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01.
Nature (Science) 2026-06-09

People are turning to AI chatbots to plug gaps in health information

A systematic assessment of health-related queries to a chatbot powered by artificial intelligence highlights shortfalls in health-care provision and the responsibilities of AI companies. A systematic assessment of health-related queries to a chatbot powered by artificial intelligence highlights shortfalls in health-care provision and the responsibilities of AI companies.

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

Computational Methods and Challenges in Cell-Free DNA Analysis for Multi-Cancer Early Detection

arXiv:2606.20174v1 Announce Type: new Abstract: Cell-free DNA (cfDNA) is a promising avenue for non-invasive multicancer early detection (MCED), in that, it can enable multiple cancer detection simultaneously from a single blood draw, with particular sensitivity to cancers that currently lack established screening programs. Here we review the computational methods developed between 2022 and 2025 for cfDNA-based MCED. We focus on how fragmentomics and epigenetic features are extracted and analyzed to detect cancer at early stages. We first briefly outline the biological basis of cfDNA signals, then review classical statistical and machine learning approaches alongside deep learning frameworks including autoencoder-based models. For each method we discuss biological interpretability, validation strategy, and readiness for clinical integration. Furthermore, we categorize the current challenges into technical, computational, and methodological while outlining open problems in the field. This review shows that multimodal ensemble approaches have the strongest promise for clinical integration and the highest readiness. However, for better assessment of future work and side-by-side comparison, standardization of evaluation protocols and reporting results will be crucial.

03.
arXiv (CS.CL) 2026-06-12

Recursive Agent Harnesses

Recursive language models (RLMs) showed that recursion over model calls is an effective strategy for long-context reasoning, and production coding agents have begun to write code that spawns subagents at scale, most recently in Anthropic's dynamic workflows. We name and study the pattern between these two lines of work, where the recursive unit is a full agent harness with filesystem tools, code execution, and planning rather than a model call with no tools. We call this the Recursive Agent Harness (RAH) and frame it as harness recursion, the code-first extension to the model recursion of RLMs. A parent agent generates and runs an executable script that spawns subagent harnesses in parallel for fine-grained workloads and uses structured function calls for small subtasks. We provide a controlled evaluation on long-context reasoning. With the backbone held fixed at GPT-5 to match the published Codex and RLM baselines, RAH improves the Codex coding-agent baseline from 71.75% to 81.36% on Oolong-Synthetic (199 samples, 13 context-length buckets up to 4M tokens), a gain attributable to the harness rather than the model. With a stronger backbone, Claude Sonnet 4.5, the same design reaches 89.77%.

04.
bioRxiv (Bioinfo) 2026-06-18

A unified smoothing framework for protein domain bigram model

Biomolecular sequences can be represented as strings over an alphabet, an analogy that has motivated many applications of computational linguistic techniques to biological problems. However, such methods must be adapted to the characteristic scale and organization of biomolecular data. Here, we consider the problem of bigram smoothing for multidomain protein architectures, where domain bigram frequency data is extremely sparse and differs from textual data in alphabet size, string length distribution, the relationship between bigram and unigram frequencies, tandem repeat lengths, and the distribution of domain adjacencies. Moreover, some domain combinations are unobserved because they are biologically incompatible, others because the data are incomplete. A smoothing method that distinguishes these two cases is required. We propose a unified smoothing framework based on interpolation that can be tuned to accommodate different bigram data characteristics. Within this framework, we design specific model variants suited to protein domain bigram data: these assign low adjusted counts to pairs that are likely incompatible, while making appropriate adjustments for undersampled pairs. We demonstrate empirically that this approach distinguishes the two cases while preserving the characteristic signatures of multidomain data.

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

Random Erasing vs. Model Inversion: A Promising Defense or a False Hope?

Model Inversion (MI) attacks pose a significant privacy threat by reconstructing private training data from machine learning models. While existing defenses primarily concentrate on model-centric approaches, the impact of data on MI robustness remains largely unexplored. In this work, we explore Random Erasing (RE), a technique traditionally used for improving model generalization under occlusion, and uncover its surprising effectiveness as a defense against MI attacks. Specifically, our novel feature space analysis shows that models trained with RE-images introduce a significant discrepancy between the features of MI-reconstructed images and those of the private data. At the same time, features of private images remain distinct from other classes and well-separated from different classification regions. These effects collectively degrade MI reconstruction quality and attack accuracy while maintaining reasonable natural accuracy. Furthermore, we explore two critical properties of RE including Partial Erasure and Random Location. Partial Erasure prevents the model from observing entire objects during training. We find this has a significant impact on MI, which aims to reconstruct the entire objects. Random Location of erasure plays a crucial role in achieving a strong privacy-utility trade-off. Our findings highlight RE as a simple yet effective defense mechanism that can be easily integrated with existing privacy-preserving techniques. Extensive experiments across 37 setups demonstrate that our method achieves state-of-the-art (SOTA) performance in the privacy-utility trade-off. The results consistently demonstrate the superiority of our defense over existing methods across different MI attacks, network architectures, and attack configurations. For the first time, we achieve a significant degradation in attack accuracy without a decrease in utility for some configurations.

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

Adapting Vision-Language Models from Iconic to Inclusive for Multi-Label Recognition Without Labels

Understanding multi-label images remains a challenging task in computer vision. With the rapid progress of vision-language multimodal learning, vision-language models (VLMs) enable zero-shot recognition without labeled data. However, due to their intrinsic design, these models often prioritize the most iconic object and omit other contextual positives. This intrinsic bias conflicts with the nature of multi-label learning, thereby limiting their applicability. In this work, we propose an unsupervised framework that adapts VLMs from iconic recognition toward inclusive understanding, enabling label-free multi-label image recognition. Our approach consists of two key stages, ``cutting'' and ``sewing'': In the cutting stage, we present the multi-sampling response estimator to prevent the model from concentrating only on one single object. In the second sewing stage, the multi-object blend adaptation is introduced to adjust the labels to better conform to the multi-label distribution while preserving the intrinsic characteristics of the original model within only one epoch. Extensive experiments show that our framework significantly outperforms existing unsupervised approaches on four public datasets, even surpassing several representative weakly supervised baselines. These results demonstrate the potential of adapting pre-trained VLMs for more comprehensive visual understanding without manual annotations. Our code is publicly available at https://github.com/iCVTEAM/TailorCLIP.

07.
arXiv (CS.LG) 2026-06-15

Contract-Based Compositional Shielding for Safe Multi-Agent Reinforcement Learning

arXiv:2606.14130v1 Announce Type: new Abstract: Safe coordination problems surface in multi-agent reinforcement learning when global safety cannot be enforced by any agent unilaterally: the admissibility of one agent's action may depend on the dynamics of other agents. Decentralised shields can enforce safety at runtime, but purely factorised permissions often exclude optimal team behaviour that is safe only through coordination. We study deterministic safety guarantees for agents trained and deployed under decentralised execution, recovering team-optimal safe behaviour without centralised runtime control. Agents have a shared global specification $\phi$ in the safety fragment of Linear Temporal Logic ($\mathsf{LTL}_{\mathsf{safe}}$ ), and select among tuples of local $\mathsf{LTL}_{\mathsf{safe}}$ obligations whose conjunction implies the global specification $\phi$. Each agent may rely on the other agents' local obligations as assumptions because the whole contract tuple is certified simultaneously and allows projection into local action masks. At learning time, a non-stationary multi-armed bandit chooses among a library of local $\mathsf{LTL}_{\mathsf{safe}}$ obligations to select the tuple that optimises team reward, all without forgoing end-to-end safety. We evaluate the approach across 6 environments and 15 algorithmic variants.

08.
arXiv (CS.AI) 2026-06-12

Real-rootedness of the Poincaré polynomials of $\overline{\mathcal M}_{0,n}$: an AI-assisted proof

arXiv:2605.29151v2 Announce Type: replace-cross Abstract: We prove real-rootedness for the Poincaré polynomial \[ P_n(t)=\sum_{i=0}^{n-3} \dim H^{2i}(\overline{\mathcal M}_{0,n};\mathbb{Q})t^i \] of the Deligne–Mumford moduli space $\overline{\mathcal M}_{0,n}$ of stable $n$-pointed rational curves, proving a conjecture of Aluffi–Chen–Marcolli. The proof starts from the Keel–Manin–Getzler recurrence, but its main new idea is a bivariate deformation $F_m(y,t)$ of the Poincaré polynomial. This deformation reveals a hidden interlacing structure not visible in the one-variable recurrence. For fixed $t

09.
medRxiv (Medicine) 2026-06-22

A Randomized, Controlled, Double Blind Clinical Study to Evaluate Use of Hydron Alkaline Ionised Water (HAIW) in Healthy Participants

Background and Objectives: Alkaline Ionized Water (AIW) is considered among the highest quality healthy drinking water worldwide and is widely discussed for its various health benefits. Hydron Alkaline Ionized Water (HAIW) is produced through electrolysis, resulting in a stable pH of approximately 9.5 with a negative Oxidation Reduction Potential (ORP), making it an antioxidant beverage. The objective of this study was to evaluate the safety of HAIW and its effects on digestion, sleep, energy, and overall quality of life in healthy participants compared to Packaged Drinking Water (PDW). Materials and Methods: A randomized, controlled, double blind, prospective clinical study was conducted in which a total of 24 healthy participants between the age group of 21 to 40 years were randomized in a 1:1 ratio to either HAIW Group or Packaged Drinking Water Group with equal gender distribution. Participants were hospitalized for 7 days and asked to consume at least 3 litres of the assigned water daily. Primary outcomes were safety-related laboratory parameters and adverse event monitoring. Secondary outcomes included assessment of digestion (appetite, digestion, bowel habits), urine parameters, sleep quality, freshness after waking, fatigue, energy/stamina/strength, quality of life, and global assessment Results: All 24 participants completed the study with no dropouts. Baseline demographics were comparable between the two groups. Assessment of primary safety-related laboratory parameters including Complete Blood count, liver function tests, renal function tests, blood sugar, Electrocardiogram and serum electrolytes showed non-significant change from baseline to 7 days and remained within normal limits in both groups, with non-significant difference between groups (p>0.05). HAIW showed significantly better improvement in appetite, digestion, and bowel habits from Day 2 onwards compared to Packaged drinking water. Sleep quality and freshness after waking up showed significant improvement from Day 3 and Day 2 respectively in the HAIW and PDW group, with significantly better improvement in HAIW group. Fatigue scores showed significant reduction at Day 6 and 7 in both groups with non-significant difference between groups. A total of 5 adverse events were reported (3 in HAIW, 2 in PDW), all unrelated to study products and were mild in nature. Global assessment showed excellent to good overall safety and tolerability in both groups. Conclusion: HAIW was well tolerated by all participants without any adverse effects. All laboratory safety parameters remained within normal range. HAIW demonstrated significant improvements in digestive function (appetite, digestion, bowel habits), sleep quality, and freshness after waking as compared to PDW. The study concludes that HAIW can be safely consumed. HAIW improves digestive and sleep-related functions.

10.
arXiv (CS.AI) 2026-06-16

AlignCoder: Aligning Retrieval with Target Intent for Repository-Level Code Completion

arXiv:2601.19697v2 Announce Type: replace-cross Abstract: Repository-level code completion remains a challenging task for existing code large language models (code LLMs) due to their limited understanding of repository-specific context and domain knowledge. While retrieval-augmented generation (RAG) approaches have shown promise by retrieving relevant code snippets as cross-file context, they suffer from two fundamental problems: misalignment between the query and the target code in the retrieval process, and the inability of existing retrieval methods to effectively utilize the inference information. To address these challenges, we propose AlignCoder, a repository-level code completion framework that introduces a query enhancement mechanism and a reinforcement learning based retriever training method. Our approach generates multiple candidate completions to construct an enhanced query that bridges the semantic gap between the initial query and the target code. Additionally, we employ reinforcement learning to train an AlignRetriever that learns to leverage inference information in the enhanced query for more accurate retrieval. We evaluate AlignCoder on two widely-used benchmarks (CrossCodeEval and RepoEval) across five backbone code LLMs, demonstrating an 18.1% improvement in EM score compared to baselines on the CrossCodeEval benchmark. The results show that our framework achieves superior performance and exhibits high generalizability across various code LLMs and programming languages.

11.
arXiv (CS.CL) 2026-06-12

InnoEval: On Research Idea Evaluation as a Knowledge-Grounded, Multi-Perspective Reasoning Problem

The rapid evolution of Large Language Models has catalyzed a surge in scientific idea production, yet this leap has not been accompanied by a matching advance in idea evaluation. The fundamental nature of scientific evaluation needs knowledgeable grounding, collective deliberation, and multi-criteria decision-making. However, existing idea evaluation methods often suffer from narrow knowledge horizons, flattened evaluation dimensions, and the inherent bias in LLM-as-a-Judge. To address these, we regard idea evaluation as a knowledge-grounded, multi-perspective reasoning problem and introduce InnoEval, a deep innovation evaluation framework designed to emulate human-level idea assessment. We apply a heterogeneous deep knowledge search engine that retrieves and grounds dynamic evidence from diverse online sources. We further achieve review consensus with an innovation review board containing reviewers with distinct academic backgrounds, enabling a multi-dimensional decoupled evaluation across multiple metrics. We construct comprehensive datasets derived from authoritative peer-reviewed submissions to benchmark InnoEval. Experiments demonstrate that InnoEval can consistently outperform baselines in point-wise, pair-wise, and group-wise evaluation tasks, exhibiting judgment patterns and consensus highly aligned with human experts.

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

RAVEN: Long-Horizon Reasoning & Navigation with a Visuo-Spatio-Temporal Memory

Long-term robot deployment requires a compact and scalable memory that preserves fine-grained visual semantics, grounds observations in space and time, and enables efficient storage and retrieval. In this paper, we propose RAVEN, an agentic memory system for long-horizon robotic question answering and navigation. RAVEN stores visual embeddings with pose and time in a vector database, and grounds retrieval in a spatial map to answer queries and navigate to goals. By operating directly on visual embeddings, RAVEN avoids lossy image-to-text captioning and enables accurate semantic, spatial, and temporal retrieval at scale. Across several simulated and real-world video question-answering benchmarks, RAVEN consistently surpasses caption-based memory systems and matches frontier VLMs on long-horizon tasks at 10$\times$ lower retrieval cost. Finally, we instantiate RAVEN on a Unitree Go1 robot for the task of long-horizon navigation for natural language goal-reaching, and show successful deployment over several large indoor environments.

13.
arXiv (CS.CL) 2026-06-18

PragReST: Self-Reinforcing Counterfactual Reasoning for Pragmatic Language Understanding

Natural language understanding often depends on meanings that are implied rather than explicitly stated, requiring pragmatic reasoning. Despite strong performance on math and logical reasoning, large language models (LLMs) still struggle with making pragmatic inferences, often choosing literal interpretations. To improve LLM pragmatic reasoning, we introduce PragReST, a self-supervised framework that constructs pragmatic QA data, generates counterfactual reasoning traces, and trains models to internalize them through supervised fine-tuning and reinforcement learning, without human-labeled training data or distillation from a stronger teacher. Across four pragmatic benchmarks (PragMega, Ludwig, MetoQA, and AltPrag), PragReST improves over backbone models, task-specific pragmatic tuning baselines, and non-counterfactual variants of the same pipeline. On accuracy-based benchmarks, PragReST improves over the instruct backbone by 5.37 and 5.50% (absolute) for Qwen3-8B and Qwen3-14B, respectively. Our error analysis and ablations underscore the importance of counterfactual reasoning: PragReST primarily reduces errors caused by failures to contrast observed utterances with plausible alternatives, and removing counterfactual reasoning substantially reduces performance. Moreover, our training preserves out-of-domain performance on general-knowledge and mathematical reasoning benchmarks.

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

Acoustic Prompting via Stage-wise Modulation for Few-Shot Learning in Audio Language Models

arXiv:2606.15751v1 Announce Type: cross Abstract: Audio-Language Models (ALMs) have shown remarkable success in zero-shot audio classification by aligning audio waveforms with text. Recent efforts to improve downstream performance focus on learning optimal text prompts. However, previous approaches focus on the text encoder, leaving the potential of learnable prompts within the audio encoder unexplored. In this paper, we propose a novel framework that introduces trainable prompts into the audio encoder to capture task-specific acoustic features. We demonstrate that integrating audio-side prompt learning with existing text-side approaches enhances few-shot adaptation. Through extensive experiments across 11 datasets show that integrating our method as a plug-and-play module alongside existing text prompt tuning generally leads to performance improvements. These findings suggest that explicitly modulating the audio representation space effectively complements text-only prompting approaches. The code is available at https://github.com/hyebin-c/aspl.

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

Track2View: 4D-Consistent Camera-Controlled Video Generation via Paired 3D Point Tracks

Re-rendering an existing video from a novel camera viewpoint requires the output to follow the prescribed camera trajectory while preserving the appearance and dynamics of the original scene across every frame. Existing methods rely on per-frame pose embeddings, noisy point-cloud renderings, or implicit learned correspondences, none of which provides an explicit, temporally continuous link between source and target pixels. We propose Track2View, which conditions a video diffusion transformer on paired 3D point tracks: sparse trajectories of scene points projected into both the source and target camera views. These tracks provide explicit spatiotemporal correspondences that are temporally continuous by construction, encoding what content should appear where and when. At the core of Track2View is a dual-view track conditioner that transfers visual context from source to target view through parameter-free geometric operations and learned temporal aggregation, ensuring generalization to arbitrary camera trajectories without memorizing specific motions. We further introduce a data curation pipeline that extracts one-to-one track correspondences by running a 3D point tracker on temporally concatenated multi-camera view pairs. On a 400-video benchmark spanning static and dynamic scenes, Track2View achieves state-of-the-art results across visual quality, view synchronization, and camera accuracy, reducing rotation error by 30-65% and translation error by 61-72% relative to leading baselines. Project page is available at this https URL: https://qjizhi.github.io/track2view

16.
arXiv (CS.LG) 2026-06-25

$DT^2$: Decision-Targeted Digital Twins

arXiv:2606.25923v1 Announce Type: new Abstract: A digital twin (DT) is a virtual model of a real-world system that can assist decision-making by simulating scenarios induced by different policies. However, typical machine learning-based DTs do not optimise for this use case. We prove that, when model capacity is limited, training DTs to minimise one-step transition errors can produce suboptimal models for ranking sets of policies according to a reward function. We further show that this holds empirically, even with expressive model classes. To address this, we introduce $DT^2$, a decision-targeted DT training paradigm. Firstly, $DT^2$ uses fitted Q-evaluation to estimate values of candidate policies from offline data. A DT is then trained to generate rollouts that preserve pairwise policy rankings derived from these proxy ground-truth values with an architecture-agnostic loss function. We empirically demonstrate the efficacy of our method across a range of settings and architectures. $DT^2$ consistently improves policy ranking and reduces decision regret during policy selection relative to conventional DT training, both for policies used during training and for unseen policies, while maintaining a good level of raw simulation fidelity.

17.
arXiv (CS.CV) 2026-06-12

Analyzing and Improving Fine-grained Preference Optimization in Medical LVLMs

Large Vision-Language Models (LVLMs) have achieved strong performance across medical imaging tasks, yet they remain prone to factual inconsistencies, poor visual grounding, and misalignment with clinically meaningful feedback. Existing post-training alignment approaches, including Direct Preference Optimization (DPO) and its variants, face three critical limitations in the medical domain: (1) sequence-level reward signals treat clinically critical tokens identically to generic filler text; (2) reliance on static supervised fine-tuning references as preferred responses introduces an off-policy distribution shift, steering optimization toward stylistic artifacts over clinical correctness; and (3) alignment objectives lack explicit visual grounding constraints, leaving models insensitive to subtle yet diagnostically decisive pathological features. Our method leverages a bidirectional token-wise KL regularizer alongside a visual-contrastive grounding objective that pairs clean and lesion-corrupted images to penalize responses generated without adequate visual evidence. Together, these components form a fine-grained, on-policy alignment framework that constructs preference pairs by minimally editing model-generated outputs, correcting only clinically erroneous spans while preserving the original linguistic style. Extensive experiments across medical imaging tasks and clinical text generation benchmarks validate the effectiveness of our approach.

18.
arXiv (CS.LG) 2026-06-24

Hybrid Sequence Modeling and Reinforced Verification for Controllable Target-Conditioned Decision Making

arXiv:2508.16420v3 Announce Type: replace Abstract: Target-conditioned sequence models provide a simple interface for controllable offline decision making, but the requested target return can be an unreliable control signal, especially when the target return lies in underrepresented regions of the dataset. This paper proposes Doctor, a hybrid sequence modeling and reinforced verification framework for controllable target-conditioned offline decision making. Doctor trains a shared masked trajectory Transformer with two complementary objectives: masked trajectory reconstruction for candidate generation and in-sample value learning for action-value verification. At inference time, the model samples multiple nearby target returns, generates candidate actions in parallel, and selects the action whose verified value is closest to the requested target return. We analyze this verifier-guided selection rule and show that its value-level alignment error is bounded by candidate-value coverage around the target return and verifier accuracy. Experiments on D4RL and EpiCare show that Doctor improves target-return alignment under reduced high-return coverage, remains competitive on standard offline return-maximization benchmarks, and enables a single policy to modulate between conservative and aggressive operating points in a simulated clinical decision-making task. These results suggest that reinforced verification can improve the controllability of target-conditioned policies.

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

CogniFold: Always-On Proactive Memory via Cognitive Folding

Existing agent memory remains predominantly reactive and retrieval-based, lacking the capacity to autonomously organize experience into persistent cognitive structure. Toward genuinely autonomous agents, we introduce CogniFold, a brain-inspired "always-on" agent memory designed for the next generation of proactive assistants. CogniFold continuously folds fragmented event streams into self-emerging cognitive structures, bootstrapping progressively higher-level cognition from incoming events and accumulated knowledge. We ground this by extending Complementary Learning Systems (CLS) theory from two layers (hippocampus, neocortex) to three, adding a prefrontal intent layer. Emulating the prefrontal cortex as the locus of intentional control and decision-making, CogniFold achieves this through graph-topology self-organization: cognitive structures proactively assemble under the stream, merge when semantically similar, decay when stale, relink through associative recall, and surface intents when concept-cluster density crosses a threshold. We evaluate structural formation using CogEval-Bench, demonstrating that CogniFold uniquely produces memory structures that match cognitive expectations and concept emergence. Furthermore, across eight downstream benchmarks – two probing long-term conversational memory (LoCoMo, LongMemEval) and six spanning other cognitive domains – we validate that CogniFold simultaneously performs robustly on conventional memory tasks. Our code is available at https://github.com/OpenNorve/CogniFold.

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

MiniFool – Physics-Constraint-Aware Minimizer-Based Adversarial Attacks in Deep Neural Networks

arXiv:2511.01352v2 Announce Type: replace Abstract: In this paper, we present a new algorithm, MiniFool, that implements physics-inspired adversarial attacks for testing neural network-based classification tasks in particle and astroparticle physics. While we initially developed the algorithm for the search for astrophysical tau neutrinos with the IceCube Neutrino Observatory, we apply it to further data from other science domains, thus demonstrating its general applicability. Here, we apply the algorithm to the well-known MNIST data set and furthermore, to Open Data data from the CMS experiment at the Large Hadron Collider. The algorithm is based on minimizing a cost function that combines a $\chi^2$ based test-statistic with the deviation from the desired target score. The test statistic quantifies the probability of the perturbations applied to the data based on the experimental uncertainties. For our studied use cases, we find that the likelihood of a flipped classification differs for both the initially correctly and incorrectly classified events. When testing changes of the classifications as a function of an attack parameter that scales the experimental uncertainties, the robustness of the network decision can be quantified. Furthermore, this allows testing the robustness of the classification of unlabeled experimental data.

21.
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.

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

A Human-in-the-Loop Label Error Detection Framework Applied to Arabic-Script HTR Datasets

Despite recent advances, Handwritten Text Recognition (HTR) for Arabic-script languages still lags behind Latin-script HTR. Part of the problem is dataset quality. To help closing this gap, we propose a two-stage framework (CER-HV) for detecting label errors. Stage 1 (CER) is a Character-Error-Rate-based noise detector built on a Convolutional Recurrent Neural Network (CRNN) architecture. Stage 2 (HV) is the Human-In-The-Loop (HITL) Verification of noisy samples detected by the first stage. Applying the CER-HV framework on multiple Arabic-script datasets can identify samples with label errors including transcription, segmentation, orientation, and non-text content errors that can markedly affect HTR performance. These errors were identified by the first stage of the framework with up to 90percent (top-50) precision. We also show that our CRNN achieves state-of-the-art performance across five of the six evaluated datasets, reaching 8.46 percent Character Error Rate (CER) on KHATT (Arabic), 8.22 percent on PHTI (Pashto), 10.59 percent on Ajami, and 10.11% on Muharaf (Arabic), all without any data cleaning. We establish a new baseline of 11.3 percent CER on the PHTD (Persian) dataset. Applying CER-HV improves evaluation CER by up to 1.8 percentage points after dataset cleaning and retraining. Although our experiments focus on documents written in an Arabic-script language, the framework is general and can be applied to other text recognition datasets

23.
arXiv (CS.CL) 2026-06-25

Memory Contagion: Cross-Temporal Propagation of Evaluator Bias via Agent Memory

Authors:

Large Language Model (LLM) agents increasingly rely on memory systems to maintain long-term coherence. Recent work shows that agent memories degrade during continuous consolidation. However, existing research assumes memories are derived from unbiased experiences. In this work, we identify and formalize a novel phenomenon: Memory Contagion – the cross-temporal propagation of evaluator bias through agent memory. We show that when agents are trained or guided by biased evaluators, their experiences become biased; when these trajectories are stored and consolidated into memory, the bias propagates to future agents retrieving from the same memory store, even when consolidation is perfect (oracle). Across two bias types (length preference, authority bias) and four experimental phases, we demonstrate: (1) Memory Contagion occurs for length bias even with perfect consolidation on older models (Gamma_A = 13.18, DeepSeek V4-Chat), while newer models (V4-Pro, Claude) are immune, proving both that biased input is a sufficient cause and that contagion is model-generation-dependent; (2) authority bias fails to propagate in all 15 controlled multi-seed experiments (Gamma_A = 0.00), revealing that not all evaluator biases can cross temporal boundaries through current memory architectures; (3) No observed safe threshold: length bias propagation is detected at contamination rates as low as p=0.2. Our findings expose a critical but contingent vulnerability in current agent memory designs and provide formal tools for measuring cross-temporal bias propagation.

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

TelcoAgent: A Scalable 5G Multi-KPM Forecasting With 3GPP-Grounded Explainability

arXiv:2606.19821v1 Announce Type: new Abstract: Key Performance Measurement (KPM) forecasting is essential for proactive network management of 5G and next-generation telecom networks. However, existing machine learning (ML) approaches face significant limitations in scalability and explainability, restricting their effectiveness in real-world deployments. We propose TelcoAgent, a foundation model-based framework that enables accurate, scalable, and explainable forecasting of multiple KPMs across diverse network cells without the need for site-specific training. Specifically, the framework comprises three key components: (i) an automated three-agent pipeline that constructs a 3rd Generation Partnership Project (3GPP) knowledge graph directly from specification documents, (ii) a scalable, time-series foundation model (TSFM)-based prediction pipeline to deliver accurate, zero-shot forecasting, and finally (iii) a reasoning and explanation pipeline that provides actionable, domain-grounded diagnostics. Evaluated using a 3-month, real-world, city-scale 5G KPM dataset from a U.S.-based network operator, TelcoAgent demonstrates high forecasting accuracy for all 7 considered KPMs per cell across 200 cells, while delivering explainable insights and actionable instructions to address network degradations.

25.
arXiv (math.PR) 2026-06-15

Limiting partition function for the Mallows model: a conjecture and partial evidence

Authors:

arXiv:2406.18855v2 Announce Type: replace Abstract: Let $S_n$ denote the set of permutations of $n$ labels. We consider a class of Gibbs probability models on $S_n$ that is a subfamily of the so-called Mallows model of random permutations. The Gibbs energy is given by a class of right invariant divergences on $S_n$ that includes common choices such as the Spearman foot rule and the Spearman rank correlation. Mukherjee in 2016 computed the limit of the (scaled) log partition function (i.e. normalizing factor) of such models as $n\rightarrow \infty$. Our objective is to compute the exact limit, as $n\rightarrow \infty$, without the log. We conjecture that this limit is given by the Fredholm determinant of an integral operator related to the so-called Schrödinger bridge probability distributions from optimal transport theory. We provide partial evidence for this conjecture, although the argument lacks a final error bound that is needed for it to become a complete proof.