Does semantic communication require a semantic information theory parallel to Shannon's information theory, or can Shannon's work be generalized for semantic communication? This paper advocates for the latter and introduces a semantic generalization of Shannon's information theory (G theory for short). The core idea is to replace the distortion constraint with the semantic constraint, achieved by utilizing a set of truth functions as a semantic channel. These truth functions enable the expressions of semantic distortion, semantic information measures, and semantic information loss. Notably, the maximum semantic information criterion is equivalent to the maximum likelihood criterion and similar to the Regularized Least Squares criterion. This paper shows G theory's applications to daily and electronic semantic communication, machine learning, constraint control, Bayesian confirmation, portfolio theory, and information value. The improvements in machine learning methods involve multilabel learning and classification, maximum mutual information classification, mixture models, and solving latent variables. Furthermore, insights from statistical physics are discussed: Shannon information is similar to free energy; semantic information to free energy in local equilibrium systems; and information efficiency to the efficiency of free energy in performing work. The paper also proposes refining Friston's minimum free energy principle into the maximum information efficiency principle. Lastly, it compares G theory with other semantic information theories and discusses its limitation in representing the semantics of complex data.

Building effective knowledge graphs (KGs) for Retrieval-Augmented Generation (RAG) is pivotal for advancing question answering (QA) systems. However, its effectiveness is hindered by a fundamental disconnect: the knowledge graph (KG) construction process is decoupled from its downstream application, yielding suboptimal graph structures. To bridge this gap, we introduce AutoGraph-R1, the first framework to directly optimize KG construction for task performance using Reinforcement Learning (RL). AutoGraph-R1 trains an LLM constructor by framing graph generation as a policy learning problem, where the reward is derived from the graph's functional utility in a RAG pipeline. We design two novel, task-aware reward functions, one for graphs as knowledge carriers and another as knowledge indices. Across multiple QA benchmarks, AutoGraph-R1 consistently enables graph RAG methods to achieve significant performance gains over using task-agnostic baseline graphs. Our work shows it is possible to close the loop between construction and application, shifting the paradigm from building intrinsically ``good'' graphs to building demonstrably ``useful'' ones.

Large language models (LLMs) are primarily accessed via commercial APIs, but this often requires users to expose their data to service providers. In this paper, we explore how users can stay in control of their data by using privacy profiles: simple natural language instructions that say what should and should not be revealed. We build a framework where a local model uses these instructions to rewrite queries, only hiding details deemed sensitive by the user, before sending them to an external model, thus balancing privacy with performance. To support this research, we introduce PEEP, a multilingual dataset of real user queries annotated to mark private content and paired with synthetic privacy profiles. Experiments with lightweight local LLMs show that, after fine-tuning, they not only achieve markedly better privacy preservation but also match or exceed the performance of much larger zero-shot models. At the same time, the system still faces challenges in fully adhering to user instructions, underscoring the need for models with a better understanding of user-defined privacy preferences.

Code generation is a core capability of large language models (LLMs), yet mainstream benchmarks (e.g., APPs and LiveCodeBench) contain questions with medium-level difficulty and pose no challenge to advanced LLMs. To better reflected the advanced reasoning and code generation ability, We introduce Humanity's Last Code Exam (HLCE), comprising 235 most challenging problems from the International Collegiate Programming Contest (ICPC World Finals) and the International Olympiad in Informatics (IOI) spanning 2010 - 2024. As part of HLCE, we design a harmonized online-offline sandbox that guarantees fully reproducible evaluation. Through our comprehensive evaluation, we observe that even the strongest reasoning LLMs: o4-mini(high) and Gemini-2.5 Pro, achieve pass@1 rates of only 15.9% and 11.4%, respectively. Meanwhile, we propose a novel "self-recognition" task to measure LLMs' awareness of their own capabilities. Results indicate that LLMs' self-recognition abilities are not proportionally correlated with their code generation performance. Finally, our empirical validation of test-time scaling laws reveals that current advanced LLMs have substantial room for improvement on complex programming tasks. We expect HLCE to become a milestone challenge for code generation and to catalyze advances in high-performance reasoning and human-AI collaborative programming. Our code and dataset are also public available(https://github.com/Humanity-s-Last-Code-Exam/HLCE).

Biological machine learning is often bottlenecked by a lack of scaled data. One promising route to relieving data bottlenecks is through high throughput screens, which can experimentally test the activity of $10^6-10^{12}$ protein sequences in parallel. In this article, we introduce algorithms to optimize high throughput screens for data creation and model training. We focus on the large scale regime, where dataset sizes are limited by the cost of measurement and sequencing. We show that when active sequences are rare, we maximize information gain if we only collect positive examples of active sequences, i.e. $x$ with $y>0$. We can correct for the missing negative examples using a generative model of the library, producing a consistent and efficient estimate of the true $p(y | x)$. We demonstrate this approach in simulation and on a large scale screen of antibodies. Overall, co-design of experiments and inference lets us accelerate learning dramatically.

Time series data are often affected by various forms of corruption, such as missing values, noise, and outliers, which pose significant challenges for tasks such as forecasting and anomaly detection. To address these issues, inverse problems focus on reconstructing the original signal from corrupted data by leveraging prior knowledge about its underlying structure. While deep learning methods have demonstrated potential in this domain, they often require extensive pretraining and struggle to generalize under distribution shifts. In this work, we propose RINS-T (Robust Implicit Neural Solvers for Time Series Linear Inverse Problems), a novel deep prior framework that achieves high recovery performance without requiring pretraining data. RINS-T leverages neural networks as implicit priors and integrates robust optimization techniques, making it resilient to outliers while relaxing the reliance on Gaussian noise assumptions. To further improve optimization stability and robustness, we introduce three key innovations: guided input initialization, input perturbation, and convex output combination techniques. Each of these contributions strengthens the framework's optimization stability and robustness. These advancements make RINS-T a flexible and effective solution for addressing complex real-world time series challenges. Our code is available at https://github.com/EPFL-IMOS/RINS-T.

Symmetries are known to improve the empirical performance of machine learning models, yet theoretical guarantees explaining these gains remain limited. Prior work has focused mainly on compact group symmetries and often assumes that the data distribution itself is invariant, an assumption rarely satisfied in real-world applications. In this work, we extend generalization guarantees to the broader setting of non-compact symmetries, such as translations and to non-invariant data distributions. Building on the PAC-Bayes framework, we adapt and tighten existing bounds, demonstrating the approach on McAllester's PAC-Bayes bound while showing that it applies to a wide range of PAC-Bayes bounds. We validate our theory with experiments on a rotated MNIST dataset with a non-uniform rotation group, where the derived guarantees not only hold but also improve upon prior results. These findings provide theoretical evidence that, for symmetric data, symmetric models are preferable beyond the narrow setting of compact groups and invariant distributions, opening the way to a more general understanding of symmetries in machine learning.

Regression with non-Euclidean responses -- e.g., probability distributions, networks, symmetric positive-definite matrices, and compositions -- has become increasingly important in modern applications. In this paper, we propose deep Fréchet neural networks (DFNNs), an end-to-end deep learning framework for predicting non-Euclidean responses -- which are considered as random objects in a metric space -- from Euclidean predictors. Our method leverages the representation-learning power of deep neural networks (DNNs) to the task of approximating conditional Fréchet means of the response given the predictors, the metric-space analogue of conditional expectations, by minimizing a Fréchet risk. The framework is highly flexible, accommodating diverse metrics and high-dimensional predictors. We establish a universal approximation theorem for DFNNs, advancing the state-of-the-art of neural network approximation theory to general metric-space-valued responses without making model assumptions or relying on local smoothing. Empirical studies on synthetic distributional and network-valued responses, as well as a real-world application to predicting employment occupational compositions, demonstrate that DFNNs consistently outperform existing methods.

We study nonparametric regression and classification for path-valued data. We introduce a functional Nadaraya-Watson estimator that combines the signature transform from rough path theory with local kernel regression. The signature transform provides a principled way to encode sequential data through iterated integrals, enabling direct comparison of paths in a natural metric space. Our approach leverages signature-induced distances within the classical kernel regression framework, achieving computational efficiency while avoiding the scalability bottlenecks of large-scale kernel matrix operations. We establish finite-sample convergence bounds demonstrating favorable statistical properties of signature-based distances compared to traditional metrics in infinite-dimensional settings. We propose robust signature variants that provide stability against outliers, enhancing practical performance. Applications to both synthetic and real-world data - including stochastic differential equation learning and time series classification - demonstrate competitive accuracy while offering significant computational advantages over existing methods.

A variety of infinitely wide neural architectures (e.g., dense NNs, CNNs, and transformers) induce Gaussian process (GP) priors over their outputs. These relationships provide both an accurate characterization of the prior predictive distribution and enable the use of GP machinery to improve the uncertainty quantification of deep neural networks. In this work, we extend this connection to neural operators (NOs), a class of models designed to learn mappings between function spaces. Specifically, we show conditions for when arbitrary-depth NOs with Gaussian-distributed convolution kernels converge to function-valued GPs. Based on this result, we show how to compute the covariance functions of these NO-GPs for two NO parametrizations, including the popular Fourier neural operator (FNO). With this, we compute the posteriors of these GPs in regression scenarios, including PDE solution operators. This work is an important step towards uncovering the inductive biases of current FNO architectures and opens a path to incorporate novel inductive biases for use in kernel-based operator learning methods.