Large Language Model is Secretly a Protein Sequence Optimizer

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an iterative process to generate variants and select via experimental feedback. We demonstrate large language models (LLMs), despite being trained on massive texts, are secretly protein sequence optimizers. With a directed evolutionary method, LLM can perform protein engineering through Pareto and experiment-budget constrained optimization, demonstrating success on both synthetic and experimental fitness landscapes.

Graph Generative Pre-trained Transformer

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

GraphCroc: Cross-Correlation Autoencoder for Graph Structural Reconstruction

Graph-structured data is integral to many applications, prompting the development of various graph representation methods. Graph autoencoders (GAEs), in particular, reconstruct graph structures from node embeddings. Current GAE models primarily utilize self-correlation to represent graph structures and focus on node-level tasks, often overlooking multi-graph scenarios. Our theoretical analysis indicates that self-correlation generally falls short in accurately representing specific graph features such as islands, symmetrical structures, and directional edges, particularly in smaller or multiple graph contexts. To address these limitations, we introduce a cross-correlation mechanism that significantly enhances the GAE representational capabilities. Additionally, we propose GraphCroc, a new GAE that supports flexible encoder architectures tailored for various downstream tasks and ensures robust structural reconstruction, through a mirrored encoding-decoding process. This model also tackles the challenge of representation bias during optimization by implementing a loss-balancing strategy. Both theoretical analysis and numerical evaluations demonstrate that our methodology significantly outperforms existing self-correlation-based GAEs in graph structure reconstruction.

AdaPI: Facilitating DNN Model Adaptivity for Efficient Private Inference in Edge Computing

Private inference (PI) has emerged as a promising solution to execute computations on encrypted data, safeguarding user privacy and model parameters in edge computing. However, existing PI methods are predominantly developed considering constant resource constraints, overlooking the varied and dynamic resource constraints in diverse edge devices, like energy budgets. Consequently, model providers have to design specialized models for different devices, where all of them have to be stored on the edge server, resulting in inefficient deployment. To fill this gap, this work presents AdaPI, a novel approach that achieves adaptive PI by allowing a model to perform well across edge devices with diverse energy budgets. AdaPI employs a PI-aware training strategy that optimizes the model weights alongside weight-level and feature-level soft masks. These soft masks are subsequently transformed into multiple binary masks to enable adjustments in communication and computation workloads. Through sequentially training the model with increasingly dense binary masks, AdaPI attains optimal accuracy for each energy budget, which outperforms the state-of-the-art PI methods by 7.3\% in terms of test accuracy on CIFAR-100. The code of AdaPI can be accessed via https://github.com/jiahuiiiiii/AdaPI.

Bileve: Securing Text Provenance in Large Language Models Against Spoofing with Bi-level Signature

Text watermarks for large language models (LLMs) have been commonly used to identify the origins of machine-generated content, which is promising for assessing liability when combating deepfake or harmful content. While existing watermarking techniques typically prioritize robustness against removal attacks, unfortunately, they are vulnerable to spoofing attacks: malicious actors can subtly alter the meanings of LLM-generated responses or even forge harmful content, potentially misattributing blame to the LLM developer. To overcome this, we introduce a bi-level signature scheme, Bileve, which embeds fine-grained signature bits for integrity checks (mitigating spoofing attacks) as well as a coarse-grained signal to trace text sources when the signature is invalid (enhancing detectability) via a novel rank-based sampling strategy. Compared to conventional watermark detectors that only output binary results, Bileve can differentiate 5 scenarios during detection, reliably tracing text provenance and regulating LLMs. The experiments conducted on OPT-1.3B and LLaMA-7B demonstrate the effectiveness of Bileve in defeating spoofing attacks with enhanced detectability.

SSNet: A Lightweight Multi-Party Computation Scheme for Practical Privacy-Preserving Machine Learning Service in the Cloud

As privacy-preserving becomes a pivotal aspect of deep learning (DL) development, multi-party computation (MPC) has gained prominence for its efficiency and strong security. However, the practice of current MPC frameworks is limited, especially when dealing with large neural networks, exemplified by the prolonged execution time of 25.8 seconds for secure inference on ResNet-152. The primary challenge lies in the reliance of current MPC approaches on additive secret sharing, which incurs significant communication overhead with non-linear operations such as comparisons. Furthermore, additive sharing suffers from poor scalability on party size. In contrast, the evolving landscape of MPC necessitates accommodating a larger number of compute parties and ensuring robust performance against malicious activities or computational failures. In light of these challenges, we propose SSNet, which for the first time, employs Shamir's secret sharing (SSS) as the backbone of MPC-based ML framework. We meticulously develop all framework primitives and operations for secure DL models tailored to seamlessly integrate with the SSS scheme. SSNet demonstrates the ability to scale up party numbers straightforwardly and embeds strategies to authenticate the computation correctness without incurring significant performance overhead. Additionally, SSNet introduces masking strategies designed to reduce communication overhead associated with non-linear operations. We conduct comprehensive experimental evaluations on commercial cloud computing infrastructure from Amazon AWS, as well as across diverse prevalent DNN models and datasets. SSNet demonstrates a substantial performance boost, achieving speed-ups ranging from 3x to 14x compared to SOTA MPC frameworks. Moreover, SSNet also represents the first framework that is evaluated on a five-party computation setup, in the context of secure DL inference.

TBNet: A Neural Architectural Defense Framework Facilitating DNN Model Protection in Trusted Execution Environments

Trusted Execution Environments (TEEs) have become a promising solution to secure DNN models on edge devices. However, the existing solutions either provide inadequate protection or introduce large performance overhead. Taking both security and performance into consideration, this paper presents TBNet, a TEE-based defense framework that protects DNN model from a neural architectural perspective. Specifically, TBNet generates a novel Two-Branch substitution model, to respectively exploit (1) the computational resources in the untrusted Rich Execution Environment (REE) for latency reduction and (2) the physically-isolated TEE for model protection. Experimental results on a Raspberry Pi across diverse DNN model architectures and datasets demonstrate that TBNet achieves efficient model protection at a low cost.

Scheduled Knowledge Acquisition on Lightweight Vector Symbolic Architectures for Brain-Computer Interfaces

Brain-Computer interfaces (BCIs) are typically designed to be lightweight and responsive in real-time to provide users timely feedback. Classical feature engineering is computationally efficient but has low accuracy, whereas the recent neural networks (DNNs) improve accuracy but are computationally expensive and incur high latency. As a promising alternative, the low-dimensional computing (LDC) classifier based on vector symbolic architecture (VSA), achieves small model size yet higher accuracy than classical feature engineering methods. However, its accuracy still lags behind that of modern DNNs, making it challenging to process complex brain signals. To improve the accuracy of a small model, knowledge distillation is a popular method. However, maintaining a constant level of distillation between the teacher and student models may not be the best way for a growing student during its progressive learning stages. In this work, we propose a simple scheduled knowledge distillation method based on curriculum data order to enable the student to gradually build knowledge from the teacher model, controlled by an $\alpha$ scheduler. Meanwhile, we employ the LDC/VSA as the student model to enhance the on-device inference efficiency for tiny BCI devices that demand low latency. The empirical results have demonstrated that our approach achieves better tradeoff between accuracy and hardware efficiency compared to other methods.

LinGCN: Structural Linearized Graph Convolutional Network for Homomorphically Encrypted Inference

The growth of Graph Convolution Network (GCN) model sizes has revolutionized numerous applications, surpassing human performance in areas such as personal healthcare and financial systems. The deployment of GCNs in the cloud raises privacy concerns due to potential adversarial attacks on client data. To address security concerns, Privacy-Preserving Machine Learning (PPML) using Homomorphic Encryption (HE) secures sensitive client data. However, it introduces substantial computational overhead in practical applications. To tackle those challenges, we present LinGCN, a framework designed to reduce multiplication depth and optimize the performance of HE based GCN inference. LinGCN is structured around three key elements: (1) A differentiable structural linearization algorithm, complemented by a parameterized discrete indicator function, co-trained with model weights to meet the optimization goal. This strategy promotes fine-grained node-level non-linear location selection, resulting in a model with minimized multiplication depth. (2) A compact node-wise polynomial replacement policy with a second-order trainable activation function, steered towards superior convergence by a two-level distillation approach from an all-ReLU based teacher model. (3) an enhanced HE solution that enables finer-grained operator fusion for node-wise activation functions, further reducing multiplication level consumption in HE-based inference. Our experiments on the NTU-XVIEW skeleton joint dataset reveal that LinGCN excels in latency, accuracy, and scalability for homomorphically encrypted inference, outperforming solutions such as CryptoGCN. Remarkably, LinGCN achieves a 14.2x latency speedup relative to CryptoGCN, while preserving an inference accuracy of 75% and notably reducing multiplication depth.

AutoReP: Automatic ReLU Replacement for Fast Private Network Inference

The growth of the Machine-Learning-As-A-Service (MLaaS) market has highlighted clients' data privacy and security issues. Private inference (PI) techniques using cryptographic primitives offer a solution but often have high computation and communication costs, particularly with non-linear operators like ReLU. Many attempts to reduce ReLU operations exist, but they may need heuristic threshold selection or cause substantial accuracy loss. This work introduces AutoReP, a gradient-based approach to lessen non-linear operators and alleviate these issues. It automates the selection of ReLU and polynomial functions to speed up PI applications and introduces distribution-aware polynomial approximation (DaPa) to maintain model expressivity while accurately approximating ReLUs. Our experimental results demonstrate significant accuracy improvements of 6.12% (94.31%, 12.9K ReLU budget, CIFAR-10), 8.39% (74.92%, 12.9K ReLU budget, CIFAR-100), and 9.45% (63.69%, 55K ReLU budget, Tiny-ImageNet) over current state-of-the-art methods, e.g., SNL. Morever, AutoReP is applied to EfficientNet-B2 on ImageNet dataset, and achieved 75.55% accuracy with 176.1 times ReLU budget reduction.