De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep learning-based methods have shown progress, they reduce the problem to a translation task, potentially overlooking critical nuances between spectra and peptides. In our research, we present ContraNovo, a pioneering algorithm that leverages contrastive learning to extract the relationship between spectra and peptides and incorporates the mass information into peptide decoding, aiming to address these intricacies more efficiently. Through rigorous evaluations on two benchmark datasets, ContraNovo consistently outshines contemporary state-of-the-art solutions, underscoring its promising potential in enhancing de novo peptide sequencing. The source code is available at https://github.com/BEAM-Labs/ContraNovo.
Federated Learning (FL) is a machine learning paradigm, which enables multiple and decentralized clients to collaboratively train a model under the orchestration of a central aggregator. Traditional FL solutions rely on the trust assumption of the centralized aggregator, which forms cohorts of clients in a fair and honest manner. However, a malicious aggregator, in reality, could abandon and replace the client's training models, or launch Sybil attacks to insert fake clients. Such malicious behaviors give the aggregator more power to control clients in the FL setting and determine the final training results. In this work, we introduce zkFL, which leverages zero-knowledge proofs (ZKPs) to tackle the issue of a malicious aggregator during the training model aggregation process. To guarantee the correct aggregation results, the aggregator needs to provide a proof per round. The proof can demonstrate to the clients that the aggregator executes the intended behavior faithfully. To further reduce the verification cost of clients, we employ a blockchain to handle the proof in a zero-knowledge way, where miners (i.e., the nodes validating and maintaining the blockchain data) can verify the proof without knowing the clients' local and aggregated models. The theoretical analysis and empirical results show that zkFL can achieve better security and privacy than traditional FL, without modifying the underlying FL network structure or heavily compromising the training speed.
In the era of deep learning, federated learning (FL) presents a promising approach that allows multi-institutional data owners, or clients, to collaboratively train machine learning models without compromising data privacy. However, most existing FL approaches rely on a centralized server for global model aggregation, leading to a single point of failure. This makes the system vulnerable to malicious attacks when dealing with dishonest clients. In this work, we address this problem by proposing a secure and reliable FL system based on blockchain and distributed ledger technology. Our system incorporates a peer-to-peer voting mechanism and a reward-and-slash mechanism, which are powered by on-chain smart contracts, to detect and deter malicious behaviors. Both theoretical and empirical analyses are presented to demonstrate the effectiveness of the proposed approach, showing that our framework is robust against malicious client-side behaviors.
Self-supervised pre-training, based on the pretext task of instance discrimination, has fueled the recent advance in label-efficient object detection. However, existing studies focus on pre-training only a feature extractor network to learn transferable representations for downstream detection tasks. This leads to the necessity of training multiple detection-specific modules from scratch in the fine-tuning phase. We argue that the region proposal network (RPN), a common detection-specific module, can additionally be pre-trained towards reducing the localization error of multi-stage detectors. In this work, we propose a simple pretext task that provides an effective pre-training for the RPN, towards efficiently improving downstream object detection performance. We evaluate the efficacy of our approach on benchmark object detection tasks and additional downstream tasks, including instance segmentation and few-shot detection. In comparison with multi-stage detectors without RPN pre-training, our approach is able to consistently improve downstream task performance, with largest gains found in label-scarce settings.
Federated learning (FL) is a promising way to allow multiple data owners (clients) to collaboratively train machine learning models without compromising data privacy. Yet, existing FL solutions usually rely on a centralized aggregator for model weight aggregation, while assuming clients are honest. Even if data privacy can still be preserved, the problem of single-point failure and data poisoning attack from malicious clients remains unresolved. To tackle this challenge, we propose to use distributed ledger technology (DLT) to achieve FLock, a secure and reliable decentralized Federated Learning system built on blockchain. To guarantee model quality, we design a novel peer-to-peer (P2P) review and reward/slash mechanism to detect and deter malicious clients, powered by on-chain smart contracts. The reward/slash mechanism, in addition, serves as incentives for participants to honestly upload and review model parameters in the FLock system. FLock thus improves the performance and the robustness of FL systems in a fully P2P manner.
Using decentralized data for federated training is one promising emerging research direction for alleviating data scarcity in the medical domain. However, in contrast to large-scale fully labeled data commonly seen in general object recognition tasks, the local medical datasets are more likely to only have images annotated for a subset of classes of interest due to high annotation costs. In this paper, we consider a practical yet under-explored problem, where underrepresented classes only have few labeled instances available and only exist in a few clients of the federated system. We show that standard federated learning approaches fail to learn robust multi-label classifiers with extreme class imbalance and address it by proposing a novel federated learning framework, FedFew. FedFew consists of three stages, where the first stage leverages federated self-supervised learning to learn class-agnostic representations. In the second stage, the decentralized partially labeled data are exploited to learn an energy-based multi-label classifier for the common classes. Finally, the underrepresented classes are detected based on the energy and a prototype-based nearest-neighbor model is proposed for few-shot matching. We evaluate FedFew on multi-label thoracic disease classification tasks and demonstrate that it outperforms the federated baselines by a large margin.
Due to the high human cost of annotation, it is non-trivial to curate a large-scale medical dataset that is fully labeled for all classes of interest. Instead, it would be convenient to collect multiple small partially labeled datasets from different matching sources, where the medical images may have only been annotated for a subset of classes of interest. This paper offers an empirical understanding of an under-explored problem, namely partially supervised multi-label classification (PSMLC), where a multi-label classifier is trained with only partially labeled medical images. In contrast to the fully supervised counterpart, the partial supervision caused by medical data scarcity has non-trivial negative impacts on the model performance. A potential remedy could be augmenting the partial labels. Though vicinal risk minimization (VRM) has been a promising solution to improve the generalization ability of the model, its application to PSMLC remains an open question. To bridge the methodological gap, we provide the first VRM-based solution to PSMLC. The empirical results also provide insights into future research directions on partially supervised learning under data scarcity.
As a scalable data-driven approach, multi-agent reinforcement learning (MARL) has made remarkable advances in solving the cooperative residential load scheduling problems. However, the common centralized training strategy of MARL algorithms raises privacy risks for involved households. In this work, we propose a privacy-preserving multi-agent actor-critic framework where the decentralized actors are trained with distributed critics, such that both the decentralized execution and the distributed training do not require the global state information. The proposed framework can preserve the privacy of the households while simultaneously learn the multi-agent credit assignment mechanism implicitly. The simulation experiments demonstrate that the proposed framework significantly outperforms the existing privacy-preserving actor-critic framework, and can achieve comparable performance to the state-of-the-art actor-critic framework without privacy constraints.
A label-efficient paradigm in computer vision is based on self-supervised contrastive pre-training on unlabeled data followed by fine-tuning with a small number of labels. Making practical use of a federated computing environment in the clinical domain and learning on medical images poses specific challenges. In this work, we propose FedMoCo, a robust federated contrastive learning (FCL) framework, which makes efficient use of decentralized unlabeled medical data. FedMoCo has two novel modules: metadata transfer, an inter-node statistical data augmentation module, and self-adaptive aggregation, an aggregation module based on representational similarity analysis. To the best of our knowledge, this is the first FCL work on medical images. Our experiments show that FedMoCo can consistently outperform FedAvg, a seminal federated learning framework, in extracting meaningful representations for downstream tasks. We further show that FedMoCo can substantially reduce the amount of labeled data required in a downstream task, such as COVID-19 detection, to achieve a reasonable performance.