Hierarchically Encapsulated Representation for Protocol Design in Self-Driving Labs

Self-driving laboratories have begun to replace human experimenters in performing single experimental skills or predetermined experimental protocols. However, as the pace of idea iteration in scientific research has been intensified by Artificial Intelligence, the demand for rapid design of new protocols for new discoveries become evident. Efforts to automate protocol design have been initiated, but the capabilities of knowledge-based machine designers, such as Large Language Models, have not been fully elicited, probably for the absence of a systematic representation of experimental knowledge, as opposed to isolated, flatten pieces of information. To tackle this issue, we propose a multi-faceted, multi-scale representation, where instance actions, generalized operations, and product flow models are hierarchically encapsulated using Domain-Specific Languages. We further develop a data-driven algorithm based on non-parametric modeling that autonomously customizes these representations for specific domains. The proposed representation is equipped with various machine designers to manage protocol design tasks, including planning, modification, and adjustment. The results demonstrate that the proposed method could effectively complement Large Language Models in the protocol design process, serving as an auxiliary module in the realm of machine-assisted scientific exploration.

LocalEscaper: A Weakly-supervised Framework with Regional Reconstruction for Scalable Neural TSP Solvers

Neural solvers have shown significant potential in solving the Traveling Salesman Problem (TSP), yet current approaches face significant challenges. Supervised learning (SL)-based solvers require large amounts of high-quality labeled data, while reinforcement learning (RL)-based solvers, though less dependent on such data, often suffer from inefficiencies. To address these limitations, we propose LocalEscaper, a novel weakly-supervised learning framework for large-scale TSP. LocalEscaper effectively combines the advantages of both SL and RL, enabling effective training on datasets with low-quality labels. To further enhance solution quality, we introduce a regional reconstruction strategy, which mitigates the problem of local optima, a common issue in existing local reconstruction methods. Additionally, we propose a linear-complexity attention mechanism that reduces computational overhead, enabling the efficient solution of large-scale TSPs without sacrificing performance. Experimental results on both synthetic and real-world datasets demonstrate that LocalEscaper outperforms existing neural solvers, achieving state-of-the-art results. Notably, it sets a new benchmark for scalability and efficiency, solving TSP instances with up to 50,000 cities.

Rethinking Tokenized Graph Transformers for Node Classification

Node tokenized graph Transformers (GTs) have shown promising performance in node classification. The generation of token sequences is the key module in existing tokenized GTs which transforms the input graph into token sequences, facilitating the node representation learning via Transformer. In this paper, we observe that the generations of token sequences in existing GTs only focus on the first-order neighbors on the constructed similarity graphs, which leads to the limited usage of nodes to generate diverse token sequences, further restricting the potential of tokenized GTs for node classification. To this end, we propose a new method termed SwapGT. SwapGT first introduces a novel token swapping operation based on the characteristics of token sequences that fully leverages the semantic relevance of nodes to generate more informative token sequences. Then, SwapGT leverages a Transformer-based backbone to learn node representations from the generated token sequences. Moreover, SwapGT develops a center alignment loss to constrain the representation learning from multiple token sequences, further enhancing the model performance. Extensive empirical results on various datasets showcase the superiority of SwapGT for node classification.

Refining Adaptive Zeroth-Order Optimization at Ease

Recently, zeroth-order (ZO) optimization plays an essential role in scenarios where gradient information is inaccessible or unaffordable, such as black-box systems and resource-constrained environments. While existing adaptive methods such as ZO-AdaMM have shown promise, they are fundamentally limited by their underutilization of moment information during optimization, usually resulting in underperforming convergence. To overcome these limitations, this paper introduces Refined Adaptive Zeroth-Order Optimization (R-AdaZO). Specifically, we first show the untapped variance reduction effect of first moment estimate on ZO gradient estimation, which improves the accuracy and stability of ZO updates. We then refine the second moment estimate based on these variance-reduced gradient estimates to better capture the geometry of the optimization landscape, enabling a more effective scaling of ZO updates. We present rigorous theoretical analysis to show (I) the first analysis to the variance reduction of first moment estimate in ZO optimization, (II) the improved second moment estimates with a more accurate approximation of its variance-free ideal, (III) the first variance-aware convergence framework for adaptive ZO methods, which may be of independent interest, and (IV) the faster convergence of R-AdaZO than existing baselines like ZO-AdaMM. Our extensive experiments, including synthetic problems, black-box adversarial attack, and memory-efficient fine-tuning of large language models (LLMs), further verify the superior convergence of R-AdaZO, indicating that R-AdaZO offers an improved solution for real-world ZO optimization challenges.

Rethinking Membership Inference Attacks Against Transfer Learning

Transfer learning, successful in knowledge translation across related tasks, faces a substantial privacy threat from membership inference attacks (MIAs). These attacks, despite posing significant risk to ML model's training data, remain limited-explored in transfer learning. The interaction between teacher and student models in transfer learning has not been thoroughly explored in MIAs, potentially resulting in an under-examined aspect of privacy vulnerabilities within transfer learning. In this paper, we propose a new MIA vector against transfer learning, to determine whether a specific data point was used to train the teacher model while only accessing the student model in a white-box setting. Our method delves into the intricate relationship between teacher and student models, analyzing the discrepancies in hidden layer representations between the student model and its shadow counterpart. These identified differences are then adeptly utilized to refine the shadow model's training process and to inform membership inference decisions effectively. Our method, evaluated across four datasets in diverse transfer learning tasks, reveals that even when an attacker only has access to the student model, the teacher model's training data remains susceptible to MIAs. We believe our work unveils the unexplored risk of membership inference in transfer learning.

Multi-armed Bandit and Backbone boost Lin-Kernighan-Helsgaun Algorithm for the Traveling Salesman Problems

The Lin-Kernighan-Helsguan (LKH) heuristic is a classic local search algorithm for the Traveling Salesman Problem (TSP). LKH introduces an $\alpha$-value to replace the traditional distance metric for evaluating the edge quality, which leads to a significant improvement. However, we observe that the $\alpha$-value does not make full use of the historical information during the search, and single guiding information often makes LKH hard to escape from some local optima. To address the above issues, we propose a novel way to extract backbone information during the TSP local search process, which is dynamic and can be updated once a local optimal solution is found. We further propose to combine backbone information, $\alpha$-value, and distance to evaluate the edge quality so as to guide the search. Moreover, we abstract their different combinations to arms in a multi-armed bandit (MAB) and use an MAB model to help the algorithm select an appropriate evaluation metric dynamically. Both the backbone information and MAB can provide diverse guiding information and learn from the search history to suggest the best metric. We apply our methods to LKH and LKH-3, which is an extension version of LKH that can be used to solve about 40 variant problems of TSP and Vehicle Routing Problem (VRP). Extensive experiments show the excellent performance and generalization capability of our proposed method, significantly improving LKH for TSP and LKH-3 for two representative TSP and VRP variants, the Colored TSP (CTSP) and Capacitated VRP with Time Windows (CVRPTW).

Neural Collapse Inspired Knowledge Distillation

Existing knowledge distillation (KD) methods have demonstrated their ability in achieving student network performance on par with their teachers. However, the knowledge gap between the teacher and student remains significant and may hinder the effectiveness of the distillation process. In this work, we introduce the structure of Neural Collapse (NC) into the KD framework. NC typically occurs in the final phase of training, resulting in a graceful geometric structure where the last-layer features form a simplex equiangular tight frame. Such phenomenon has improved the generalization of deep network training. We hypothesize that NC can also alleviate the knowledge gap in distillation, thereby enhancing student performance. This paper begins with an empirical analysis to bridge the connection between knowledge distillation and neural collapse. Through this analysis, we establish that transferring the teacher's NC structure to the student benefits the distillation process. Therefore, instead of merely transferring instance-level logits or features, as done by existing distillation methods, we encourage students to learn the teacher's NC structure. Thereby, we propose a new distillation paradigm termed Neural Collapse-inspired Knowledge Distillation (NCKD). Comprehensive experiments demonstrate that NCKD is simple yet effective, improving the generalization of all distilled student models and achieving state-of-the-art accuracy performance.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.

Privacy-preserving Universal Adversarial Defense for Black-box Models

Deep neural networks (DNNs) are increasingly used in critical applications such as identity authentication and autonomous driving, where robustness against adversarial attacks is crucial. These attacks can exploit minor perturbations to cause significant prediction errors, making it essential to enhance the resilience of DNNs. Traditional defense methods often rely on access to detailed model information, which raises privacy concerns, as model owners may be reluctant to share such data. In contrast, existing black-box defense methods fail to offer a universal defense against various types of adversarial attacks. To address these challenges, we introduce DUCD, a universal black-box defense method that does not require access to the target model's parameters or architecture. Our approach involves distilling the target model by querying it with data, creating a white-box surrogate while preserving data privacy. We further enhance this surrogate model using a certified defense based on randomized smoothing and optimized noise selection, enabling robust defense against a broad range of adversarial attacks. Comparative evaluations between the certified defenses of the surrogate and target models demonstrate the effectiveness of our approach. Experiments on multiple image classification datasets show that DUCD not only outperforms existing black-box defenses but also matches the accuracy of white-box defenses, all while enhancing data privacy and reducing the success rate of membership inference attacks.

Diverse Generation while Maintaining Semantic Coordination: A Diffusion-Based Data Augmentation Method for Object Detection

Recent studies emphasize the crucial role of data augmentation in enhancing the performance of object detection models. However,existing methodologies often struggle to effectively harmonize dataset diversity with semantic coordination.To bridge this gap, we introduce an innovative augmentation technique leveraging pre-trained conditional diffusion models to mediate this balance. Our approach encompasses the development of a Category Affinity Matrix, meticulously designed to enhance dataset diversity, and a Surrounding Region Alignment strategy, which ensures the preservation of semantic coordination in the augmented images. Extensive experimental evaluations confirm the efficacy of our method in enriching dataset diversity while seamlessly maintaining semantic coordination. Our method yields substantial average improvements of +1.4AP, +0.9AP, and +3.4AP over existing alternatives on three distinct object detection models, respectively.