molecules, providing a unique opportunity to study transcriptional and epitranscriptomic regulation within a single experiment. However, comprehensive analysis of DRS data remains challenging, as existing workflows typically focus on individual processing steps and often require manual integration of multiple software packages for expression analysis, modification detection, statistical testing, and visualization. Furthermore, integrated differential expression and differential RNA modification analysis at both gene and isoform resolution remains poorly supported by current workflows. Here, we present DModE (Differential Modification and Expression Analysis), an end-to-end framework for integrated analysis of Nanopore DRS data. DModE combines an Epi2ME-compatible Nextflow preprocessing workflow with a dedicated Python package for downstream statistical analysis, visualization, and reporting. The framework supports differential gene and isoform expression analysis, differential RNA modification analysis at genome and transcript level, metagene profiling, exploratory epitranscriptomic analyses, and integrated assessment of relationships between expression and modification dynamics. Results are automatically summarized in interactive HTML reports, facilitating reproducible and accessible data interpretation. By integrating transcriptomic and epitranscriptomic analyses within a single framework, DModE substantially simplifies comprehensive DRS data analysis and lowers the barrier for studying RNA modification biology using Nanopore sequencing.

08.
bioRxiv (Bioinfo) 2026-06-12

PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics

Data-independent acquisition (DIA) mass spectrometry has become increasingly prevalent in proteomics as advances in instrumentation, chromatography, and computational analysis have enabled robust proteome identification across complex biological samples. However, analytical depth achieved with fast chromatographic gradients remains lower than that obtained using long-gradients, reflecting a throughput-depth trade-off. Here, we present PeptiDIA, a machine learning framework that enhances peptide identification in fast-gradient DIA data by leveraging paired fast and long-gradient acquisitions from identical samples. PeptiDIA processes DIA-NN outputs generated at relaxed false discovery rate thresholds to obtain expanded candidate peptide pools and trains gradient-boosted decision tree models using long-gradient identifications as reference labels. The model integrates DIA-NN features with engineered peptide descriptors and applies isotonic regression to calibrate probabilities, enabling controlled peptide recovery relative to the long-gradient reference. Applied to human and murine datasets spanning six tissues acquired on an Orbitrap Exploris 480, PeptiDIA increased peptide identifications by 25-34% at 1% target reference-discordance rate (RDR) and increased the number of protein groups containing at least one rescued peptide by 15-17%. Overall, PeptiDIA improves the identification depth of fast-gradient DIA-NN workflows without altering acquisition strategies. The framework is available as a web application and command-line tool at https://github.com/Jordano700/PeptiDIA.

09.
arXiv (quant-ph) 2026-06-17

Superconductor-"Metal" Transition of One-dimensional Interacting Bosons with Ohmic Quantum Dissipation

arXiv:2605.30746v2 Announce Type: replace-cross Abstract: The phase diagram of a system of interacting bosons (Cooper pairs) hoping on a one-dimensional (1D) lattice with onsite phase dissipation describing the Josephson tunneling to a nearby diffusive normal-metal electrode is studied. Starting from the system at commensurate lattice filling, it is shown by a combination of analytical techniques that the phase diagram contains two quantum phases: A dissipative Bose-Einstein condensate (D-BEC) or superconductor with long-range phase coherence, and a dissipative Mott insulator (D-Mott) or "metal" with exponentially decaying phase correlations in space and local imaginary-time correlations decaying as the local pairing correlations of the electrode. The D-Mott/metal phase can be described as a 1D array of dissipative boson puddles, weakly coupled by Josephson tunneling. The puddle size roughly corresponds to the length scale beyond which phase slips suppress phase coherence. The dissipative time-dependent Ginsburg-Landau theory phenomenologically used by Sachdev, Werner, and Troyer [Phys. Rev. Lett. {\bf 92} 237003 (2004)] for the superconductor-metal transition in quasi-1D wires is derived from this microscopic puddle picture. Thus, the criticality of the D-Mott/D-BEC transition is shown to belong to the Wilson-Fisher universality class with dynamical exponent $z\approx 2$. At small doping, the D-Mott/metal phase remains stable due to its finite compressibility, which is computed to leading order in a perturbation expansion of the dissipation strength and the inter-puddle Josephson coupling. At larger doping, using a mapping to a pseudospin chain combined with bosonization, the D-BEC/superconductor phase is the ground state for non-vanishing but arbitrarily small dissipation. Similarities and differences with deconfinement transition of an array 1D bosonic Mott insulators in anisotropic optical lattices are also discussed.

10.
arXiv (CS.AI) 2026-06-11

HiGR: Industrial-Scale Hierarchical Generative Slate Recommendation Framework in Tencent

arXiv:2512.24787v4 Announce Type: replace-cross Abstract: Slate recommendation, which presents users with a ranked item list in a single display, is ubiquitous across mainstream online platforms. While recent generative recommendation methods have shown strong potential in modeling item sequences with semantic IDs, directly applying them to industrial-scale slate recommendation faces a fundamental disconnect: entangled SID spaces confound high-level list planning, fine-grained autoregressive decoding over long sequences limits semantic planning efficiency, and token-level objectives misalign with holistic slate quality. In this paper, we propose HiGR, an industrial-scale hierarchical generative framework for slate recommendation that bridges this disconnect through a co-designed pipeline. First, HiGR learns structured SIDs via a Prefix-Contrastive Residual Quantized VAE (PCRQ-VAE). By enforcing high-level prefixes to capture shared semantics, PCRQ-VAE creates a controllable discrete space that acts as a prerequisite for efficient planning. Leveraging this structured space, our Hierarchical Slate Decoder (HSD) shifts autoregressive modeling from entangled token-level decoding to coarse-grained preference embeddings. This design significantly reduces inference latency while allowing explicit global slate structure planning. Finally, this stable planning space enables an ORPO-based listwise alignment mechanism to optimize triple-objective implicit feedback-ranking fidelity, genuine user interest, and diversity. Extensive offline experiments show that HiGR outperforms state-of-the-art baselines by over 10% in offline recommendation quality while achieving a $5\times$ inference speedup. Online A/B tests on Tencent platforms further improve watch time by 1.22% and video plays by 1.73%. HiGR has been deployed on multiple Tencent platform surfaces, serving hundreds of millions of users and proving its industrial-scale applicability.

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

Future Dynamic 3D Reconstruction: A 3D World Model with Disentangled Ego-Motion

Forecasting the evolution of dynamic environments is crucial for autonomous agents. While generative world models have recently achieved high photorealism in 2D video synthesis by mixing ego-motion and environmental dynamics within the image plane, they exhibit physical inconsistencies, such as morphing or vanishing objects, especially over long time horizons. In this paper, we propose FR3D, a world model that predicts a persistent 3D latent representation for future dynamic 3D reconstruction. Unlike prior works that treat the world as a sequence of image-based features, FR3D explicitly decouples the 3D evolution of the scene from the agent's trajectory, treating the inferred ego-motion as a latent proxy for action. This disentanglement resolves the ambiguities between self-motion and world-motion, ensuring geometric consistency into the future. Furthermore, we introduce a teacher-student distillation strategy that leverages the spatial "common sense" of off-the-shelf foundation models, leading to robust zero-shot generalization. Extensive experiments demonstrate FR3D's strong performance for future dynamic 3D reconstruction from monocular observations across multiple datasets, even 2 seconds into the future. Project page: https://fr3d-wm.github.io.

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

Robust Regularized Policy Iteration under Transition Uncertainty

arXiv:2603.09344v3 Announce Type: replace Abstract: Offline reinforcement learning (RL) enables data-efficient and safe policy learning without online exploration, but its performance often degrades under distribution shift. The learned policy may visit out-of-distribution state-action pairs where value estimates and learned dynamics are unreliable. To address policy-induced extrapolation and transition uncertainty in a unified framework, we formulate offline RL as robust policy optimization, treating the transition kernel as a decision variable within an uncertainty set and optimizing the policy against the worst-case dynamics. We propose Robust Regularized Policy Iteration (RRPI), which replaces the intractable max-min bilevel objective with a tractable KL-regularized surrogate and derives an efficient policy iteration procedure based on a robust regularized Bellman operator. We provide theoretical guarantees by showing that the proposed operator is a $\gamma$-contraction and that iteratively updating the surrogate yields monotonic improvement of the original robust objective with convergence. Experiments on D4RL benchmarks demonstrate that RRPI achieves strong average performance, outperforming recent baselines including percentile-based methods on the majority of environments while remaining competitive on the rest. Moreover, RRPI exhibits robust performance by aligning lower $Q$-values with high epistemic uncertainty, which prevents the policy from executing unreliable out-of-distribution actions.

13.
arXiv (math.PR) 2026-06-11

Approximation Properties of Evolutionary Dynamics in Continuous-Time Finite State Space Games

Authors:

arXiv:2606.11193v1 Announce Type: cross Abstract: This thesis studies the convergence of finite-population stochastic evolutionary dynamics to their deterministic mean-field limit in continuous-time finite state space games. We first develop refined ergodic theorems for Markov chains with a single positive-recurrent class, guaranteeing the existence of a unique invariant distribution and almost-sure convergence of time averages. Next, we prove that the mean-field model, described by a system of Lipschitz-continuous ordinary differential equations, admits a unique solution that depends continuously on its initial condition and that constitutes the almost-sure limit for the empirical distributions with fixed policy. Furthermore, we show that every Mixed Stationary Nash Equilibrium of the mean-field game is approximated by a Nash equilibrium of the corresponding $N$-player game within an error $\epsilon$ for sufficiently large $N$. We finally demonstrate, by Kurtz's theorem, that the empirical state-policy distribution converges in probability to the mean-field trajectory. Numerical simulations conducted in MATLAB confirm the theoretical $\mathcal{O}(N^{-1/2})$ convergence rate in both models across a range of population sizes.

14.
arXiv (CS.AI) 2026-06-15

MA-ProofBench: A Two-Tiered Evaluation of LLMs for Theorem Proving in Mathematical Analysis

arXiv:2606.13782v1 Announce Type: new Abstract: Large Language Models (LLMs) have made notable progress in automated theorem proving, yet existing formal benchmarks remain limited in both mathematical coverage and difficulty. Most are concentrated in areas that are easier to formalize, such as algebra and elementary number theory, and provide limited coverage of subfields that require deeper reasoning, including mathematical analysis. To address this gap, we introduce MA-ProofBench, to the best of our knowledge, the first formal theorem-proving benchmark dedicated to Mathematical Analysis. The benchmark contains 200 formalized theorems covering 6 core topics and 27 subcategories, including measure and integration theory, complex analysis, and functional analysis. The problems are divided into two difficulty levels, an undergraduate level (Level I, 100 problems) and a Ph.D. qualifying level (Level II, 100 problems), to evaluate how well LLMs perform formal reasoning at different mathematical depths. Each problem is constructed through a human-led, LLM-assisted formalization pipeline followed by independent expert review, ensuring that the formal statements remain faithful to the original mathematics. We evaluate a range of recent general-purpose reasoning models and formal theorem provers on MA-ProofBench. However, most models perform poorly: even the best-performing model, GPT-5.5, achieves only 16% Pass@8 on Level I and 5% on Level II, while most models stay close to 0% on Level II. Further analysis identifies Mathlib hallucinations and incomplete proofs as the two dominant failure modes, while an evaluation on the natural-language version of the benchmark exposes a clear gap between informal and formal reasoning. MA-ProofBench is intended to serve as a reliable reference for tracking progress in formal mathematical reasoning in advanced domains.

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

LabVLA: Grounding Vision-Language-Action Models in Scientific Laboratories

Scientific laboratories increasingly rely on AI systems to reason about experiments, but the physical act of doing science remains largely outside their reach. AI can help read literature, generate hypotheses, and plan protocols, yet the execution of those protocols at the bench still requires a human operator. Vision-Language-Action (VLA) models provide one possible interface between written protocols and robot execution, but existing policies are trained mostly on household and tabletop demonstrations and rarely encounter the instruments, transparent liquids, or fixed protocol workflows found in scientific laboratories. Closing this gap requires both laboratory-specific supervision and a unified learning framework that can accommodate the diverse robot embodiments used to execute experimental protocols. We therefore identify data and embodiment as central bottlenecks alongside model design. To address the data side, we build RoboGenesis, a simulation-based workflow and data engine that composes configured laboratory workflows from atomic skills, validates and filters rollouts, and exports structured demonstrations across supported robot profiles. On the policy side, we present LabVLA, trained with a two-stage recipe: FAST action token pretraining first makes the Qwen3-VL-4B-Instruct backbone action aware before any continuous control is learned, and flow matching posttraining then attaches a DiT action expert under knowledge insulation. On the LabUtopia benchmark, LabVLA achieves the highest average success rate among all evaluated baselines under both in-distribution and out-of-distribution settings.

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

Identifiable Markov Switching Models with Instantaneous Effects and Exponential Families

arXiv:2606.02231v2 Announce Type: replace-cross Abstract: Temporal systems often exhibit non-stationary behaviour, such as seasonal climate variation or glucose fluctuations in patients with type-1 diabetes. One way to model non-stationarity is through discrete latent regimes, i.e., stationary segments of time. Such systems induce a Markov Switching Model (MSM), a class of Hidden Markov Models with autoregressive dependencies among latent regimes and observed variables. Identifying latent regimes is challenging in the presence of frequent regime switches and nonlinear and non-Gaussian dynamics, particularly when there are instantaneous effects between the variables, e.g., due to slow rates of measurements. In this work, we establish the identifiability of both latent regimes and regime-dependent causal structures under temporal regime dependencies, nonlinear lagged and instantaneous effects, and independent noise from the exponential family. Our identifiability theory subsumes non-temporal mixtures of causal models. Furthermore, we introduce FlowMSM, a regime detection framework that can be paired with any stationary causal discovery method to recover regime-dependent causal structures. Experiments on synthetic benchmarks and a financial economics dataset demonstrate the effectiveness of our approach to detect latent regimes and discover causal structures from non-stationary time series.

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

Doc-to-Atom: Learning to Compile and Compose Memory Atoms

Long input sequences are central to document understanding and multi-step reasoning in Large Language Models, yet the quadratic cost of attention makes inference both memory-intensive and slow. Context distillation mitigates this by compressing contextual information into model parameters, and recent work such as Doc-to-LoRA amortizes context distillation into a single forward pass that generates one LoRA adapter per document. However, producing a single monolithic adapter for all queries leads to irrelevant-query interference, limited compositional recall, and poor scalability to long-document reasoning. To address these challenges, we propose Doc-to-Atom (Doc2Atom), a compositional parametric memory framework that decomposes each document into semantically typed knowledge atoms. Each atom is compiled into an independent micro-LoRA adapter and a provenance retrieval key. At inference time, a lightweight query router selects and assembles only the relevant atoms into a query-specific adapter, which is then injected into a frozen base model. The entire system is trained end-to-end through a multi-objective distillation framework. Experiments on six diverse QA benchmarks demonstrate that Doc2Atom outperforms Doc-to-LoRA baselines while reducing the memory cost of document internalization.

18.
arXiv (math.PR) 2026-06-12

Averaging principles for nonautonomous multiscale McKean-Vlasov stochastic systems

arXiv:2606.12820v1 Announce Type: new Abstract: This paper investigates a class of nonautonomous multiscale McKean-Vlasov stochastic systems. By leveraging the nonautonomous Poisson equation, we rigorously establish both strong and weak averaging principles, accompanied by explicit convergence rates. Notably, the coefficients of the averaging equations derived in the general case retain dependence on the scaling parameter $\varepsilon$. However, under the additional assumptions that the fast-scale coefficients are either asymptotically convergent or time-periodic, we demonstrate that the slow component converges, in the strong or weak sense, to averaging equations with coefficients independent of $\varepsilon$.

19.
arXiv (CS.LG) 2026-06-18

MetaboNet-Bench: A Multi-modal Benchmark for Glucose Forecasting in Type 1 Diabetes

arXiv:2606.18640v1 Announce Type: new Abstract: Glucose forecasting algorithms are an important aspect of glycemic control management in type 1 diabetes. So far, the research community has developed numerous algorithms and models for forecasting. However, it is well-recognized that the lack of standardized model performance evaluation benchmarks makes fair comparison difficult and hinders further innovation, and thus benchmark standardization is in urgent need. Furthermore, many published glucose forecasting algorithms are limited to CGM data alone, ignoring other multimodal signals such as insulin dosing and carbohydrate intake. Here, we introduce MetaboNet-Bench, a benchmark for multimodal glucose forecasting for patients with type 1 diabetes that provides an extensible open-source evaluation framework for comparison of glucose forecasting algorithms that leverage glucose, insulin, and carbohydrate data. We then demonstrate its utility by benchmarking several recently published glucose forecasting models and a custom multimodal time-series model, representing different model architectures. The results show that the benefit of adding data modalities is conditioned on the complexity of the model and that incorporating more clinical metrics helps identify meaningful gaps to fill for future research.

20.
arXiv (CS.AI) 2026-06-17

CogGen: Cognitive-Load-Inspired Fully Unsupervised Deep Generative Modeling for Compressively Sampled MRI Reconstruction

arXiv:2603.04438v3 Announce Type: replace-cross Abstract: Fully unsupervised deep generative modeling (FU-DGM) offers significant potential for compressively sampled magnetic resonance imaging (CS-MRI) reconstruction. Representative FU-DGM formulations, such as deep image prior (DIP) and implicit neural representation (INR), employ architectural bias to induce a low-dimensional manifold in the image space that aligns with the forward observation. However, as the underlying inverse system is highly ill-posed, prolonged iterative fitting in FU-DGM typically leads to poor efficiency and noise amplification. In this paper, guided by the cognitive principle of easy-to-hard learning, we propose CogGen, an FU-DGM framework that reformulates CS-MRI reconstruction as a staged inversion problem. Specifically, CogGen implements an self-paced curriculum learning (SPCL)-driven progressive scheduling strategy through an MRI-aware dual-threshold weighting criterion, which adaptively regulates k-space measurement participation. The data-consistency residual thresholding evaluates the fitting reliability of the current generator, while the k-space radius thresholding controls stage-wise measurement exposure, thereby avoiding uniform fitting throughout optimization. Theoretically, our analysis shows that, when early stages favor easy-to-fit measurements, CogGen yields a reduced local sufficient-iteration bound and a smaller cumulative noise-amplification bound, explaining the improved convergence behavior and reconstruction fidelity of CogGen within a finite iteration budget. Numerical experiments demonstrate that both CogGen instantiations, CogGen-DIP and CogGen-INR, achieve superior performance over prevailing CS-MRI reconstruction techniques, including unsupervised and supervised pipelines.

21.
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.

22.
medRxiv (Medicine) 2026-06-22

Early-life nutritional environment is associated with late-life cognition in the Health and Retirement Study, a pellagra epidemic natural experiment

Early-life exposures are important to several late-life health outcomes. We sought to study the effect of an in utero nutritional environment and its interaction with Alzheimer's disease (AD) genetic risk on late-life cognitive function. We used a natural experiment created by the pellagra epidemic, a nutritional disease caused by a vitamin B3 deficiency, to evaluate the association between in utero pellagra epidemic exposure and late-life cognitive function in the Health and Retirement Study (N = 18,285). We also evaluated whether the in utero exposure could modify the AD polygenic score's (PGS) effect on cognition. In utero pellagra epidemic exposure was significantly associated with cognition ({beta} = -0.025). However, these effects were not isolated to the prenatal period as exposure during childhood periods also had an effect. The interaction between the in utero exposure and the AD PGS was significant, where the genetic effect on cognition was amplified with increasing (progressively worse) in utero exposure levels. These associations imply that the early-life nutritional environment affects late-life cognitive function and that these effects can modify genetic risk.

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

Proximal Policy Optimization for Amortized Discrete Sampling

arXiv:2606.15793v1 Announce Type: cross Abstract: This paper explores policy gradient algorithms for training stochastic policies to sample from structured discrete probability distributions under the Generative Flow Network (GFlowNet) framework. Building on extensive theoretical connections between GFlowNets and entropy-regularized reinforcement learning, we derive equivalents of standard policy gradient algorithms for training GFlowNets, as well as experimentally explore their various methodological aspects, including baseline training and advantage estimation. Most importantly, our work is the first to derive and successfully apply proximal policy optimization to GFlowNets, showing its improved convergence speed and data efficiency compared to standard GFlowNet training objectives on benchmarks ranging from synthetic energies to molecular graph generation.

24.
bioRxiv (Bioinfo) 2026-06-20

Systematic Evaluation of Feature Representations for Cancer-Associated sORF Prediction in Non-coding RNA

Short open reading frames (sORFs) within non-coding RNAs (ncRNAs) have arisen as a hidden layer of gene regulation, encoding small peptides that represent a new class of cancer regulators with diagnostic and therapeutic potential. However, inferring associations between sORFs to specific cancer types remains challenging and requires computational approaches for accurate prediction. Recently, the CoraL framework introduced the first computational approach for predicting cancer-associated peptides, focusing primarily on model architecture while overlooking how feature extraction strategies influence predictive accuracy. We present a systematic evaluation of machine learning models and feature extraction approaches to predict cancer-associated sORFs across 15 cancer types. We benchmarked seven traditional machine learning algorithms combined with three feature extraction methods: k-mer frequency, Word2Vec embeddings, and genomic language model (gLM)-based embeddings. To our knowledge, this is the first study applying gLM-derived embeddings to the prediction of cancer-associated sORFs in ncRNA. Our results show that traditional machine learning models with appropriate feature extraction outperform the CoraL baseline across all cancer types, achieving up to 10% higher accuracy in some of the 15 evaluated datasets. Interestingly, k-mer features consistently outperformed gLM embeddings without fine-tuning, suggesting that local sequence composition may provide more discriminative information for this task and that pre-trained genomic representations may require task-specific adaptation to fully capture these patterns. Additionally, we observed that the way sequences are tokenized, such as the k-mer length, can affect performance: longer fragments (e.g., k=7) sometimes reduced accuracy for Random Forest but had a smaller effect on MLP. Our findings suggest that appropriate feature engineering can provide greater improvements than increasing model complexity.

25.
arXiv (CS.CV) 2026-06-12

Iterative Tool Usage Exploration for Multimodal Agents via Step-wise Preference Tuning

Multimodal agents, which integrate a controller e.g., a vision language model) with external tools, have demonstrated remarkable capabilities in tackling complex multimodal tasks. Existing approaches for training these agents, both supervised fine-tuning and reinforcement learning, depend on extensive human-annotated task-answer pairs and tool trajectories. However, for complex multimodal tasks, such annotations are prohibitively expensive or impractical to obtain. In this paper, we propose an iterative tool usage exploration method for multimodal agents without any pre-collected data, namely SPORT, via step-wise preference optimization to refine the trajectories of tool usage. Our method enables multimodal agents to autonomously discover effective tool usage strategies through self-exploration and optimization, eliminating the bottleneck of human annotation. SPORT has four iterative components: task synthesis, step sampling, step verification, and preference tuning. We first synthesize multimodal tasks using language models. Then, we introduce a novel trajectory exploration scheme, where step sampling and step verification are executed alternately to solve synthesized tasks. In step sampling, the agent tries different tools and obtains corresponding results. In step verification, we employ a verifier to provide AI feedback to construct step-wise preference data. The data is subsequently used to update the controller for tool usage through preference tuning, producing a SPORT agent. By interacting with real environments, the SPORT agent gradually evolves into a more refined and capable system. Evaluation in the GTA and GAIA benchmarks shows that the SPORT agent achieves 6.41% and 3.64% improvements, underscoring the generalization and effectiveness introduced by our method. The project page is https://SPORT-Agents.github.io.