Agents based on large language models (LLMs) for machine learning engineering (MLE) can automatically implement ML models via code generation. However, existing approaches to build such agents often rely heavily on inherent LLM knowledge and employ coarse exploration strategies that modify the entire code structure at once. This limits their ability to select effective task-specific models and perform deep exploration within specific components, such as experimenting extensively with feature engineering options. To overcome these, we propose MLESTAR, a novel approach to build MLE agents. MLE-STAR first leverages external knowledge by using a search engine to retrieve effective models from the web, forming an initial solution, then iteratively refines it by exploring various strategies targeting specific ML components. This exploration is guided by ablation studies analyzing the impact of individual code blocks. Furthermore, we introduce a novel ensembling method using an effective strategy suggested by MLE-STAR. Our experimental results show that MLE-STAR achieves medals in 64% of the Kaggle competitions on the MLE-bench, significantly outperforming the best alternative.1

Prompt learning has emerged as a promising paradigm for adapting pre-trained vision-language models (VLMs) to few-shot whole slide image (WSI) classification by aligning visual features with textual representations, thereby reducing annotation cost and enhancing model generalization. Nevertheless, existing methods typically rely on slide-level prompts and fail to capture the subtype-specific phenotypic variations of histological entities (e.g., nuclei, glands) that are critical for cancer diagnosis. To address this gap, we propose Multi-scale Attribute-enhanced Prompt Learning (MAPLE), a hierarchical framework for few-shot WSI classification that jointly integrates multi-scale visual semantics and performs prediction at both the entity and slide levels. Specifically, we first leverage large language models (LLMs) to generate entity-level prompts that can help identify multi-scale histological entities and their phenotypic attributes, as well as slide-level prompts to capture global visual descriptions. Then, an entity-guided cross-attention module is proposed to generate entity-level features, followed by aligning with their corresponding subtype-specific attributes for fine-grained entity-level prediction. To enrich entity representations, we further develop a cross-scale entity graph learning module that can update these representations by capturing their semantic correlations within and across scales. The refined representations are then aggregated into a slide-level representation and aligned with the corresponding prompts for slide-level prediction. Finally, we combine both entity-level and slide-level outputs to produce the final prediction results. Results on three cancer cohorts confirm the effectiveness of our approach in addressing few-shot pathology diagnosis tasks.

Endoscopic imaging is indispensable for visualizing internal organs, yet conventional systems remain bulky and costly because they rely on large, multi-element optics, which limits their ability to access and image certain areas of the body. Achieving high-quality endomicroscopy with hundred micron-scale and inexpensive hardware remains a grand challenge. Optical fibers offer a sub-millimeter-scale imaging conduit that could meet this need, but existing fiber-based approaches typically require either raster scanning or multicore bundles, which limit resolution and speed of imaging. In this work, we overcome these limitations by combining dualcomb interferometry with optical ghost imaging and advanced algorithm. Optical frequency combs enable precise and parallel speckle illumination via wavelengthdivision multiplexing through a single-core fiber, while our dual-comb compressive ghost imaging approach enables snapshot detection of bucket-sum signals using a single-pixel detector, eliminating the need for both spatial and spectral scanning. To reconstruct images from these highly compressed measurements, we introduce Optical Ghost-GPT, a transformer-based image reconstruction model that enables fast, high-fidelity recovery at low sampling ratios. Our dual-comb ghost imaging approach, combined with the novel algorithm, outperforms classical ghost imaging techniques in both speed and accuracy, enabling real-time, high-resolution endoscopic imaging with a significantly reduced device footprint. This advancement paves the way for non-invasive, high-resolution, low-cost endomicroscopy and other sensing applications constrained by hardware size and complexity.

The deployment of large language models (LLMs) is frequently hindered by prohibitive memory and computational requirements. While quantization mitigates these bottlenecks, maintaining model fidelity in the sub-1-bit regime remains a persistent challenge. In this paper, we introduce LITTLEBIT, a novel framework for extreme LLM compression. We target quantization rates as low as 0.1bits per weight (BPW), achieving a memory reduction of approximately 31, which effectively compresses Llama2-13B to under 0.9GB. We represent weights via low-rank latent matrix factorization and subsequently binarize the resulting factors. To counteract the information loss inherent to such drastic precision reduction, we integrate a multi-scale compensation mechanism that learns importance parameters across row, column, and latent dimensions. Two primary contributions enable effective training: Dual Sign-Value-Independent Decomposition (Dual-SVID) for quantization-aware training (QAT) initialization, and Residual Compensation to minimize approximation errors. Extensive experiments confirm the superiority of LITTLEBIT in the sub-1-bit domain; for instance, our method at 0.1 BPW surpasses the performance of leading techniques operating at 0.7BPW on Llama2-7B. We establish a new sizeperformance trade-off--unlocking a potential 11.6 inference speedup relative to FP16--and render powerful LLMs practical for resource-constrained environments.

Rigorous security-focused evaluation of large language model (LLM) agents is imperative for establishing trust in their safe deployment throughout the software development lifecycle. However, existing benchmarks largely rely on synthetic challenges or simplified vulnerability datasets that fail to capture the complexity and ambiguity encountered by security engineers in practice. We introduce SEC-bench, the first fully automated benchmarking framework for evaluating LLM agents on authentic security engineering tasks. SEC-bench employs a novel multi-agent scaffold that automatically constructs code repositories with harnesses, reproduces vulnerabilities in isolated environments, and generates gold patches for reliable evaluation. Our framework automatically creates high-quality software vulnerability datasets with reproducible artifacts at a cost of only $0.87 per instance. Using SEC-bench, we implement two critical software security tasks to rigorously evaluate LLM agents' capabilities: proof-of-concept (PoC) generation and vulnerability patching. A comprehensive evaluation of state-of-the-art LLM code agents reveals significant performance gaps, achieving at most 18.0% success in PoC generation and 34.0% in vulnerability patching on our complete dataset. These results highlight the crucial steps needed toward developing LLM agents that are more practical, intelligent, and autonomous for security engineering.

Graphs are complex, non-Euclidean structures that require specialized models, such as Graph Neural Networks (GNNs), Graph Transformers, or kernel-based approaches, to effectively capture their relational patterns. This inherent complexity makes explaining GNNs decisions particularly challenging. Most existing explainable AI (XAI) methods for GNNs focus on identifying influential nodes or extracting subgraphs that highlight relevant motifs. However, these approaches often fall short of clarifying how such elements contribute to the final prediction. To overcome this limitation, logic-based explanations aim to derive explicit logical rules that reflect the model's decision-making process.

Spatial transcriptomics (ST) technologies provide gene expression measurements with spatial resolution, enabling the dissection of tissue structure and function. A fundamental challenge in ST analysis is clustering spatial spots into coherent functional regions. While existing models effectively integrate expression and spatial signals, they largely overlook sequence-level biological priors encoded in the DNA sequences of expressed genes. To bridge this gap, we propose SAINT (Sequence-Aware Integration for Nucleotide-informed Transcriptomics), a unified framework that augments spatial representation learning with nucleotide-derived features. We construct sequence-augmented datasets across 14 tissue sections from three widely used ST benchmarks (DLPFC, HBC, and MBA), retrieving reference DNA sequences for each expressed gene and encoding them using a pretrained Nucleotide Transformer. For each spot, gene-level embeddings are aggregated via expression-weighted and attention-based pooling, then fused with spatial-expression representations through a late fusion module. Extensive experiments demonstrate that SAINT consistently improves clustering performance across multiple datasets.

Nuclear Magnetic Resonance (NMR) spectroscopy is a cornerstone technique for determining the structures of small molecules and is especially critical in the discovery of novel natural products and clinical therapeutics. Yet, interpreting NMR spectra remains a time-consuming, manual process requiring extensive domain expertise. We introduce CHEFNMR (CHemical Elucidation From NMR), an endto-end framework that directly predicts an unknown molecule's structure solely from its 1DNMR spectra and chemical formula. We frame structure elucidation as conditional generation from an atomic diffusion model built on a non-equivariant transformer architecture. To model the complex chemical groups found in natural products, we generated a dataset of simulated 1DNMR spectra for over 111,000 natural products. CHEFNMR predicts the structures of challenging natural product compounds with an unsurpassed accuracy of over 65%. This work takes a significant step toward solving the grand challenge of automating small-molecule structure elucidation and highlights the potential of deep learning in accelerating molecular discovery.

Modern machine learning algorithms, especially deep learning-based techniques, typically involve careful hyperparameter tuning to achieve the best performance. Despite the surge of intense interest in practical techniques like Bayesian optimization and random search-based approaches to automating this laborious and compute-intensive task, the fundamental learning-theoretic complexity of tuning hyperparameters for deep neural networks is poorly understood. Inspired by this glaring gap, we initiate the formal study of hyperparameter tuning complexity in deep learning through a recently introduced data-driven setting. We assume that we have a series of learning tasks, and we have to tune hyperparameters to do well on average over the distribution of tasks. A major difficulty is that the utility function as a function of the hyperparameter is very volatile and furthermore, it is given implicitly by an optimization problem over the model parameters. To tackle this challenge, we introduce a new technique to characterize the discontinuities and oscillations of the utility function on any fixed problem instance as we vary the hyperparameter; our analysis relies on subtle concepts including tools from algebraic geometry, differential geometry and constrained optimization. We use this to show that the learning-theoretic complexity of the corresponding family of utility functions is bounded. We instantiate our results and provide sample complexity bounds for concrete applications--tuning a hyperparameter that interpolates neural activation functions and setting the kernel parameter in graph neural networks.

We consider the problem of sampling distributions stemming from non-convex potentials with Unadjusted Langevin Algorithm (ULA). We prove the stability of the discrete-time ULA to drift approximations under the assumption that the potential is strongly convex at infinity.