CLCLSA: Cross-omics Linked embedding with Contrastive Learning and Self Attention for multi-omics integration with incomplete multi-omics data

Integration of heterogeneous and high-dimensional multi-omics data is becoming increasingly important in understanding genetic data. Each omics technique only provides a limited view of the underlying biological process and integrating heterogeneous omics layers simultaneously would lead to a more comprehensive and detailed understanding of diseases and phenotypes. However, one obstacle faced when performing multi-omics data integration is the existence of unpaired multi-omics data due to instrument sensitivity and cost. Studies may fail if certain aspects of the subjects are missing or incomplete. In this paper, we propose a deep learning method for multi-omics integration with incomplete data by Cross-omics Linked unified embedding with Contrastive Learning and Self Attention (CLCLSA). Utilizing complete multi-omics data as supervision, the model employs cross-omics autoencoders to learn the feature representation across different types of biological data. The multi-omics contrastive learning, which is used to maximize the mutual information between different types of omics, is employed before latent feature concatenation. In addition, the feature-level self-attention and omics-level self-attention are employed to dynamically identify the most informative features for multi-omics data integration. Extensive experiments were conducted on four public multi-omics datasets. The experimental results indicated that the proposed CLCLSA outperformed the state-of-the-art approaches for multi-omics data classification using incomplete multi-omics data.

P-MMF: Provider Max-min Fairness Re-ranking in Recommender System

In this paper, we address the issue of recommending fairly from the aspect of providers, which has become increasingly essential in multistakeholder recommender systems. Existing studies on provider fairness usually focused on designing proportion fairness (PF) metrics that first consider systematic fairness. However, sociological researches show that to make the market more stable, max-min fairness (MMF) is a better metric. The main reason is that MMF aims to improve the utility of the worst ones preferentially, guiding the system to support the providers in weak market positions. When applying MMF to recommender systems, how to balance user preferences and provider fairness in an online recommendation scenario is still a challenging problem. In this paper, we proposed an online re-ranking model named Provider Max-min Fairness Re-ranking (P-MMF) to tackle the problem. Specifically, P-MMF formulates provider fair recommendation as a resource allocation problem, where the exposure slots are considered the resources to be allocated to providers and the max-min fairness is used as the regularizer during the process. We show that the problem can be further represented as a regularized online optimizing problem and solved efficiently in its dual space. During the online re-ranking phase, a momentum gradient descent method is designed to conduct the dynamic re-ranking. Theoretical analysis showed that the regret of P-MMF can be bounded. Experimental results on four public recommender datasets demonstrated that P-MMF can outperformed the state-of-the-art baselines. Experimental results also show that P-MMF can retain small computationally costs on a corpus with the large number of items.

Bridging The Gap: Entailment Fused-T5 for Open-retrieval Conversational Machine Reading Comprehension

Open-retrieval conversational machine reading comprehension (OCMRC) simulates real-life conversational interaction scenes. Machines are required to make a decision of "Yes/No/Inquire" or generate a follow-up question when the decision is "Inquire" based on retrieved rule texts, user scenario, user question, and dialogue history. Recent studies explored the methods to reduce the information gap between decision-making and question generation and thus improve the performance of generation. However, the information gap still exists because these pipeline structures are still limited in decision-making, span extraction, and question rephrasing three stages. Decision-making and generation are reasoning separately, and the entailment reasoning utilized in decision-making is hard to share through all stages. To tackle the above problem, we proposed a novel one-stage end-to-end framework, called Entailment Fused-T5 (EFT), to bridge the information gap between decision-making and generation in a global understanding manner. The extensive experimental results demonstrate that our proposed framework achieves new state-of-the-art performance on the OR-ShARC benchmark.

PseudoAugment: Learning to Use Unlabeled Data for Data Augmentation in Point Clouds

Data augmentation is an important technique to improve data efficiency and save labeling cost for 3D detection in point clouds. Yet, existing augmentation policies have so far been designed to only utilize labeled data, which limits the data diversity. In this paper, we recognize that pseudo labeling and data augmentation are complementary, thus propose to leverage unlabeled data for data augmentation to enrich the training data. In particular, we design three novel pseudo-label based data augmentation policies (PseudoAugments) to fuse both labeled and pseudo-labeled scenes, including frames (PseudoFrame), objecta (PseudoBBox), and background (PseudoBackground). PseudoAugments outperforms pseudo labeling by mitigating pseudo labeling errors and generating diverse fused training scenes. We demonstrate PseudoAugments generalize across point-based and voxel-based architectures, different model capacity and both KITTI and Waymo Open Dataset. To alleviate the cost of hyperparameter tuning and iterative pseudo labeling, we develop a population-based data augmentation framework for 3D detection, named AutoPseudoAugment. Unlike previous works that perform pseudo-labeling offline, our framework performs PseudoAugments and hyperparameter tuning in one shot to reduce computational cost. Experimental results on the large-scale Waymo Open Dataset show our method outperforms state-of-the-art auto data augmentation method (PPBA) and self-training method (pseudo labeling). In particular, AutoPseudoAugment is about 3X and 2X data efficient on vehicle and pedestrian tasks compared to prior arts. Notably, AutoPseudoAugment nearly matches the full dataset training results, with just 10% of the labeled run segments on the vehicle detection task.

Partial Information as Full: Reward Imputation with Sketching in Bandits

We focus on the setting of contextual batched bandit (CBB), where a batch of rewards is observed from the environment in each episode. But the rewards of the non-executed actions are unobserved (i.e., partial-information feedbacks). Existing approaches for CBB usually ignore the rewards of the non-executed actions, resulting in feedback information being underutilized. In this paper, we propose an efficient reward imputation approach using sketching for CBB, which completes the unobserved rewards with the imputed rewards approximating the full-information feedbacks. Specifically, we formulate the reward imputation as a problem of imputation regularized ridge regression, which captures the feedback mechanisms of both the non-executed and executed actions. To reduce the time complexity of reward imputation, we solve the regression problem using randomized sketching. We prove that our reward imputation approach obtains a relative-error bound for sketching approximation, achieves an instantaneous regret with a controllable bias and a smaller variance than that without reward imputation, and enjoys a sublinear regret bound against the optimal policy. Moreover, we present two extensions of our approach, including the rate-scheduled version and the version for nonlinear rewards, making our approach more feasible. Experimental results demonstrated that our approach can outperform the state-of-the-art baselines on synthetic and real-world datasets.

ET5: A Novel End-to-end Framework for Conversational Machine Reading Comprehension

Conversational machine reading comprehension (CMRC) aims to assist computers to understand an natural language text and thereafter engage in a multi-turn conversation to answer questions related to the text. Existing methods typically require three steps: (1) decision making based on entailment reasoning; (2) span extraction if required by the above decision; (3) question rephrasing based on the extracted span. However, for nearly all these methods, the span extraction and question rephrasing steps cannot fully exploit the fine-grained entailment reasoning information in decision making step because of their relative independence, which will further enlarge the information gap between decision making and question phrasing. Thus, to tackle this problem, we propose a novel end-to-end framework for conversational machine reading comprehension based on shared parameter mechanism, called entailment reasoning T5 (ET5). Despite the lightweight of our proposed framework, experimental results show that the proposed ET5 achieves new state-of-the-art results on the ShARC leaderboard with the BLEU-4 score of 55.2. Our model and code are publicly available at https://github.com/Yottaxx/ET5.

MICO: Selective Search with Mutual Information Co-training

In contrast to traditional exhaustive search, selective search first clusters documents into several groups before all the documents are searched exhaustively by a query, to limit the search executed within one group or only a few groups. Selective search is designed to reduce the latency and computation in modern large-scale search systems. In this study, we propose MICO, a Mutual Information CO-training framework for selective search with minimal supervision using the search logs. After training, MICO does not only cluster the documents, but also routes unseen queries to the relevant clusters for efficient retrieval. In our empirical experiments, MICO significantly improves the performance on multiple metrics of selective search and outperforms a number of existing competitive baselines.

Adversarial Attacks on ASR Systems: An Overview

With the development of hardware and algorithms, ASR(Automatic Speech Recognition) systems evolve a lot. As The models get simpler, the difficulty of development and deployment become easier, ASR systems are getting closer to our life. On the one hand, we often use APPs or APIs of ASR to generate subtitles and record meetings. On the other hand, smart speaker and self-driving car rely on ASR systems to control AIoT devices. In past few years, there are a lot of works on adversarial examples attacks against ASR systems. By adding a small perturbation to the waveforms, the recognition results make a big difference. In this paper, we describe the development of ASR system, different assumptions of attacks, and how to evaluate these attacks. Next, we introduce the current works on adversarial examples attacks from two attack assumptions: white-box attack and black-box attack. Different from other surveys, we pay more attention to which layer they perturb waveforms in ASR system, the relationship between these attacks, and their implementation methods. We focus on the effect of their works.

Handling Data Heterogeneity in Federated Learning via Knowledge Fusion

Federated learning (FL) supports distributed training of a global machine learning model across multiple clients with the help from a central server. The local dataset held by each client is never exchanged in FL, so the local dataset privacy is protected. Although FL is increasingly popular, data heterogeneity across different clients leads to the client model drift issue and results in model performance degradation and poor model fairness. To address the issue, we design Federated learning with global-local Knowledge Fusion (FedKF) scheme in this paper. The key idea in FedKF is to let the server return the global knowledge to be fused with the local knowledge in each training round so that the local model can be regularized towards the global optima. Thus, the client model drift issue can be mitigated. In FedKF, we first propose the active-inactive model aggregation technique that supports a precise global knowledge representation. Then, we propose a data-free knowledge distillation (KD) approach to facilitate the KD from the global model to the local model while the local model can still learn the local knowledge (embedded in the local dataset) simultaneously, thereby realizing the global-local knowledge fusion process. The theoretical analysis and intensive experiments demonstrate that FedKF achieves high model performance, high fairness, and privacy-preserving simultaneously. The project source codes will be released on GitHub after the paper review.

Training Large-Vocabulary Neural Language Models by Private Federated Learning for Resource-Constrained Devices

Federated Learning (FL) is a technique to train models using data distributed across devices. Differential Privacy (DP) provides a formal privacy guarantee for sensitive data. Our goal is to train a large neural network language model (NNLM) on compute-constrained devices while preserving privacy using FL and DP. However, the DP-noise introduced to the model increases as the model size grows, which often prevents convergence. We propose Partial Embedding Updates (PEU), a novel technique to decrease noise by decreasing payload size. Furthermore, we adopt Low Rank Adaptation (LoRA) and Noise Contrastive Estimation (NCE) to reduce the memory demands of large models on compute-constrained devices. This combination of techniques makes it possible to train large-vocabulary language models while preserving accuracy and privacy.