论文检索

Deep Learning · Everything Else

Yuan Feng, Yukun Cao, Hairu Wang, Xike Xie, S Kevin Zhou

Sketches, probabilistic structures for estimating item frequencies in infinite data streams with limited space, are widely used across various domains. Recent studies have shifted the focus from handcrafted sketches to neural sketches, leveraging memory-augmented neural networks (MANNs) to enhance the streaming compression capabilities and achieve better space-accuracy trade-offs.However, existing neural sketches struggle to scale across different data domains and space budgets due to inflexible MANN configurations. In this paper, we introduce a scalable MANN architecture that brings to life the Lego sketch, a novel sketch with superior scalability and accuracy.Much like assembling creations with modular Lego bricks, the Lego sketch dynamically coordinates multiple memory bricks to adapt to various space budgets and diverse data domains.Theoretical analysis and empirical studies demonstrate its scalability and superior space-accuracy trade-offs, outperforming existing handcrafted and neural sketches.

General Machine Learning · Everything Else

Enming Liang, Minghua Chen

Neural networks (NNs) have emerged as promising tools for solving constrained optimization problems in real-time. However, ensuring constraint satisfaction for NN-generated solutions remains challenging due to prediction errors. Existing methods to ensure NN feasibility either suffer from high computational complexity or are limited to specific constraint types.We present Bisection Projection, an efficient approach to ensure NN solution feasibility for optimization over general compact sets with non-empty interiors.Our method comprises two key components:(i) a dedicated NN (called IPNN) that predicts interior points (IPs) with low eccentricity, which naturally accounts for approximation errors;(ii) a bisection algorithm that leverages these IPs to recover solution feasibility when initial NN solutions violate constraints.We establish theoretical guarantees by providing sufficient conditions for IPNN feasibility and proving bounded optimality loss of the bisection operation under IP predictions. Extensive evaluations on real-world non-convex problems demonstrate that Bisection Projection achieves superior feasibility and computational efficiency compared to existing methods, while maintaining comparable optimality gaps.

Applications · Everything Else

Zijie Qiu, Jiaqi Wei, Xiang Zhang, Sheng Xu, Kai Zou, Zhi Jin, ZhiQiang Gao, Nanqing Dong, Siqi Sun

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (**P**eptide **M**ass **D**eviation) and RMD (**R**esidual**M**ass **D**eviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models—those whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

Applications · Everything Else

Boyu Zhang, Aocheng Shen, Bing Liu, Qiankun Zhang, Bin Yuan, Wang, Shenghao Liu, Xianjun Deng

We explore the potential of \emph{AI-enhanced combinatorial optimization theory}, taking online bipartite matching (OBM) as a case study.In the theoretical study of OBM, the \emph{hardness} corresponds to a performance \emph{upper bound} of a specific online algorithm or any possible online algorithms.Typically, these upper bounds derive from challenging instances meticulously designed by theoretical computer scientists.Zhang et al. (ICML 2024) recently provide an example demonstrating how reinforcement learning techniques enhance the hardness result of a specific OBM model.Their attempt is inspiring but preliminary.It is unclear whether their methods can be applied to other OBM problems with similar breakthroughs.This paper takes a further step by introducing DiMa, a unified and novel framework that aims at understanding the hardness of OBM problems based on denoising diffusion probabilistic models (DDPMs).DiMa models the process of generating hard instances as denoising steps, and optimizes them by a novel reinforcement learning algorithm, named \emph{shortcut policy gradient} (SPG).We first examine DiMa on the classic OBM problem by reproducing its known hardest input instance in literature.Further, we apply DiMa to two well-known variants of OBM, for which the exact hardness remains an open problem, and we successfully improve their theoretical state-of-the-art upper bounds.

Deep Learning · Everything Else

Gaurav Menghani, Ravi Kumar, Sanjiv Kumar

One of the core pillars of efficient deep learning methods are architectural improvements, such as residual/skip connections, which have led to significantly better model convergence and quality. Since their introduction, residual connections have become ubiquitous not only in convolutional neural networks but also in transformer-based architectures, the backbone of LLMs.In this paper, we introduce the Learned Augmented Residual Layer (LAuReL) --- a novel generalization of the canonical residual connection --- designed to serve as an in-situ replacement while outperforming it in both model quality and footprint metrics. Our experiments show that LAuReL can enhance quality for both vision and language models while adding fewer parameters and incurring less latency and memory overhead than naively increasing parameter count.For example, on the ImageNet-1K task, LAuReL achieves the same model quality improvements as naively adding an extra layer while using $2.6 \times$ fewer parameters. Similarly, when pre-training 1B and 4B parameter LLMs, LAuReL improves performance on a variety of challenging downstream evaluation tasks by 2.54\% to 20.05\%, while adding only 0.012\% and 0.1\% additional parameters, respectively.

Deep Learning · Everything Else

Qitian Wu, Chenxiao Yang, Kaipeng Zeng, Michael Bronstein

The capability of generalization is a cornerstone for the success of modern learning systems. For non-Euclidean data, e.g., graphs, that particularly involves topological structures, one important aspect neglected by prior studies is how machine learning models generalize under topological shifts. This paper proposes AdvDIFFormer, a physics-inspired graph Transformer model designed to address this challenge. The model is derived from advective diffusion equations which describe a class of continuous message passing process with observed and latent topological structures. We show that AdvDIFFormer has provable capability for controlling generalization error with topological shifts, which in contrast cannot be guaranteed by graph diffusion models, i.e., the generalization of common graph neural networks in continuous space. Empirically, the model demonstrates superiority in various predictive tasks across information networks, molecular screening and protein interactions

Applications · Everything Else

Prashanth Vijayaraghavan, Luyao Shi, Ehsan Degan, Vandana Mukherjee, Xin Zhang

Analog circuit topology synthesis is integral to Electronic Design Automation (EDA), enabling the automated creation of circuit structures tailored to specific design requirements. However, the vast design search space and strict constraint adherence make efficient synthesis challenging. Leveraging the versatility of Large Language Models (LLMs), we propose AUTOCIRCUIT-RL, a novel reinforcement learning (RL)-based framework for automated analog circuit synthesis. The framework operates in two phases: instruction tuning, where an LLM learns to generate circuit topologies from structured prompts encoding design constraints, and RL refinement, which further improves the instruction-tuned model using reward models that evaluate validity, efficiency, and output voltage. The refined model is then used directly to generate topologies that satisfy the design constraints. Empirical results show that AUTOCIRCUIT-RL generates ~12% more valid circuits and improves efficiency by ~14% compared to the best baselines, while reducing duplicate generation rates by ~38%. It achieves over 60% success in synthesizing valid circuits with limited training data, demonstrating strong generalization. These findings highlight the framework's effectiveness in scaling to complex circuits while maintaining efficiency and constraint adherence, marking a significant advancement in AI-driven circuit design.

Applications · Everything Else

Yiheng Xu, Zekun Wang, Junli Wang, Dunjie Lu, Tianbao Xie, Amrita Saha, Doyen Sahoo, Tao Yu, Caiming Xiong

Automating GUI tasks remains challenging due to reliance on textual representations, platform-specific action spaces, and limited reasoning capabilities. We introduce Aguvis, a unified vision-based framework for autonomous GUI agents that directly operates on screen images, standardizes cross-platform interactions and incorporates structured reasoning via inner monologue. To enable this, we construct Aguvis data collection, a large-scale dataset with multimodal grounding and reasoning annotations, and develop a two-stage training pipeline that separates GUI grounding from planning and reasoning. Experiments show that Aguvis achieves state-of-the-art performance across offline and real-world online benchmarks, marking the first fully autonomous vision-based GUI agent that operates without closed-source models. We open-source all datasets, models, and training recipes at https://aguvis-project.github.io to advance future research.

General Machine Learning · Everything Else

Samuel Holt, Max Ruiz Luyten, Antonin Berthon, Mihaela van der Schaar

Constructing robust simulators is essential for asking "what if?" questions and guiding policy in critical domains like healthcare and logistics. However, existing methods often struggle, either failing to generalize beyond historical data or, when using Large Language Models (LLMs), suffering from inaccuracies and poor empirical alignment. We introduce **G-Sim**, a hybrid framework that automates simulator construction by synergizing LLM-driven structural design with rigorous empirical calibration. G-Sim employs an LLM in an iterative loop to propose and refine a simulator's core components and causal relationships, guided by domain knowledge. This structure is then grounded in reality by estimating its parameters using flexible calibration techniques. Specifically, G-Sim can leverage methods that are both **likelihood-free** and **gradient-free** with respect to the simulator, such as **gradient-free optimization** for direct parameter estimation or **simulation-based inference** for obtaining a posterior distribution over parameters. This allows it to handle non-differentiable and stochastic simulators. By integrating domain priors with empirical evidence, G-Sim produces reliable, causally-informed simulators, mitigating data-inefficiency and enabling robust system-level interventions for complex decision-making.

Theory · Everything Else

Chenghua Liu, Minbo Gao, Zhengfeng Ji, Ying

Graph sparsification serves as a foundation for many algorithms, such as approximation algorithms for graph cuts and Laplacian system solvers. As its natural generalization, hypergraph sparsification has recently gained increasing attention, with broad applications in graph machine learning and other areas. In this work, we propose the first quantum algorithm for hypergraph sparsification, addressing an open problem proposed by Apers and de Wolf (FOCS'20). For a weighted hypergraph with $n$ vertices, $m$ hyperedges, and rank $r$, our algorithm outputs a near-linear size $\varepsilon$-spectral sparsifier in time $\widetilde O(r\sqrt{mn}/\varepsilon)$. This algorithm matches the quantum lower bound for constant $r$ and demonstrates quantum speedup when compared with the state-of-the-art $\widetilde O(mr)$-time classical algorithm. As applications, our algorithm implies quantum speedups for computing hypergraph cut sparsifiers, approximating hypergraph mincuts and hypergraph $s$-$t$ mincuts.

Applications · Everything Else

Yao Zhu, Zhenyuan LI, yangyang wei, Shouling Ji

Provenance graphs describe data flows and causal dependencies of host activities, enabling to track the data propagation and manipulation throughout the systems, which provide a foundation for intrusion detection. However, these Provenance-based Intrusion Detection Systems (PIDSes) face significant challenges in storage, representation, and analysis, which impede the efficacy of machine learning models such as Graph Neural Networks (GNNs) in processing and learning from these graphs. This paper presents a novel learning-based anomaly detection method designed to efficiently embed and analyze large-scale provenance graphs. Our approach integrates dynamic graph processing with adaptive encoding, facilitating compact embeddings that effectively address out-of-vocabulary (OOV) elements and adapt to normality shifts in dynamic real-world environments. Subsequently, we incorporate this refined baseline into a tag-propagation framework for real-time detection. Our evaluation demonstrates the method's accuracy and adaptability in anomaly path mining, significantly advancing the state-of-the-art in handling and analyzing provenance graphs for anomaly detection.

Optimization · Everything Else

Lucas Fabian Naumann, Jannik Irmai, Bjoern Andres

The Quantum Alternating Operator Ansatz (QAOA) is a hybrid quantum-classical variational algorithm for approximately solving combinatorial optimization problems on Noisy Intermediate-Scale Quantum (NISQ) devices. Although it has been successfully applied to a variety of problems, there is only limited work on correlation clustering due to the difficulty of modelling the problem constraints with the ansatz. Motivated by this, we present a generalization of QAOA that is more suitable for this problem. In particular, we modify QAOA in two ways: Firstly, we use nucleus sampling for the computation of the expected cost. Secondly, we split the problem into sub-problems, solving each individually with QAOA. We call this generalization the Sub-Problem Quantum Alternating Operator Ansatz (SQAOA) and show theoretically that optimal solutions for correlation clustering instances can be obtained with certainty when the depth of the ansatz tends to infinity. Further, we show experimentally that SQAOA achieves better approximation ratios than QAOA for correlation clustering, while using only one qubit per node of the respective problem instance and reducing the runtime (of simulations).

Applications · Everything Else

Xiang Zhang, Jiaqi Wei, Zijie Qiu, Sheng Xu, Nanqing Dong, ZhiQiang Gao, Siqi Sun

Peptide sequencing—the process of identifying amino acid sequences from mass spectrometry data—is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate tokens sequentially, NATs predict all positions simultaneously, leveraging bidirectional context through unmasked self-attention.However, existing NAT approaches often rely on Connectionist Temporal Classification (CTC) loss, which presents significant optimization challenges due to CTC's complexity and increases the risk of training failures. To address these issues, we propose an improved non-autoregressive peptide sequencing model that incorporates a structured protein sequence curriculum learning strategy. This approach adjusts protein's learning difficulty based on the model’s estimated protein generational capabilities through a sampling process, progressively learning peptide generation from simple to complex sequences. Additionally, we introduce a self-refining inference-time module that iteratively enhances predictions using learned NAT token embeddings, improving sequence accuracy at a fine-grained level. Our curriculum learning strategy reduces NAT training failures frequency by more than 90% based on sampled training over various data distributions. Evaluations on nine benchmark species demonstrate that our approach outperforms all previous methods across multiple metrics and species. Model and source code are available at https://github.com/BEAM-Labs/denovo.

Applications · Everything Else

Anqi Lu, Junchi Yan

For the fundamental linear programming (LP) problems, the simplex method remains popular, which usually requires an appropriate initial basis as a warm start to accelerate the solving process. Predicting an initial basis close to an optimal one can often accelerate the solver, but a closer initial basis does not always result in greater acceleration. To achieve better acceleration, we propose a GNN model based on a tripartite graph representation inspired by LP duality. This approach enables more effective feature extraction for general LP problems and enhances the expressiveness of GNNs. Additionally, we introduce novel loss functions targeting basic variable selection and basis feasibility, along with data preprocessing schemes, to further improve learning capability. In addition to achieving high prediction accuracy, we enhance the quality of the initial basis for practical use. Experimental results show that our approach greatly surpasses the state-of-the-art method in predicting initial basis with greater accuracy and in reducing the number of iterations and solving time of the LP solver.

Deep Learning · Everything Else

Míriam Barrabés, Daniel Mas Montserrat, Kapal Dev, Alexander Ioannidis

Feature shifts between data sources are present in many applications involving healthcare, biomedical, socioeconomic, financial, survey, and multi-sensor data, among others, where unharmonized heterogeneous data sources, noisy data measurements, or inconsistent processing and standardization pipelines can lead to erroneous features. Localizing shifted features is important to address the underlying cause of the shift and correct or filter the data to avoid degrading downstream analysis. While many techniques can detect distribution shifts, localizing the features originating them is still challenging, with current solutions being either inaccurate or not scalable to large and high-dimensional datasets. In this work, we introduce the Feature Shift Localization Network (FSL-Net), a neural network that can localize feature shifts in large and high-dimensional datasets in a fast and accurate manner. The network, trained with a large number of datasets, learns to extract the statistical properties of the datasets and can localize feature shifts from previously unseen datasets and shifts without the need for re-training. The code and ready-to-use trained model are available at \url{https://github.com/AI-sandbox/FSL-Net}.

General Machine Learning · Everything Else

Florence Regol, Leo Schwinn, Kyle Sprague, Mark Coates, Thomas L Markovich

A significant challenge in maintaining real-world machine learning models is responding to the continuous and unpredictable evolution of data. Most practitioners are faced with the difficult question: when should I retrain or update my machine learning model? This seemingly straightforward problem is particularly challenging for three reasons: 1) decisions must be made based on very limited information - we usually have access to only a few examples, 2) the nature, extent, and impact of the distribution shift are unknown, and 3) it involves specifying a cost ratio between retraining and poor performance, which can be hard to characterize. Existing works address certain aspects of this problem, but none offer a comprehensive solution. Distribution shift detection falls short as it cannot account for the cost trade-off; the scarcity of the data, paired with its unusual structure, makes it a poor fit for existing offline reinforcement learning methods, and the online learning formulation overlooks key practical considerations. To address this, we present a principled formulation of the retraining problem and propose an uncertainty-based method that makes decisions by continually forecasting the evolution of model performance evaluated with a bounded metric. Our experiments, addressing classification tasks, show that the method consistently outperforms existing baselines on 7 datasets. We thoroughly assess its robustness to varying cost trade-off values and mis-specified cost trade-offs.

Applications · Everything Else

Yuxiang Zhao, zhuomin chai, Xun Jiang, Qiang Xu, Runsheng Wang, Yibo Lin

Recent advancements have integrated various deep-learning methodologies into physical design, aiming for workflows acceleration and surpasses human-devised solutions. However, prior research has primarily concentrated on developing task-specific networks, which necessitate a significant investment of time to construct large, specialized datasets, and the unintended isolation of models across different tasks. In this paper, we introduce DeepLayout, the first general representation learning framework specifically designed for backend circuit design. To address the distinct characteristics of post-placement circuits, including topological connectivity and geometric distribution, we propose a hybrid encoding architecture that integrates GNN with spatial transformers. Additionally, the framework includes a flexible decoder module that accommodates a variety of task types, supporting multiple hierarchical outputs such as nets and layouts. To mitigate the high annotation costs associated with layout data, we introduce a mask-based self-supervised learning approach designed explicitly for layout representation. This strategy involves a carefully devised masking approach tailored to layout features, precise reconstruction guidance, and most critically—two key supervised learning tasks. We conduct extensive experiments on large-scale industrial datasets, demonstrating that DeepLayout surpasses state-of-the-art (SOTA) methods specialized for individual tasks on two crucial layout quality assessment benchmarks. The experiment results underscore the framework’s robust capability to learn the intrinsic properties of circuits.

Theory · Everything Else

Adam Block, Alexander Rakhlin, Ayush Sekhari

Watermarking, the process by which Large Language Model (LLM) servers imbed an imperceptible signal at inference time in order to detect text generated by their own models, has grown in importance due to the significant improvements in natural language processing tasks by modern LLMs. Current approaches are often impractical due to generation latency, detection time, degradation in text quality, or robustness; such problems often arise due to the focus on token level watermarking, which ignores the inherent structure of text. In this work, we introduce a new scheme, GaussMark, that is simple and efficient to implement, has formal statistical guarantees, comes at no cost in generation latency, and embeds the watermark into the weights of the model itself, providing a structural watermark. Our approach is based on Gaussian independence testing and is motivated by recent empirical observations that minor additive corruptions to LLM weights can result in models of identical (or even improved) quality. We provide formal statistical bounds on the validity and power of our procedure and, through an extensive suite of experiments, demonstrate that GaussMark is reliable, efficient, relatively robust to corruption, and can be instantiated with essentially no loss in model quality.

Applications · Everything Else

Ke Liu, Hao Chen, Chunhua Shen

Developing models for protein-ligand interactions holds substantial significance for drug discovery. Supervised methods often failed due to the lack of labeled data for predicting the protein-ligand binding energy, like antibodies. Therefore, unsupervised approaches are urged to make full use of the unlabeled data. To tackle the problem, we propose an efficient, unsupervised protein-ligand binding energy prediction model via the conservation of energy (CEBind), which follows the physical laws. Specifically, given a protein-ligand complex, we randomly sample forces for each atom in the ligand. Then these forces are applied rigidly to the ligand to perturb its position, following the law of rigid body dynamics. Finally, CEBind predicts the energy of both the unperturbed complex and the perturbed complex. The energy gap between two complexes equals the work of the outer forces, following the law of conservation of energy. Extensive experiments are conducted on the unsupervised protein-ligand binding energy prediction benchmarks, comparing them with previous works. Empirical results and theoretic analysis demonstrate that CEBind is more efficient and outperforms previous unsupervised models on benchmarks.

Deep Learning · Everything Else

Xuanming Cui, Chionh Peng, Adriel Kuek, Ser-Nam Lim

Neural Theorem Provers (NTPs) present a promising framework for neuro-symbolic reasoning, combining end-to-end differentiability with the interpretability of symbolic logic programming. However, optimizing NTPs remains a significant challenge due to their complex objective landscape and gradient sparcity. On the other hand, Knowledge Graph Embedding (KGE) methods offer smooth optimization with well-defined learning objectives but often lack interpretability. In this work, we propose several strategies to integrate the strengths of NTPs and KGEs, and demonstrate substantial improvements in both accuracy and computational efficiency. Specifically, we show that by leveraging the strength of structural learning in KGEs, we can greatly improve NTPs' poorly structured embedding space, while by substituting NTPs with efficient KGE operations, we can significantly reduce evaluation time by over 1000$\times$ on large-scale dataset such as WN18RR with a mild accuracy trade-off.