In recent years, Reinforcement Learning (RL) has emerged as a powerful tool for solving a wide range of problems, including decision-making and genomics. The exponential growth of raw genomic data over the past two decades has exceeded the capacity of manual analysis, leading to a growing interest in automatic data analysis and processing. RL algorithms are capable of learning from experience with minimal human supervision, making them well-suited for genomic data analysis and interpretation. One of the key benefits of using RL is the reduced cost associated with collecting labeled training data, which is required for supervised learning. While there have been numerous studies examining the applications of Machine Learning (ML) in genomics, this survey focuses exclusively on the use of RL in various genomics research fields, including gene regulatory networks (GRNs), genome assembly, and sequence alignment. We present a comprehensive technical overview of existing studies on the application of RL in genomics, highlighting the strengths and limitations of these approaches. We then discuss potential research directions that are worthy of future exploration, including the development of more sophisticated reward functions as RL heavily depends on the accuracy of the reward function, the integration of RL with other machine learning techniques, and the application of RL to new and emerging areas in genomics research. Finally, we present our findings and conclude by summarizing the current state of the field and the future outlook for RL in genomics.
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The Network Revenue Management (NRM) problem is a well-known challenge in dynamic decision-making under uncertainty. In this problem, fixed resources must be allocated to serve customers over a finite horizon, while customers arrive according to a stochastic process. The typical NRM model assumes that customer arrivals are independent over time. However, in this paper, we explore a more general setting where customer arrivals over different periods can be correlated. We propose a model that assumes the existence of a system state, which determines customer arrivals for the current period. This system state evolves over time according to a time-inhomogeneous Markov chain. We show our model can be used to represent correlation in various settings. To solve the NRM problem under our correlated model, we derive a new linear programming (LP) approximation of the optimal policy. Our approximation provides an upper bound on the total expected value collected by the optimal policy. We use our LP to develop a new bid price policy, which computes bid prices for each system state and time period in a backward induction manner. The decision is then made by comparing the reward of the customer against the associated bid prices. Our policy guarantees to collect at least $1/(1+L)$ fraction of the total reward collected by the optimal policy, where $L$ denotes the maximum number of resources required by a customer. In summary, our work presents a Markovian model for correlated customer arrivals in the NRM problem and provides a new LP approximation for solving the problem under this model. We derive a new bid price policy and provides a theoretical guarantee of the performance of the policy.
Over the past few years, there has been growing interest in developing a broad, universal, and general-purpose computer vision system. Such systems have the potential to address a wide range of vision tasks simultaneously, without being limited to specific problems or data domains. This universality is crucial for practical, real-world computer vision applications. In this study, our focus is on a specific challenge: the large-scale, multi-domain universal object detection problem, which contributes to the broader goal of achieving a universal vision system. This problem presents several intricate challenges, including cross-dataset category label duplication, label conflicts, and the necessity to handle hierarchical taxonomies. To address these challenges, we introduce our approach to label handling, hierarchy-aware loss design, and resource-efficient model training utilizing a pre-trained large vision model. Our method has demonstrated remarkable performance, securing a prestigious second-place ranking in the object detection track of the Robust Vision Challenge 2022 (RVC 2022) on a million-scale cross-dataset object detection benchmark. We believe that our comprehensive study will serve as a valuable reference and offer an alternative approach for addressing similar challenges within the computer vision community. The source code for our work is openly available at //github.com/linfeng93/Large-UniDet.
Federated Learning (FL) is a well-known paradigm of distributed machine learning on mobile and IoT devices, which preserves data privacy and optimizes communication efficiency. To avoid the single point of failure problem in FL, decentralized federated learning (DFL) has been proposed to use peer-to-peer communication for model aggregation, which has been considered an attractive solution for machine learning tasks on distributed personal devices. However, this process is vulnerable to attackers who share false models and data. If there exists a group of malicious clients, they might harm the performance of the model by carrying out a poisoning attack. In addition, in DFL, clients often lack the incentives to contribute their computing powers to do model training. In this paper, we proposed Blockchain-based Decentralized Federated Learning (BDFL), which leverages a blockchain for decentralized model verification and auditing. BDFL includes an auditor committee for model verification, an incentive mechanism to encourage the participation of clients, a reputation model to evaluate the trustworthiness of clients, and a protocol suite for dynamic network updates. Evaluation results show that, with the reputation mechanism, BDFL achieves fast model convergence and high accuracy on real datasets even if there exist 30\% malicious clients in the system.
Graph Neural Networks (GNNs) have shown promising results on a broad spectrum of applications. Most empirical studies of GNNs directly take the observed graph as input, assuming the observed structure perfectly depicts the accurate and complete relations between nodes. However, graphs in the real world are inevitably noisy or incomplete, which could even exacerbate the quality of graph representations. In this work, we propose a novel Variational Information Bottleneck guided Graph Structure Learning framework, namely VIB-GSL, in the perspective of information theory. VIB-GSL advances the Information Bottleneck (IB) principle for graph structure learning, providing a more elegant and universal framework for mining underlying task-relevant relations. VIB-GSL learns an informative and compressive graph structure to distill the actionable information for specific downstream tasks. VIB-GSL deduces a variational approximation for irregular graph data to form a tractable IB objective function, which facilitates training stability. Extensive experimental results demonstrate that the superior effectiveness and robustness of VIB-GSL.
Recently, contrastive learning (CL) has emerged as a successful method for unsupervised graph representation learning. Most graph CL methods first perform stochastic augmentation on the input graph to obtain two graph views and maximize the agreement of representations in the two views. Despite the prosperous development of graph CL methods, the design of graph augmentation schemes -- a crucial component in CL -- remains rarely explored. We argue that the data augmentation schemes should preserve intrinsic structures and attributes of graphs, which will force the model to learn representations that are insensitive to perturbation on unimportant nodes and edges. However, most existing methods adopt uniform data augmentation schemes, like uniformly dropping edges and uniformly shuffling features, leading to suboptimal performance. In this paper, we propose a novel graph contrastive representation learning method with adaptive augmentation that incorporates various priors for topological and semantic aspects of the graph. Specifically, on the topology level, we design augmentation schemes based on node centrality measures to highlight important connective structures. On the node attribute level, we corrupt node features by adding more noise to unimportant node features, to enforce the model to recognize underlying semantic information. We perform extensive experiments of node classification on a variety of real-world datasets. Experimental results demonstrate that our proposed method consistently outperforms existing state-of-the-art baselines and even surpasses some supervised counterparts, which validates the effectiveness of the proposed contrastive framework with adaptive augmentation.
Graph Neural Networks (GNNs) have proven to be useful for many different practical applications. However, many existing GNN models have implicitly assumed homophily among the nodes connected in the graph, and therefore have largely overlooked the important setting of heterophily, where most connected nodes are from different classes. In this work, we propose a novel framework called CPGNN that generalizes GNNs for graphs with either homophily or heterophily. The proposed framework incorporates an interpretable compatibility matrix for modeling the heterophily or homophily level in the graph, which can be learned in an end-to-end fashion, enabling it to go beyond the assumption of strong homophily. Theoretically, we show that replacing the compatibility matrix in our framework with the identity (which represents pure homophily) reduces to GCN. Our extensive experiments demonstrate the effectiveness of our approach in more realistic and challenging experimental settings with significantly less training data compared to previous works: CPGNN variants achieve state-of-the-art results in heterophily settings with or without contextual node features, while maintaining comparable performance in homophily settings.
Translational distance-based knowledge graph embedding has shown progressive improvements on the link prediction task, from TransE to the latest state-of-the-art RotatE. However, N-1, 1-N and N-N predictions still remain challenging. In this work, we propose a novel translational distance-based approach for knowledge graph link prediction. The proposed method includes two-folds, first we extend the RotatE from 2D complex domain to high dimension space with orthogonal transforms to model relations for better modeling capacity. Second, the graph context is explicitly modeled via two directed context representations. These context representations are used as part of the distance scoring function to measure the plausibility of the triples during training and inference. The proposed approach effectively improves prediction accuracy on the difficult N-1, 1-N and N-N cases for knowledge graph link prediction task. The experimental results show that it achieves better performance on two benchmark data sets compared to the baseline RotatE, especially on data set (FB15k-237) with many high in-degree connection nodes.
Incompleteness is a common problem for existing knowledge graphs (KGs), and the completion of KG which aims to predict links between entities is challenging. Most existing KG completion methods only consider the direct relation between nodes and ignore the relation paths which contain useful information for link prediction. Recently, a few methods take relation paths into consideration but pay less attention to the order of relations in paths which is important for reasoning. In addition, these path-based models always ignore nonlinear contributions of path features for link prediction. To solve these problems, we propose a novel KG completion method named OPTransE. Instead of embedding both entities of a relation into the same latent space as in previous methods, we project the head entity and the tail entity of each relation into different spaces to guarantee the order of relations in the path. Meanwhile, we adopt a pooling strategy to extract nonlinear and complex features of different paths to further improve the performance of link prediction. Experimental results on two benchmark datasets show that the proposed model OPTransE performs better than state-of-the-art methods.
It is important to detect anomalous inputs when deploying machine learning systems. The use of larger and more complex inputs in deep learning magnifies the difficulty of distinguishing between anomalous and in-distribution examples. At the same time, diverse image and text data are available in enormous quantities. We propose leveraging these data to improve deep anomaly detection by training anomaly detectors against an auxiliary dataset of outliers, an approach we call Outlier Exposure (OE). This enables anomaly detectors to generalize and detect unseen anomalies. In extensive experiments on natural language processing and small- and large-scale vision tasks, we find that Outlier Exposure significantly improves detection performance. We also observe that cutting-edge generative models trained on CIFAR-10 may assign higher likelihoods to SVHN images than to CIFAR-10 images; we use OE to mitigate this issue. We also analyze the flexibility and robustness of Outlier Exposure, and identify characteristics of the auxiliary dataset that improve performance.
Deep neural networks (DNNs) have been found to be vulnerable to adversarial examples resulting from adding small-magnitude perturbations to inputs. Such adversarial examples can mislead DNNs to produce adversary-selected results. Different attack strategies have been proposed to generate adversarial examples, but how to produce them with high perceptual quality and more efficiently requires more research efforts. In this paper, we propose AdvGAN to generate adversarial examples with generative adversarial networks (GANs), which can learn and approximate the distribution of original instances. For AdvGAN, once the generator is trained, it can generate adversarial perturbations efficiently for any instance, so as to potentially accelerate adversarial training as defenses. We apply AdvGAN in both semi-whitebox and black-box attack settings. In semi-whitebox attacks, there is no need to access the original target model after the generator is trained, in contrast to traditional white-box attacks. In black-box attacks, we dynamically train a distilled model for the black-box model and optimize the generator accordingly. Adversarial examples generated by AdvGAN on different target models have high attack success rate under state-of-the-art defenses compared to other attacks. Our attack has placed the first with 92.76% accuracy on a public MNIST black-box attack challenge.
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