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

LLM-as-Code Agentic Programming for Agent Harness

arXiv:2606.15874v1 Announce Type: new Abstract: Every major LLM agent framework gives the LLM the role of orchestrator; the model decides what to do next, when to call tools, and when to stop. We argue that token explosion, control-flow hallucination, and unreliable completion are not implementation bugs but architectural consequences of assigning the deterministic work of looping, branching, and sequencing to a probabilistic system. A better prompt or a stronger model cannot guarantee the reliability of the LLM agent. We therefore propose Agentic Programming, in which the program governs all control flow, and the LLM is itself part of it, an adaptive component we call LLM-as-Code and invoke only where a task calls for reasoning or generation. Within each call the model keeps full flexibility, but it cannot alter the program's execution path. With control in the program, the LLM's context is built from the execution history's call tree and forms a directed acyclic graph (DAG). Each call's context length is then determined by its call depth rather than by accumulation over steps. A case study of computer-use agents shows that the design is practical, not just a theoretical stance, substantially improving the stability of long visual operation sequences.

02.
Nature (Science) 2026-06-10

Gen Z scepticism towards AI is a wake-up call — universities must take it seriously

Authors:

The challenge for universities is not adopting artificial intelligence, but doing so in ways that the current generation of students can trust. The challenge for universities is not adopting artificial intelligence, but doing so in ways that the current generation of students can trust.

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

Learning Geometric Representations from Videos for Spatial Intelligent Multimodal Large Language Models

arXiv:2606.05833v2 Announce Type: replace-cross Abstract: Multimodal Large Language Models (MLLMs) excel at 2D semantic understanding but lack intrinsic 3D awareness, resulting in representations that fail to maintain geometric and spatial consistency across video frames. Given the scarcity of large-scale 3D data, we present GeoVR, a novel framework that learns geometric representations using purely 2D video sequences. This approach effectively restructures the semantic latent space within MLLMs to unlock spatial intelligence. Rather than employing superficial feature mixing, GeoVR reshapes the internal representations of the MLLM by distilling geometry knowledge from pre-trained 3D foundation models. This is accomplished through a multi-objective learning strategy driven by four complementary geometric targets: (1) estimating inter-frame camera poses to embed varying viewpoint dynamics, (2) regressing dense depth maps to anchor physical distances, (3) predicting a metric scale factor for real-world calibration, and (4) distilling multi-scale 3D features to align the intermediate feature space. Guided by these explicit physical and geometric constraints, the model's internal representations naturally develop strong 3D awareness. Extensive experiments on spatial reasoning benchmarks demonstrate that GeoVR achieves state-of-the-art performance, establishing a new paradigm for endowing foundation models with spatial intelligence.

04.
arXiv (CS.LG) 2026-06-16

Descriptive versus Regulatory Uncertainty in Bounded Predictive Systems

arXiv:2605.18909v2 Announce Type: replace Abstract: Any system that models the world under finite representational capacity must compress; any compression entails a prior; and the prior is the system's bias. What has not been established is whether uncertainty participates in the dynamics governing future behavior, or merely describes the output distribution without consequence. We introduce a structural distinction between descriptive uncertainty, which does not recursively modulate the system's policy, and regulatory uncertainty, which directly enters the optimization landscape and drives persistent adaptive restructuring. We prove formally that current transformer architectures are confined to descriptive uncertainty at inference. We ground this in thermodynamics via Landauer's principle: for uncertainty to be regulatory, epistemic error must cost real energy; in a decoupled system, hallucinations and correct derivations dissipate identical energy. We test this empirically across three locally-deployed language models (3B, 8B, 70B parameters). Token-level Shannon entropy is statistically invariant across tasks spanning pattern retrieval, causal operator application, and out-of-distribution causal generalization in all three models (all pairwise p >= 0.568; within-model ranges 0.011-0.028 nats), while task accuracy varies substantially across the same conditions (0%-100%). Entropy and accuracy are orthogonal. The decoupling is scale-invariant: larger models achieve higher accuracy but identical entropy flatness. This structural incapacity is not resolvable by additional parameters or training data. Genuine epistemic grounding requires physical coupling between thermodynamic substrate state and information processing cost.

05.
bioRxiv (Bioinfo) 2026-06-19

OmniPath Metabo: chemical structures, interactions and mechanisms to study the metabolome

Mechanistic and functional analysis of omics data largely relies on the incorporation of prior knowledge; however, connecting metabolomics data and knowledge is a major methodological challenge. This is largely driven by the diverse prior knowledge being fragmented across many databases requiring the merging of different database records across chemical structures, identifiers, and varying levels of structural specificity. Hence, this limits mechanistic interpretation and functional characterisation of the metabolome. Here, we present OmniPath Metabo, a comprehensive, harmonized, metabolome-centric database covering metabolites, lipids, food-derived compounds, and small molecule drugs, along with their associated receptors, transporters, enzymes, reactions, allosteric regulators, and disease associations. OmniPath Metabo harmonizes attributes using controlled vocabularies and ontologies, structures and built-in cheminformatics to map identifiers and track ambiguity. OmniPath Metabo is built directly from 40+ original resources and is freely accessible via an interactive web app and API at metabo.omnipathdb.org. OmniPath Metabo enables dynamic, context-specific construction of subnetworks to serve dedicated purposes, such as cell-cell communication or integrated multi-omics metabolite-driven regulation, connecting reactions, allosteric regulation, metabolite-receptor and metabolite-transporter interactions. Combining it with the over 170 other resources in OmniPath, it can be used for integrated networks of signaling, gene regulation, and metabolism. We showcase the application of OmniPath Metabo by analysing publicly available metabolomics data of lung cancer cell lines and metabolic footprints to mutational patterns. In summary, OmniPath Metabo transforms fragmented resources into a harmonised prior knowledge framework for a mechanistic and functional analysis of the metabolome.

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

AnomalyMatch: Discovering Rare Objects of Interest with Semi-supervised and Active Learning

arXiv:2505.03509v3 Announce Type: replace Abstract: Anomaly detection in large datasets is essential in astronomy and computer vision. However, due to a scarcity of labelled data, it is often infeasible to apply supervised methods to anomaly detection. We present AnomalyMatch, an anomaly detection framework combining the semi-supervised FixMatch algorithm using EfficientNet classifiers with active learning. AnomalyMatch is tailored for large-scale applications and integrated into the ESA Datalabs science platform. In this method, we treat anomaly detection as a binary classification problem and efficiently utilise limited labelled and abundant unlabelled images for training. We enable active learning via a user interface for verification of high-confidence anomalies and correction of false positives. Evaluations on the GalaxyMNIST astronomical dataset and the miniImageNet natural-image benchmark under severe class imbalance display strong performance. Starting from five to ten labelled anomalies, we achieve an average AUROC of 0.96 (miniImageNet) and 0.89 (GalaxyMNIST), with respective AUPRC of 0.82 and 0.77. After three active learning cycles, anomalies are ranked with 76% (miniImageNet) to 94% (GalaxyMNIST) precision in the top 1% of the highest-ranking images by score. We compare to the established Astronomaly software on selected 'odd' galaxies from the 'Galaxy Zoo- The Galaxy Challenge' dataset, achieving comparable performance with an average AUROC of 0.83. Our results underscore the exceptional utility and scalability of this approach for anomaly discovery, highlighting the value of specialised approaches for domains characterised by severe label scarcity

07.
arXiv (CS.LG) 2026-06-24

Federated Survival Analysis in Healthcare: A Multi-Model Evaluation on Cross-Institutional Heterogeneous Breast Cancer Data

arXiv:2606.23871v1 Announce Type: new Abstract: Survival analysis is central to clinical decision-making, yet reliable time-to-event models require large, diverse cohorts that are rarely available at a single institution, while privacy regulations restrict the centralization of patient data. Federated learning (FL) offers a privacy-preserving alternative by training shared models without exchanging raw data, but its effectiveness for survival modeling under realistic, heterogeneous conditions remains insufficiently understood. This paper presents a systematic, multi-model evaluation of federated survival analysis on a cross-institutional breast cancer cohort with naturally heterogeneous distributed clients. Three representative survival models, the Cox Proportional Hazards model, DeepSurv, and Random Survival Forest (RSF), are compared across centralized, local, and federated training, and three federated optimization strategies (FedAvg, FedProx, and FedAdam) are assessed for the gradient-based models. Results show that FL consistently outperforms local training and approaches, and occasionally exceeds, centralized performance, while RSF offers the best overall balance of discrimination, calibration, and robustness across heterogeneous clients. We further find that performance depends on the diversity of client distributions, and that FedAvg and FedProx are stronger and more stable than FedAdam. Based on these findings, we derive practical, decision-oriented guidelines mapping data, privacy, interpretability, and resource constraints to recommended model and training-paradigm choices for federated survival modeling in healthcare.

08.
arXiv (CS.LG) 2026-06-11

Visualizing LLM Latent Space Geometry Through Dimensionality Reduction

arXiv:2511.21594v3 Announce Type: replace Abstract: Large language models (LLMs) achieve state-of-the-art results across many natural language tasks, but their internal mechanisms remain difficult to interpret. In this work, we extract, process, and visualize latent state geometries in Transformer-based language models through dimensionality reduction. We capture layerwise activations at multiple points within Transformer blocks and enable systematic analysis through Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP). We demonstrate experiments on GPT-2 and LLaMa models, where we uncover interesting geometric patterns in latent space. Notably, we identify a clear separation between attention and MLP component outputs across intermediate layers, a pattern not documented in prior work to our knowledge. We also characterize the high norm of latent states at the initial sequence position and visualize the layerwise evolution of latent states. Additionally, we demonstrate the high-dimensional helical structure of GPT-2's positional embeddings and the sequence-wise geometric patterns in LLaMa. We make our code available at https://github.com/Vainateya/Feature_Geometry_Visualization. A better formatted blog-post with identical content is available at https://iclr-blogposts.github.io/2026/blog/2026/vis-llm-latent-geometry/.

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

Library-Aware Doubles and Iterative Repair for Large Language Model-Generated Unit Tests in OpenSIL Firmware

arXiv:2606.19725v1 Announce Type: cross Abstract: Validating changes in low-level C firmware is expensive because unit tests (UTs) are fragile under strict build constraints, where missing headers, unresolved symbols, and dependency mismatches frequently prevent compilation and linking. This study introduces an automated UT authoring workflow for the Open-Source Silicon Initialization Library (openSIL) firmware codebase maintained by Advanced Micro Devices (AMD) that reduces manual effort through a large language model (LLM) guided multi-agent pipeline. The workflow combines automated generation of test scaffolds, library-aware creation or reuse of stubs, mocks, and fakes, and an iterative compile-dispatch repair loop driven by build logs and line-coverage feedback. We evaluate the approach using compilation success, repair iterations, dispatch success, and line coverage, with time, cost, and token usage as secondary measures. Across 76 functions under test, the workflow generated compilable UTs for 73 functions. In a configuration without line coverage guidance or retrieval augmentation, mean line coverage reached 73.9%. On a 48-function subset evaluated under both configurations, mean line coverage reached 98.8% with line-coverage guidance alone and reached 94.7% when combined with vector-database retrieval. Results show that automated generation-and-repair pipelines can substantially improve UT creation efficiency and coverage for constrained firmware environments while reducing manual debugging effort.

10.
arXiv (quant-ph) 2026-06-17

Asymptotically Optimal Circuit Depth for Diagonal Unitary Synthesis and Compilation on Two-Dimensional Grids

arXiv:2606.17589v1 Announce Type: new Abstract: Diagonal unitaries are a fundamental but resource-intensive class of quantum operations, arising as the phase separators of QAOA and the time-evolution blocks of Hamiltonian simulation. Under all-to-all connectivity their optimal depth is established, but on nearest-neighbor hardware general-purpose compilers fall back on heuristic search, which yields no analyzable cost bound and becomes intractable at the very sizes where depth is the bottleneck. We address synthesis and compilation jointly. On the synthesis side, we develop a Gray-Path Framework (GPF) that realizes any $n$-qubit diagonal unitary in asymptotically optimal $R_z$ and CNOT depth $O(2^n/n)$ without ancillas. Our main result is that compiling GPF onto a two-dimensional nearest-neighbor grid preserves this optimality: routing adds depth $\Theta(2^n/n)$ and gate count $\Theta(2^n)$. Because GPF fixes its entire interaction structure in advance, routing reduces to scheduling a known sequence, with no heuristic search. We give the construction both with and without ancillas: the ancilla-free, cost-optimized layout is a two-row grid, and a $2k$-row layout introduces a space–time tradeoff that cuts depth by $1/k$ while remaining asymptotically optimal for the enlarged register; both are deterministic and analyzed in closed form. The same complexity is also attained on a linear nearest-neighbor chain, so the preservation is topology-independent, holding on any architecture that contains such a chain. All routing bounds are closed-form, giving the concrete resource estimates that heuristic compilers cannot provide at scale.

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

SuCo: Sufficiency-guided Continuous Adaptive Reasoning

Despite remarkable performance on complex tasks, Large Reasoning Models (LRMs) often generate excessively long Chain-of-Thoughts (CoT), inflating computational costs even for simple queries. Existing efforts to mitigate this inefficiency typically rely on discrete reasoning modes or fixed budget tiers, lacking a principled criterion of when reasoning is sufficient. In this work, we introduce Minimal Sufficient CoT (MSC), defined as the shortest prefix of a CoT trajectory which is adequate for producing the correct answer. We empirically show that MSC not only reduces reasoning tokens, but also improves accuracy across difficulty levels. Building on MSC, we propose Sufficiency-guided Continuous Adaptive Reasoning (SuCo), a two-stage training framework for autonomous reasoning control along a continuous spectrum. In stage 1, MSC-Aligned Fine-Tuning (MFT) constructs MSC data using problem-adaptive sufficiency thresholds that naturally scale with question difficulty, then fine-tunes the model to internalize concise yet sufficient reasoning patterns. In stage 2, Sufficiency-Aware Policy Optimization (SAPO) further optimizes the model through reinforcement learning with dynamic complexity tracking and sufficiency-aware rewards that penalize both over- and under-thinking. Extensive experiments across mathematics, code, and science benchmarks show that SuCo consistently achieves improvements in both accuracy and reasoning efficiency.

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

Dropout Neural Network Training Viewed from a Percolation Perspective

arXiv:2512.13853v2 Announce Type: replace Abstract: In this work, we investigate the existence and effect of percolation in training deep Neural Networks (NNs) with dropout. Dropout methods are regularisation techniques for training NNs, first introduced by G. Hinton et al. (2012). These methods temporarily remove connections in the NN, randomly at each stage of training, and update the remaining subnetwork with Stochastic Gradient Descent (SGD). The process of removing connections from a network at random is similar to percolation, a paradigm model of statistical physics. If dropout were to remove enough connections such that there is no path between the input and output of the NN, then the NN could not make predictions informed by the data. We study new percolation models that mimic dropout in NNs and characterise the relationship between network topology and this path problem. The theory shows the existence of a percolative effect in dropout. We also show that this percolative effect can cause a breakdown when training NNs without biases with dropout; and we argue heuristically that this breakdown extends to NNs with biases.

13.
arXiv (CS.CV) 2026-06-15

A Pragmatic VLA Foundation Model

Offering great potential in robotic manipulation, a capable Vision-Language-Action (VLA) foundation model is expected to faithfully generalize across tasks and platforms while ensuring cost efficiency (e.g., data and GPU hours required for adaptation). To this end, we develop LingBot-VLA with around 20,000 hours of real-world data from 9 popular dual-arm robot configurations. Through a systematic assessment on 3 robotic platforms, each completing 100 tasks with 130 post-training episodes per task, our model achieves clear superiority over competitors, showcasing its strong performance and broad generalizability. We have also built an efficient codebase, which delivers a throughput of 261 samples per second with an 8-GPU training setup, representing a 1.5~2.8$\times$ (depending on the relied VLM base model) speedup over existing VLA-oriented codebases. The above features ensure that our model is well-suited for real-world deployment. To advance the field of robot learning, we provide open access to the code, base model, and benchmark data, with a focus on enabling more challenging tasks and promoting sound evaluation standards.

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

Projection and Quantisation: A Unifying View of Learning to Hash, from Random Projections to the RAG Era

Authors:

Approximate nearest-neighbour search underpins large-scale retrieval and retrieval-augmented generation, yet its methods are studied in communities that seldom read one another. We argue that they form one field with three design choices. We develop the projection-quantisation-organisation lens: every method places its projections, places its quantisation thresholds, and organises the resulting codes for search. We test the lens with a reproducible measurement, released as the open BitBudget benchmark, and report three findings. First, the quantisation axis delivers the largest memory savings: a one-bit code with full-precision re-ranking matches uncompressed quality for six of seven embedders, the scanned code one thirty-second of the float's size. Second, the orderings the lens anticipates, including a learned-embedding regime where binary codes overtake an inverted-file product quantiser at a matched byte budget, recur as the embedding is enlarged. Third, given class labels, an eight-byte supervised code more than doubles the retrieval quality of the two-kilobyte task-agnostic float it replaces. We also recast the semantic identifiers of generative retrieval as quantisation codes. The main contribution is a single, tested account of compact-code search, from random projections to the retrieval-augmented era.

15.
medRxiv (Medicine) 2026-06-11

Incremental costs of transitioning from four to eight WHO-recommended antenatal care visits in Uganda: A costing analysis from a societal perspective

Background In 2016, the World Health Organization revised its antenatal care (ANC) recommendation from four to eight visits. For low- and middle-income countries like Uganda, where achieving even four visits remains a challenge, this transition has significant cost implications for both the health system and households. This study estimated the incremental costs of adopting the eight-visit model from a societal perspective. Methods The study was conducted in six government health facilities in southwestern Uganda. A micro-costing approach estimated health facility costs (personnel, equipment, consumables, and overhead). Costs incurred at patients end (transport, ultrasound, medical expenses, and time) were collected from 785 women using a questionnaire, with all costs in 2025 USD. Results For an average of 4.3 visits, total cost per woman was $100.1: facility costs $43.7 (43.7%), and patient costs $56.4 (56.3%). Transitioning to eight visits would increase total cost by $57.8 (57.8%), of which $36.4 (63.0%) would fall on households, equivalent to 68.8% of average monthly household income. Total costs would rise by 55.4% ($115.5 to $179.5) at Health Center IVs and 64.3% ($102.3 to $168.1) at Health Center IIIs, with facility costs up 43.4% and 62.9% and patient costs up 61.2% and 65.7%, respectively. Conclusion Transitioning to eight ANC visits would impose a large financial burden on households, with the incremental patient cost equivalent to more than two-thirds of average monthly household income. Equitable implementation requires improving availability of medicines and diagnostics, subsidizing transport, exploring telemedicine or community-based models, and improving efficiency at lower-tier health centers.

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

The Urysohn Machine: A Metric-Topological Model of Computation

Authors:

arXiv:2508.14143v2 Announce Type: replace Abstract: We introduce the Urysohn Machine, an effective model of classification-oriented computation in which metric separation, frontier structure, and contraction are explicit parts of the computational state. Its basic object is a Urysohn Triple: a support region, a target partition, and a separating classifier stored in a reusable Metric Library. The topological foundation is a constructive Urysohn Realization theorem for finite simplicial settings. It builds separators from dyadic ladders of nested polyhedral regions and equips their frontiers with a chain-level calculus: frontiers are cycles, and shells between levels have boundaries given by differences of frontiers. This construction yields two related complexity measures: decision-boundary width, the geometric measure of a single classifier's boundary, and Urysohn width, the total frontier mass represented by a library or realization. We prove an Amortized Separation Theorem showing that approximating a boundary of width to accuracy requires a number of simple basis triples proportional to boundary width and inversely proportional to resolution, under explicit boundary-footprint assumptions. We also introduce a contrastive separation operator whose graph-cut functional consistently estimates decision-boundary width from sampled metric data, while its Laplacian spectrum certifies class-component structure and conductance. Finally, we analyze the dynamic Urysohn ladder and prove four guarantees: separability under quotient collapse, stability of committed frontiers, bounded capacity under contraction, and scalability with quotient distance. Together, these results give a metric-topological account of classification complexity, amortized inference, and compositional reuse that preserves classical computability while exposing geometric structure hidden by purely symbolic descriptions.

17.
arXiv (CS.AI) 2026-06-24

ATHENA: Agentic Team for Hierarchical Evolutionary Numerical Algorithms

arXiv:2512.03476v3 Announce Type: replace-cross Abstract: Progress in computational science depends on complex numerical workflows that must faithfully encode physical laws, yet translating conceptual insight into reliable code remains a major bottleneck. Although large language models can generate isolated code fragments, they lack the structured reasoning required to design, verify, and iteratively refine complete scientific pipelines. Here we introduce ATHENA, an agentic framework explicitly designed to emulate scientific research modeled as a knowledge-driven contextual bandit process. Its core loop separates conceptual policy from numerical realization through expert-derived conceptual scaffolding, enabling principled diagnosis, reformulation, and repair of computational strategies. Across scientific computing and scientific machine learning tasks, ATHENA autonomously derives and correctly applies exact analytical solutions, constructs stable numerical solvers, diagnoses ill-posed formulations, and orchestrates hybrid symbolic-numeric workflows. Quantitatively, ATHENA matches and frequently surpasses the accuracy of expert-authored reference solutions reported in the literature on canonical benchmarks. By reframing computation as an object of agentic reasoning, our framework enables autonomous orchestration of heterogeneous algorithms across scientific domains.

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

Learning the Koopman Operator using Attention Free Transformers

arXiv:2606.23957v1 Announce Type: new Abstract: Learning Koopman operators with autoencoders enables linear prediction in a latent space, but long-horizon rollouts often drift off the learned manifold, leading to phase and amplitude errors on systems with switching, continuous spectra, or strong transients. We introduce two complementary components that make Koopman predictors more robust. First, we add an attention-free latent memory (AFT) block that aggregates a short window of past latents to produce a corrected latent before each Koopman update. Unlike multi-head attention, AFT operates in linear time and adds only $\approx$30k parameters ($3d^2 + T^2$, fewer than matched multi-head attention), yet captures the local temporal context needed to suppress error divergence. Second, we propose dynamic re-encoding: lightweight, online change-point triggers (EWMA, CUSUM, and sequential two-sample tests) that detect latent drift and project predictions back onto the autoencoder manifold. Across three benchmark systems – Duffing oscillator, Repressilator, IRMA – our model consistently reduces error accumulation compared to a Koopman autoencoder and matched-capacity multi-head attention. We also compare against GRU and Transformer autoencoders, evaluated both from initial conditions and with a 50-step context, and find that Koopman+AFT (with optional re-encoding) attains markedly lower long-horizon error while maintaining lower inference latency. We report improvements over horizons up to 1000 steps, together with ablations over trigger policies. The result is a fast, compact predictor that stays on the learned manifold over long horizons.

19.
arXiv (CS.LG) 2026-06-11

Conformal Bayes under Label Shift: Post-Hoc Calibration vs. In-Training Adaptation

Authors:

arXiv:2606.11865v1 Announce Type: cross Abstract: Conformal Bayes combines Bayesian posterior predictives with conformal calibration to produce prediction sets that are both statistically valid and geometrically efficient. We study conformal Bayes under label shift from a unified perspective, identifying two complementary approaches that restore nominal target-domain coverage through importance-weighted conformal calibration but operate through independent mechanisms. Post-hoc calibration tilts the posterior predictive toward the target domain and corrects the conformal threshold via an importance-weighted quantile, leaving the parameter posterior unchanged. In-training adaptation tilts the parameter posterior itself to the target domain, producing a corrected predictive whose highest predictive density region serves as the highest predictive density (HPD) based prediction set under the fitted target predictive; efficiency is model-dependent and does not imply finite-sample conditional optimality. Two controlled experiments show that in an unbiased training regime both strategies achieve valid coverage equally, while in a lead-optimization regime in-training adaptation acts as a debiasing operator, reducing interval width at unchanged coverage.

20.
arXiv (CS.LG) 2026-06-18

Toward Simultaneously Optimal Regret in U-Calibration

arXiv:2606.18527v1 Announce Type: cross Abstract: U-calibration studies online forecasting algorithms whose predictions can be consumed by any unknown downstream agent, guaranteeing sublinear regret simultaneously for all proper loss functions. Existing U-calibration algorithms achieve worst-case optimal $O(\sqrt{T})$ regret for every bounded proper loss, but they fail to adapt to easier losses: as we show, even for smooth losses such as squared loss, they incur $\Omega(\sqrt{T})$ regret instead of the optimal $O(\log T)$ regret. In this work, we show that this limitation is not inherent. Specifically, we design a single forecast algorithm that simultaneously achieves $\tilde O(\sqrt{T})$ regret for every bounded proper loss and $O(\log T)$ regret for every bounded smooth proper loss. More generally, our algorithm also attains logarithmic regret for losses that are smooth relative to the log-barrier, which include several non-Lipschitz examples. Our approach is based on a novel variant of Follow-the-Perturbed-Leader (FTPL) in which perturbations are applied directly in the prediction space using self-concordant noise. The resulting analysis also departs substantially from prior FTPL analyses due to the complex nature of this noise and may be of independent interest.

21.
arXiv (CS.LG) 2026-06-17

Discovering Functionally Selective Brain Regions with a Deep Topographic Multimodal Model

arXiv:2606.09770v2 Announce Type: replace-cross Abstract: Nearby neurons in cortex share similar response profiles, producing systematic spatial organization across sensory and cognitive systems. Recent topographic models reproduce aspects of this structure but remain unimodal and spatially constrain each layer separately, yielding fragmented maps that capture neither the contiguity of cortical processing streams nor their integration across modalities. We introduce Topo-Omni, a topographic multimodal model in which visual, auditory, and language/cognitive processing share a single contiguous in-silico sheet. Built by fine-tuning a pretrained foundation model with a spatial smoothness objective, this architecture develops clusters across modalities that are consistent with human neuroimaging, from sensory to cognitive systems. Driving or suppressing a cluster selectively biases or impairs perception, paralleling human intervention studies. Finally, we use our model to screen for novel clusters in-silico and discover new natural landscape and animal networks which we validate in human data. A single spatial principle thus organizes representations across modalities and processing stages, yielding testable hypotheses about cortical organization.

22.
bioRxiv (Bioinfo) 2026-06-12

CAREPath: Semantic Context-Aware Reasoning Paths with Mechanism-Augmented Embeddings for Drug Repurposing

Biomedical knowledge graphs (BKGs) that include drugs, genes, and diseases support drug repurposing by connecting drugs to diseases through gene-mediated multi-hop paths, thereby enabling mechanism-of-action reasoning. However, deeper traversal does not necessarily improve mechanistic reasoning: long paths grow combinatorially and frequently pass through hub genes, producing irrelevant gene regulatory signals, whereas overly constrained or sparse paths may miss broader biological context. We propose CAREPath, a KG-LLM framework inspired by depth-first search (DFS)-like and breadth-first search (BFS)-like reasoning to balance mechanistic specificity, scalability, and context recovery. The DFS-like module constrains traversal to short disease-gene-drug paths, converts each path into a structured prompt, and encodes it with a biomedical language model to generate semantic path embeddings. Complementarily, the BFS-like module constructs entity-level mechanism-context embeddings from one-hop gene neighborhoods and enriches them through similarity-guided augmentation using pharmacologically related drugs and gene-signature-similar diseases. Across five biomedical KGs, CAREPath achieves the best overall AUPRC among 18 baselines, improving performance by up to 3.8%. Additional analyses show that semantic short-path encoding contributes most to performance, while mechanism-context augmentation improves robustness under sparse evidence and strengthens Gene Ontology functional agreement. Case studies and recently FDAapproved indications further demonstrate its practical relevance, positioning CAREPath as an interpretable framework for scalable and mechanism-aware drug repurposing. Source code is available at https://github.com/hamppy-song/CAREPath.

23.
arXiv (CS.AI) 2026-06-19

Multi-View Decompilation for LLM-Based Malware Classification

arXiv:2606.20436v1 Announce Type: cross Abstract: Malware analysts often inspect compiled binaries through decompiled pseudo-C, when source code is unavailable. Recent work suggests that large language models (LLMs) can assist this process by classifying decompiled code as benign or malicious, but existing pipelines typically rely on a single decompiler view. We argue that this assumption is fragile: decompilers are lossy heuristic tools, and different decompilers can expose different artefacts of the same binary. We curate a benchmark of benign utilities and malicious programs spanning a range of threat behaviors. Each sample is compiled and decompiled with both Ghidra and RetDec, yielding matched pseudo-C views. Across a range of LLMs from major model families, we find that providing both decompiler views improves malicious-class F1, mainly by increasing recall on malicious samples. Agreement analyses further show that Ghidra and RetDec make partially different errors, supporting the view that decompiler outputs provide complementary evidence. Our results suggest that multi-decompiler prompting is a simple, training-free way to improve LLM-based malware triage in practical settings.

24.
medRxiv (Medicine) 2026-06-15

Genome-wide colocalization of body fat distribution GWAS and subcutaneous adipose eQTLs identifies SNX10, DGKQ, and CBX3 as candidate causal genes for cardiometabolic disease

Authors:

Background: Genome-wide association studies (GWAS) have identified hundreds of loci associated with body fat distribution, yet the causal genes and regulatory mechanisms through which these variants exert their effects remain largely unknown. Expression quantitative trait locus (eQTL) colocalization provides a powerful framework for identifying genes whose expression is genetically coregulated with complex traits. Methods: We performed a genome-wide colocalization analysis integrating waist-hip ratio adjusted for body mass index (WHRadjBMI) GWAS summary statistics from 694,649 individuals (Pulit et al., 2019) with subcutaneous adipose tissue eQTLs from the Genotype-Tissue Expression (GTEx) Project v8 (N = 581 donors). GWAS coordinates were lifted from GRCh37 to GRCh38 to enable direct alignment with GTEx data. We incorporated CAVIAR fine-mapping results to overcome the limitation of FDR-significant eQTL filtering. Colocalization was assessed using the approximate Bayes factor framework (coloc.abf) across 335 independent genome-wide significant loci. Results: Of 2,897 locus-gene pairs tested, 489 (16.9%) showed strong colocalization (PP.H4 > 0.8) and 618 (21.3%) showed moderate evidence (PP.H4 > 0.5). The strongest colocalization was observed for SNX10 (sorting nexin 10; PP.H4 = 1.000), a recently characterized regulator of adipocyte differentiation and female-specific diet-induced obesity. Other top hits included DGKQ (diacylglycerol kinase theta; PP.H4 = 0.9999999), an emerging pharmacological target for insulin resistance, and CBX3 (chromobox 3; PP.H4 = 0.9999974), an epigenetic regulator linked to cardiovascular disease. Established adiposity genes including GRB14 (PP.H4 = 0.681) and KLF14 (PP.H4 = 0.590) were recovered, validating our approach. Several loci exhibited extensive allelic heterogeneity, with 50 genes colocalizing at a single chromosome 3 locus. Conclusions: Our analysis provides a comprehensive map of adipose tissue gene regulatory mechanisms underlying genetic risk for body fat distribution. The identification of SNX10, DGKQ, and CBX3 as high-confidence candidate causal genes advances the translation of GWAS associations into mechanistic understanding and therapeutic targets for obesity-related cardiometabolic disease.

25.
Nature (Science) 2026-06-17

Rock weathering can counteract river CO<sub>2</sub> emissions induced by permafrost thaw

Authors:

Climate-induced permafrost thaw unlocks large stores of organic carbon that are mineralized and emitted as carbon dioxide (CO2) from rivers to the atmosphere1. Concurrently, warming and permafrost thaw can increase mineral weathering rates, thus affecting the release and sequestration of inorganic carbon2–4. Yet how these biological and geological carbon cycles interact and jointly affect CO2 dynamics (emission compared with drawdown) in permafrost rivers remains unknown5. Here we combine CO2 emissions, organic and inorganic solute concentrations, dual carbon isotopes (δ13C–Δ14C) and geochemical modelling to infer how permafrost thaw may affect river biogeochemistry over decades to centuries across the Qinghai–Tibet Plateau. Leveraging a gradient of thermal permafrost degradation, we find that river CO2 emissions decline, whereas solute fluxes from rock weathering increase with decreasing permafrost cover. Across this region, net CO2 drawdown fluxes from rock weathering are about 35% of river CO2 emissions, varying from around 15% in catchments with continuous permafrost to more than 100% in catchments with discontinuous or isolated permafrost. Thus, carbon fluxes from chemical weathering may become increasingly important with ongoing permafrost thaw, potentially even outpacing river CO2 emissions. Our findings disentangle the interplay between biological and geological carbon fluxes that are important for the cryosphere and the global carbon cycle. Permafrost thaw on the Qinghai–Tibet Plateau increases rock-weathering rates while reducing river CO2 emissions, suggesting geological carbon fluxes may eventually outpace thaw-driven emissions.