OpenRaiser/Intern-Atlas huggingface dataset:
AAVDiff: Experimental Validation of Enhanced Viability and Diversity in Recombinant Adeno-Associated Virus (AAV) Capsids through Diffusion Generation
Venue: arXiv cs.AI 2024
Year: 2024

Recombinant adeno-associated virus (rAAV) vectors have revolutionized gene therapy, but their broad tropism and suboptimal transduction efficiency limit their clinical applications. To overcome these limitations, researchers have focused on designing and screening capsid libraries to identify improved vectors. However, the large sequence space and limited resources present challenges in identifying viable capsid variants. In this study, we propose an end-to-end diffusion model to generate capsid sequences with enhanced viability. Using publicly available AAV2 data, we generated 38,000 diverse AAV2 viral protein (VP) sequences, and evaluated 8,000 for viral selection. The results attested the superiority of our model compared to traditional methods. Additionally, in the absence of AAV9 capsid data, apart from one wild-type sequence, we used the same model to directly generate a number of viable sequences with up to 9 mutations. we transferred the remaining 30,000 samples to the AAV9 domain. Furthermore, we conducted mutagenesis on AAV9 VP hypervariable regions VI and V, contributing to the continuous improvement of the AAV9 VP sequence. This research represents a significant advancement in the design and functional validation of rAAV vectors, offering innovative solutions to enhance specificity and transduction efficiency in gene therapy applications.
Uncertainty-guided Open-Set Source-Free Unsupervised Domain Adaptation with Target-private Class Segregation
Venue: arXiv cs.CV 2024
Year: 2024

Standard Unsupervised Domain Adaptation (UDA) aims to transfer knowledge from a labeled source domain to an unlabeled target but usually requires simultaneous access to both source and target data. Moreover, UDA approaches commonly assume that source and target domains share the same labels space. Yet, these two assumptions are hardly satisfied in real-world scenarios. This paper considers the more challenging Source-Free Open-set Domain Adaptation (SF-OSDA) setting, where both assumptions are dropped. We propose a novel approach for SF-OSDA that exploits the granularity of target-private categories by segregating their samples into multiple unknown classes. Starting from an initial clustering-based assignment, our method progressively improves the segregation of target-private samples by refining their pseudo-labels with the guide of an uncertainty-based sample selection module. Additionally, we propose a novel contrastive loss, named NL-InfoNCELoss, that, integrating negative learning into self-supervised contrastive learning, enhances the model robustness to noisy pseudo-labels. Extensive experiments on benchmark datasets demonstrate the superiority of the proposed method over existing approaches, establishing new state-of-the-art performance. Notably, additional analyses show that our method is able to learn the underlying semantics of novel classes, opening the possibility to perform novel class discovery.
EMC$^2$: Efficient MCMC Negative Sampling for Contrastive Learning with Global Convergence
Venue: arXiv cs.LG 2024
Year: 2024

A key challenge in contrastive learning is to generate negative samples from a large sample set to contrast with positive samples, for learning better encoding of the data. These negative samples often follow a softmax distribution which are dynamically updated during the training process. However, sampling from this distribution is non-trivial due to the high computational costs in computing the partition function. In this paper, we propose an Efficient Markov Chain Monte Carlo negative sampling method for Contrastive learning (EMC$^2$). We follow the global contrastive learning loss as introduced in SogCLR, and propose EMC$^2$ which utilizes an adaptive Metropolis-Hastings subroutine to generate hardness-aware negative samples in an online fashion during the optimization. We prove that EMC$^2$ finds an $\mathcal{O}(1/\sqrt{T})$-stationary point of the global contrastive loss in $T$ iterations. Compared to prior works, EMC$^2$ is the first algorithm that exhibits global convergence (to stationarity) regardless of the choice of batch size while exhibiting low computation and memory cost. Numerical experiments validate that EMC$^2$ is effective with small batch training and achieves comparable or better performance than baseline algorithms. We report the results for pre-training image encoders on STL-10 and Imagenet-100.
Do Counterfactual Examples Complicate Adversarial Training?
Venue: arXiv cs.LG 2024
Year: 2024

We leverage diffusion models to study the robustness-performance tradeoff of robust classifiers. Our approach introduces a simple, pretrained diffusion method to generate low-norm counterfactual examples (CEs): semantically altered data which results in different true class membership. We report that the confidence and accuracy of robust models on their clean training data are associated with the proximity of the data to their CEs. Moreover, robust models perform very poorly when evaluated on the CEs directly, as they become increasingly invariant to the low-norm, semantic changes brought by CEs. The results indicate a significant overlap between non-robust and semantic features, countering the common assumption that non-robust features are not interpretable.
Towards free-response paradigm: a theory on decision-making in spiking neural networks
Venue: arXiv cs.NE 2024
Year: 2024

The energy-efficient and brain-like information processing abilities of Spiking Neural Networks (SNNs) have attracted considerable attention, establishing them as a crucial element of brain-inspired computing. One prevalent challenge encountered by SNNs is the trade-off between inference speed and accuracy, which requires sufficient time to achieve the desired level of performance. Drawing inspiration from animal behavior experiments that demonstrate a connection between decision-making reaction times, task complexity, and confidence levels, this study seeks to apply these insights to SNNs. The focus is on understanding how SNNs make inferences, with a particular emphasis on untangling the interplay between signal and noise in decision-making processes. The proposed theoretical framework introduces a new optimization objective for SNN training, highlighting the importance of not only the accuracy of decisions but also the development of predictive confidence through learning from past experiences. Experimental results demonstrate that SNNs trained according to this framework exhibit improved confidence expression, leading to better decision-making outcomes. In addition, a strategy is introduced for efficient decision-making during inference, which allows SNNs to complete tasks more quickly and can use stopping times as indicators of decision confidence. By integrating neuroscience insights with neuromorphic computing, this study opens up new possibilities to explore the capabilities of SNNs and advance their application in complex decision-making scenarios.
Shining Light into the Tunnel: Understanding and Classifying Network Traffic of Residential Proxies
Venue: arXiv cs.CR 2024
Year: 2024

Emerging in recent years, residential proxies (RESIPs) feature multiple unique characteristics when compared with traditional network proxies (e.g., commercial VPNs), particularly, the deployment in residential networks rather than data center networks, the worldwide distribution in tens of thousands of cities and ISPs, and the large scale of millions of exit nodes. All these factors allow RESIP users to effectively masquerade their traffic flows as ones from authentic residential users, which leads to the increasing adoption of RESIP services, especially in malicious online activities. However, regarding the (malicious) usage of RESIPs (i.e., what traffic is relayed by RESIPs), current understanding turns out to be insufficient. Particularly, previous works on RESIP traffic studied only the maliciousness of web traffic destinations and the suspicious patterns of visiting popular websites. Also, a general methodology is missing regarding capturing large-scale RESIP traffic and analyzing RESIP traffic for security risks. Furthermore, considering many RESIP nodes are found to be located in corporate networks and are deployed without proper authorization from device owners or network administrators, it is becoming increasingly necessary to detect and block RESIP traffic flows, which unfortunately is impeded by the scarcity of realistic RESIP traffic datasets and effective detection methodologies. To fill in these gaps, multiple novel tools have been designed and implemented in this study, which include a general framework to deploy RESIP nodes and collect RESIP traffic in a distributed manner, a RESIP traffic analyzer to efficiently process RESIP traffic logs and surface out suspicious traffic flows, and multiple machine learning based RESIP traffic classifiers to timely and accurately detect whether a given traffic flow is RESIP traffic or not.
HLAT: High-quality Large Language Model Pre-trained on AWS Trainium
Venue: arXiv cs.CL 2024
Year: 2024

Getting large language models (LLMs) to perform well on the downstream tasks requires pre-training over trillions of tokens. This typically demands a large number of powerful computational devices in addition to a stable distributed training framework to accelerate the training. The growing number of applications leveraging AI/ML led to a scarcity of the expensive conventional accelerators (such as GPUs), which emphasizes the need for the alternative specialized-accelerators that are scalable and cost-efficient. AWS Trainium is the second-generation machine learning accelerator purposely built for training large deep learning models. However, training LLMs with billions of parameters on AWS Trainium is challenging due to its relatively nascent software ecosystem. In this paper, we showcase HLAT: a family of 7B and 70B decoder-only LLMs pre-trained using 4096 AWS Trainium accelerators over 1.8 trillion tokens. The performance of HLAT is benchmarked against popular open source models including LLaMA and OpenLLaMA, which have been trained on NVIDIA GPUs and Google TPUs, respectively. On various evaluation tasks, we show that HLAT achieves model quality on par with the baselines of similar model size. We also open-source all the training scripts and configurations of HLAT (https://github.com/awslabs/HLAT) and share the best practice of using the NeuronX Distributed Training (NxDT), a customized distributed training library for AWS Trainium. Our work demonstrates that AWS Trainium powered by NxDT is able to successfully pre-train state-of-the-art LLM models with high performance and cost-effectiveness.
Continual Offline Reinforcement Learning via Diffusion-based Dual Generative Replay
Venue: arXiv cs.LG 2024
Year: 2024

We study continual offline reinforcement learning, a practical paradigm that facilitates forward transfer and mitigates catastrophic forgetting to tackle sequential offline tasks. We propose a dual generative replay framework that retains previous knowledge by concurrent replay of generated pseudo-data. First, we decouple the continual learning policy into a diffusion-based generative behavior model and a multi-head action evaluation model, allowing the policy to inherit distributional expressivity for encompassing a progressive range of diverse behaviors. Second, we train a task-conditioned diffusion model to mimic state distributions of past tasks. Generated states are paired with corresponding responses from the behavior generator to represent old tasks with high-fidelity replayed samples. Finally, by interleaving pseudo samples with real ones of the new task, we continually update the state and behavior generators to model progressively diverse behaviors, and regularize the multi-head critic via behavior cloning to mitigate forgetting. Experiments demonstrate that our method achieves better forward transfer with less forgetting, and closely approximates the results of using previous ground-truth data due to its high-fidelity replay of the sample space. Our code is available at \href{https://github.com/NJU-RL/CuGRO}{https://github.com/NJU-RL/CuGRO}.
HSVI-based Online Minimax Strategies for Partially Observable Stochastic Games with Neural Perception Mechanisms
Venue: arXiv cs.GT 2024
Year: 2024

We consider a variant of continuous-state partially-observable stochastic games with neural perception mechanisms and an asymmetric information structure. One agent has partial information, with the observation function implemented as a neural network, while the other agent is assumed to have full knowledge of the state. We present, for the first time, an efficient online method to compute an $\varepsilon$-minimax strategy profile, which requires only one linear program to be solved for each agent at every stage, instead of a complex estimation of opponent counterfactual values. For the partially-informed agent, we propose a continual resolving approach which uses lower bounds, pre-computed offline with heuristic search value iteration (HSVI), instead of opponent counterfactual values. This inherits the soundness of continual resolving at the cost of pre-computing the bound. For the fully-informed agent, we propose an inferred-belief strategy, where the agent maintains an inferred belief about the belief of the partially-informed agent based on (offline) upper bounds from HSVI, guaranteeing $\varepsilon$-distance to the value of the game at the initial belief known to both agents.
Simplex Decomposition for Portfolio Allocation Constraints in Reinforcement Learning
Venue: arXiv cs.AI 2024
Year: 2024

Portfolio optimization tasks describe sequential decision problems in which the investor's wealth is distributed across a set of assets. Allocation constraints are used to enforce minimal or maximal investments into particular subsets of assets to control for objectives such as limiting the portfolio's exposure to a certain sector due to environmental concerns. Although methods for constrained Reinforcement Learning (CRL) can optimize policies while considering allocation constraints, it can be observed that these general methods yield suboptimal results. In this paper, we propose a novel approach to handle allocation constraints based on a decomposition of the constraint action space into a set of unconstrained allocation problems. In particular, we examine this approach for the case of two constraints. For example, an investor may wish to invest at least a certain percentage of the portfolio into green technologies while limiting the investment in the fossil energy sector. We show that the action space of the task is equivalent to the decomposed action space, and introduce a new reinforcement learning (RL) approach CAOSD, which is built on top of the decomposition. The experimental evaluation on real-world Nasdaq-100 data demonstrates that our approach consistently outperforms state-of-the-art CRL benchmarks for portfolio optimization.
Question Difficulty Ranking for Multiple-Choice Reading Comprehension
Venue: arXiv cs.CL 2024
Year: 2024

Multiple-choice (MC) tests are an efficient method to assess English learners. It is useful for test creators to rank candidate MC questions by difficulty during exam curation. Typically, the difficulty is determined by having human test takers trial the questions in a pretesting stage. However, this is expensive and not scalable. Therefore, we explore automated approaches to rank MC questions by difficulty. However, there is limited data for explicit training of a system for difficulty scores. Hence, we compare task transfer and zero-shot approaches: task transfer adapts level classification and reading comprehension systems for difficulty ranking while zero-shot prompting of instruction finetuned language models contrasts absolute assessment against comparative. It is found that level classification transfers better than reading comprehension. Additionally, zero-shot comparative assessment is more effective at difficulty ranking than the absolute assessment and even the task transfer approaches at question difficulty ranking with a Spearman's correlation of 40.4%. Combining the systems is observed to further boost the correlation.
Bootstrapping Linear Models for Fast Online Adaptation in Human-Agent Collaboration
Venue: arXiv cs.AI 2024
Year: 2024

Agents that assist people need to have well-initialized policies that can adapt quickly to align with their partners' reward functions. Initializing policies to maximize performance with unknown partners can be achieved by bootstrapping nonlinear models using imitation learning over large, offline datasets. Such policies can require prohibitive computation to fine-tune in-situ and therefore may miss critical run-time information about a partner's reward function as expressed through their immediate behavior. In contrast, online logistic regression using low-capacity models performs rapid inference and fine-tuning updates and thus can make effective use of immediate in-task behavior for reward function alignment. However, these low-capacity models cannot be bootstrapped as effectively by offline datasets and thus have poor initializations. We propose BLR-HAC, Bootstrapped Logistic Regression for Human Agent Collaboration, which bootstraps large nonlinear models to learn the parameters of a low-capacity model which then uses online logistic regression for updates during collaboration. We test BLR-HAC in a simulated surface rearrangement task and demonstrate that it achieves higher zero-shot accuracy than shallow methods and takes far less computation to adapt online while still achieving similar performance to fine-tuned, large nonlinear models. For code, please see our project page https://sites.google.com/view/blr-hac.
Laplace-HDC: Understanding the geometry of binary hyperdimensional computing
Venue: arXiv cs.LG 2024
Year: 2024

This paper studies the geometry of binary hyperdimensional computing (HDC), a computational scheme in which data are encoded using high-dimensional binary vectors. We establish a result about the similarity structure induced by the HDC binding operator and show that the Laplace kernel naturally arises in this setting, motivating our new encoding method Laplace-HDC, which improves upon previous methods. We describe how our results indicate limitations of binary HDC in encoding spatial information from images and discuss potential solutions, including using Haar convolutional features and the definition of a translation-equivariant HDC encoding. Several numerical experiments highlighting the improved accuracy of Laplace-HDC in contrast to alternative methods are presented. We also numerically study other aspects of the proposed framework such as robustness and the underlying translation-equivariant encoding.
Quantifying AI Vulnerabilities: A Synthesis of Complexity, Dynamical Systems, and Game Theory
Venue: arXiv cs.CR 2024
Year: 2024

The rapid integration of Artificial Intelligence (AI) systems across critical domains necessitates robust security evaluation frameworks. We propose a novel approach that introduces three metrics: System Complexity Index (SCI), Lyapunov Exponent for AI Stability (LEAIS), and Nash Equilibrium Robustness (NER). SCI quantifies the inherent complexity of an AI system, LEAIS captures its stability and sensitivity to perturbations, and NER evaluates its strategic robustness against adversarial manipulation. Through comparative analysis, we demonstrate the advantages of our framework over existing techniques. We discuss the theoretical and practical implications, potential applications, limitations, and future research directions. Our work contributes to the development of secure and trustworthy AI technologies by providing a holistic, theoretically grounded approach to AI security evaluation. As AI continues to advance, prioritising and advancing AI security through interdisciplinary collaboration is crucial to ensure its responsible deployment for the benefit of society.
The Path To Autonomous Cyber Defense
Venue: arXiv cs.CR 2024
Year: 2024

Defenders are overwhelmed by the number and scale of attacks against their networks.This problem will only be exacerbated as attackers leverage artificial intelligence to automate their workflows. We propose a path to autonomous cyber agents able to augment defenders by automating critical steps in the cyber defense life cycle.
Industrial Cabling in Constrained Environments: a Practical Approach and Current Challenges
Venue: arXiv cs.RO 2024
Year: 2024

Cabling tasks (pulling, clipping, and plug insertion) are today mostly manual work, limiting the cost-effectiveness of electrification. Feasibility for the robotic grasping and insertion of plugs, as well as the manipulation of cables, have been shown in research settings. However, in many industrial tasks the complete process from picking, insertion, routing, and validation must be solved with one system. This often means the cable must be directly manipulated for routing, and the plug must be manipulated for insertion, often in cluttered environments with tight space constraints. Here we introduce an analysis of the complete industrial cabling tasks and demonstrate a solution from grasp, plug insertion, clipping, and final plug insertion. Industrial requirements are summarized, considering the space limitations, tolerances, and possible ways that the cabling process can be integrated into the production process. This paper proposes gripper designs and general robotic assembly methods for the widely used FASTON and a cubical industrial connector. The proposed methods cover the cable gripping, handling, routing, and inserting processes of the connector. Customized grippers are designed to ensure the reliable gripping of the plugs and the pulling and manipulation of the cable segments. A passive component to correct the cable orientation is proposed, allowing the robot to re-grip the plug before insertion. In general, the proposed method can perform cable assembly with mere position control, foregoing complex control approaches. This solution is demonstrated with an industrial product with realistic space requirements and tolerances, identifying difficult aspects of current cabling scenarios and potential to improve the automation-friendliness in the product design.
Course Recommender Systems Need to Consider the Job Market
Venue: arXiv cs.IR 2024
Year: 2024

Current course recommender systems primarily leverage learner-course interactions, course content, learner preferences, and supplementary course details like instructor, institution, ratings, and reviews, to make their recommendation. However, these systems often overlook a critical aspect: the evolving skill demand of the job market. This paper focuses on the perspective of academic researchers, working in collaboration with the industry, aiming to develop a course recommender system that incorporates job market skill demands. In light of the job market's rapid changes and the current state of research in course recommender systems, we outline essential properties for course recommender systems to address these demands effectively, including explainable, sequential, unsupervised, and aligned with the job market and user's goals. Our discussion extends to the challenges and research questions this objective entails, including unsupervised skill extraction from job listings, course descriptions, and resumes, as well as predicting recommendations that align with learner objectives and the job market and designing metrics to evaluate this alignment. Furthermore, we introduce an initial system that addresses some existing limitations of course recommender systems using large Language Models (LLMs) for skill extraction and Reinforcement Learning (RL) for alignment with the job market. We provide empirical results using open-source data to demonstrate its effectiveness.