Large language models (LLMs) have transformed software development by enabling automated code generation, yet they frequently suffer from systematic errors that limit practical deployment. We identify two critical failure modes: \textit{logical hallucination} (incorrect control/data-flow reasoning) and \textit{schematic hallucination} (type mismatches, signature violations, and architectural inconsistencies). These errors stem from the absence of explicit, queryable representations of repository-wide semantics. This paper presents \textbf{SemanticForge}, which introduces four fundamental algorithmic advances for semantically-aware code generation: (1) a novel automatic reconciliation algorithm for dual static-dynamic knowledge graphs, unifying compile-time and runtime program semantics; (2) a neural approach that learns to generate structured graph queries from natural language, achieving 73\% precision versus 51\% for traditional retrieval; (3) a novel beam search algorithm with integrated SMT solving, enabling real-time constraint verification during generation rather than post-hoc validation; and (4) an incremental maintenance algorithm that updates knowledge graphs in $O(|ΔR| \cdot \log n)$ time while maintaining semantic equivalence.

A common approach to the de novo molecular generation problem from mass spectra involves a two-stage pipeline: (1) encoding mass spectra into molecular fingerprints, followed by (2) decoding these fingerprints into molecular structures. In our work, we adopt MIST (Goldman et. al., 2023) as the encoder and MolForge (Ucak et. al., 2023) as the decoder, leveraging additional training data to enhance performance. We also threshold the probabilities of each fingerprint bit to focus on the presence of substructures. This results in a tenfold improvement over previous state-of-the-art methods, generating top-1 31% / top-10 40% of molecular structures correctly from mass spectra in MassSpecGym (Bushuiev et. al., 2024). We position this as a strong baseline for future research in de novo molecule elucidation from mass spectra.

Large language models (LLMs) have demonstrated remarkable capability in function-level code generation tasks. Unlike isolated functions, real-world applications demand reasoning over the entire software system: developers must orchestrate how different components interact, maintain consistency across states over time, and ensure the application behaves correctly within the lifecycle and framework constraints. Yet, no existing benchmark adequately evaluates whether LLMs can bridge this gap and construct entire software systems from scratch. To address this gap, we propose APPFORGE, a benchmark consisting of 101 software development problems drawn from real-world Android apps. Given a natural language specification detailing the app functionality, a language model is tasked with implementing the functionality into an Android app from scratch. Developing an Android app from scratch requires understanding and coordinating app states, lifecycle management, and asynchronous operations, calling for LLMs to generate context-aware, robust, and maintainable code. To construct APPFORGE, we design a multi-agent system to automatically summarize the main functionalities from app documents and navigate the app to synthesize test cases validating the functional correctness of app implementation. Following rigorous manual verification by Android development experts, APPFORGE incorporates the test cases within an automated evaluation framework that enables reproducible assessment without human intervention, making it easily adoptable for future research. Our evaluation on 12 flagship LLMs show that all evaluated models achieve low effectiveness, with the best-performing model (GPT-5) developing only 18.8% functionally correct applications, highlighting fundamental limitations in current models' ability to handle complex, multi-component software engineering challenges.

Combinatorial optimization problems are ubiquitous in science and engineering. Still, learning-based approaches to accelerate combinatorial optimization often require solving a large number of difficult instances to collect training data, incurring significant computational cost. Existing learning-based methods require training dedicated models for each problem distribution, for each downstream task, severely limiting their scalability and generalization. We introduce Forge: Foundational Optimization Representations from Graph Embeddings, a framework that pre-trains a vector-quantized graph autoencoder on a large, diverse collection of mixed-integer programming (MIP) instances in an unsupervised manner, without relying on optimization solvers or optimal solutions. Vector quantization produces discrete code assignments that serve as a vocabulary for representing optimization instances. We evaluate Forge in both unsupervised and supervised settings. In the unsupervised setting, Forge embeddings effectively cluster unseen instances across problem domains and sizes. In the supervised setting, we fine-tune Forge embeddings and show that a single pre-trained model helps predicting both the integrality gap for cut-generation and variable hints for search guidance across multiple problem and size distributions. In both tasks, we improve the performance of a commercial optimization solver and outperform state-of-the-art learning-based methods. Finally, we open-source our training code, pre-trained Forge weights, and embeddings for multiple MIP distributions to foster further research in representation learning for optimization problems.

Survey paper plays a crucial role in scientific research, especially given the rapid growth of research publications. Recently, researchers have begun using LLMs to automate survey generation for better efficiency. However, the quality gap between LLM-generated surveys and those written by human remains significant, particularly in terms of outline quality and citation accuracy. To close these gaps, we introduce SurveyForge, which first generates the outline by analyzing the logical structure of human-written outlines and referring to the retrieved domain-related articles. Subsequently, leveraging high-quality papers retrieved from memory by our scholar navigation agent, SurveyForge can automatically generate and refine the content of the generated article. Moreover, to achieve a comprehensive evaluation, we construct SurveyBench, which includes 100 human-written survey papers for win-rate comparison and assesses AI-generated survey papers across three dimensions: reference, outline, and content quality. Experiments demonstrate that SurveyForge can outperform previous works such as AutoSurvey.

Federated learning (FL) provides an effective machine learning (ML) architecture to protect data privacy in a distributed manner. However, the inevitable network asynchrony, the over-dependence on a central coordinator, and the lack of an open and fair incentive mechanism collectively hinder its further development. We propose \textsc{IronForge}, a new generation of FL framework, that features a Directed Acyclic Graph (DAG)-based data structure and eliminates the need for central coordinators to achieve fully decentralized operations. \textsc{IronForge} runs in a public and open network, and launches a fair incentive mechanism by enabling state consistency in the DAG, so that the system fits in networks where training resources are unevenly distributed. In addition, dedicated defense strategies against prevalent FL attacks on incentive fairness and data privacy are presented to ensure the security of \textsc{IronForge}. Experimental results based on a newly developed testbed FLSim highlight the superiority of \textsc{IronForge} to the existing prevalent FL frameworks under various specifications in performance, fairness, and security. To the best of our knowledge, \textsc{IronForge} is the first secure and fully decentralized FL framework that can be applied in open networks with realistic network and training settings.