Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has entered a new phase, and many methods are proposed based on the component of AlphaFold2. The importance of a unified research framework in protein folding contains implementations and benchmarks to consistently and fairly compare various approaches. To achieve this, we present Solvent, an protein folding framework that supports significant components of state-of-th-arts models in the manner of off-the-shelf interface Solvent contains different models implemented in a unified codebase and supports training and evaluation for defined models on the same dataset. We benchmark well-known algorithms and their components and provide experiments that give helpful insights into the protein structure modeling field. We hope that Solvent will increase the reliability and consistency of proposed models and gives efficiency in both speed and costs, resulting in acceleration on protein folding modeling research. The code is available at //github.com/kakaobrain/solvent, and the project will continue to be developed.
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With the rapid growth of information, recommender systems have become integral for providing personalized suggestions and overcoming information overload. However, their practical deployment often encounters "dirty" data, where noise or malicious information can lead to abnormal recommendations. Research on improving recommender systems' robustness against such dirty data has thus gained significant attention. This survey provides a comprehensive review of recent work on recommender systems' robustness. We first present a taxonomy to organize current techniques for withstanding malicious attacks and natural noise. We then explore state-of-the-art methods in each category, including fraudster detection, adversarial training, certifiable robust training against malicious attacks, and regularization, purification, self-supervised learning against natural noise. Additionally, we summarize evaluation metrics and common datasets used to assess robustness. We discuss robustness across varying recommendation scenarios and its interplay with other properties like accuracy, interpretability, privacy, and fairness. Finally, we delve into open issues and future research directions in this emerging field. Our goal is to equip readers with a holistic understanding of robust recommender systems and spotlight pathways for future research and development.
Gender inequalities in science have long been observed globally. Studies have demonstrated it through survey data or published literature, focusing on the interests of subjects or authors; few, however, examined the manifestation of gender inequalities on researchers' knowledge status. This study analyzes the relationship between regional and gender identities, topics, and knowledge status while revealing the female labor division in science and scientific research using online Q&A from researchers. We find that gender inequalities are merged with both regional-specific characteristics and global common patterns. Women's field and topic distribution within fields are influenced by regions, yet the prevalent topics are consistent in all regions. Women are more involved in specific topics, particularly topics about experiments with weaker levels of knowledge and they are of less assistance. To promote inequality in science, the scientific community should pay more attention to reducing the knowledge gap and encourage women to work on unexplored topics and areas.
Vision Transformers (ViTs) have emerged as the fundamental architecture for most computer vision fields, but the considerable memory and computation costs hinders their application on resource-limited devices. As one of the most powerful compression methods, binarization reduces the computation of the neural network by quantizing the weights and activation values as $\pm$1. Although existing binarization methods have demonstrated excellent performance on Convolutional Neural Networks (CNNs), the full binarization of ViTs is still under-studied and suffering a significant performance drop. In this paper, we first argue empirically that the severe performance degradation is mainly caused by the weight oscillation in the binarization training and the information distortion in the activation of ViTs. Based on these analyses, we propose $\textbf{BinaryViT}$, an accurate full binarization scheme for ViTs, which pushes the quantization of ViTs to the limit. Specifically, we propose a novel gradient regularization scheme (GRS) for driving a bimodal distribution of the weights to reduce oscillation in binarization training. Moreover, we design an activation shift module (ASM) to adaptively tune the activation distribution to reduce the information distortion caused by binarization. Extensive experiments on ImageNet dataset show that our BinaryViT consistently surpasses the strong baseline by 2.05% and improve the accuracy of fully binarized ViTs to a usable level. Furthermore, our method achieves impressive savings of 16.2$\times$ and 17.7$\times$ in model size and OPs compared to the full-precision DeiT-S.
Large language models such as GPT-3 & ChatGPT have transformed deep learning (DL), powering applications that have captured the public's imagination. These models are rapidly being adopted across domains for analytics on various modalities, often by finetuning pre-trained base models. Such models need multiple GPUs due to both their size and computational load, driving the development of a bevy of "model parallelism" techniques & tools. Navigating such parallelism choices, however, is a new burden for end users of DL such as data scientists, domain scientists, etc. who may lack the necessary systems knowhow. The need for model selection, which leads to many models to train due to hyper-parameter tuning or layer-wise finetuning, compounds the situation with two more burdens: resource apportioning and scheduling. In this work, we tackle these three burdens for DL users in a unified manner by formalizing them as a joint problem that we call SPASE: Select a Parallelism, Allocate resources, and SchedulE. We propose a new information system architecture to tackle the SPASE problem holistically, representing a key step toward enabling wider adoption of large DL models. We devise an extensible template for existing parallelism schemes and combine it with an automated empirical profiler for runtime estimation. We then formulate SPASE as an MILP. We find that direct use of an MILP-solver is significantly more effective than several baseline heuristics. We optimize the system runtime further with an introspective scheduling approach. We implement all these techniques into a new data system we call Saturn. Experiments with benchmark DL workloads show that Saturn achieves 39-49% lower model selection runtimes than typical current DL practice.
Nowadays, research into personalization has been focusing on explainability and fairness. Several approaches proposed in recent works are able to explain individual recommendations in a post-hoc manner or by explanation paths. However, explainability techniques applied to unfairness in recommendation have been limited to finding user/item features mostly related to biased recommendations. In this paper, we devised a novel algorithm that leverages counterfactuality methods to discover user unfairness explanations in the form of user-item interactions. In our counterfactual framework, interactions are represented as edges in a bipartite graph, with users and items as nodes. Our Bipartite Graph Explainer perturbs the topological structure to find an altered version (counterfactual explanation) that minimizes the disparity in utility between the protected and unprotected demographic groups. Experiments on four real-world graphs coming from various domains showed that our method can systematically explain user unfairness on three state-of-the-art GNN-based recommendation models. Moreover, an empirical evaluation of the perturbed network uncovered relevant patterns that justify the nature of the unfairness discovered by the generated explanations. The source code and the preprocessed data sets are available at //github.com/jackmedda/RS-BGExplainer.
Despite recent advances in the field of explainability, much remains unknown about the algorithms that neural networks learn to represent. Recent work has attempted to understand trained models by decomposing them into functional circuits (Csord\'as et al., 2020; Lepori et al., 2023). To advance this research, we developed NeuroSurgeon, a python library that can be used to discover and manipulate subnetworks within models in the Huggingface Transformers library (Wolf et al., 2019). NeuroSurgeon is freely available at //github.com/mlepori1/NeuroSurgeon.
Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful prediction of molecule property by GNNs is the scarcity of labeled data. Though graph contrastive learning (GCL) methods have achieved extraordinary performance with insufficient labeled data, most focused on designing data augmentation schemes for general graphs. However, the fundamental property of a molecule could be altered with the augmentation method (like random perturbation) on molecular graphs. Whereas, the critical geometric information of molecules remains rarely explored under the current GNN and GCL architectures. To this end, we propose a novel graph contrastive learning method utilizing the geometry of the molecule across 2D and 3D views, which is named GeomGCL. Specifically, we first devise a dual-view geometric message passing network (GeomMPNN) to adaptively leverage the rich information of both 2D and 3D graphs of a molecule. The incorporation of geometric properties at different levels can greatly facilitate the molecular representation learning. Then a novel geometric graph contrastive scheme is designed to make both geometric views collaboratively supervise each other to improve the generalization ability of GeomMPNN. We evaluate GeomGCL on various downstream property prediction tasks via a finetune process. Experimental results on seven real-life molecular datasets demonstrate the effectiveness of our proposed GeomGCL against state-of-the-art baselines.
With the capability of modeling bidirectional contexts, denoising autoencoding based pretraining like BERT achieves better performance than pretraining approaches based on autoregressive language modeling. However, relying on corrupting the input with masks, BERT neglects dependency between the masked positions and suffers from a pretrain-finetune discrepancy. In light of these pros and cons, we propose XLNet, a generalized autoregressive pretraining method that (1) enables learning bidirectional contexts by maximizing the expected likelihood over all permutations of the factorization order and (2) overcomes the limitations of BERT thanks to its autoregressive formulation. Furthermore, XLNet integrates ideas from Transformer-XL, the state-of-the-art autoregressive model, into pretraining. Empirically, XLNet outperforms BERT on 20 tasks, often by a large margin, and achieves state-of-the-art results on 18 tasks including question answering, natural language inference, sentiment analysis, and document ranking.
Graph convolutional networks (GCNs) have recently become one of the most powerful tools for graph analytics tasks in numerous applications, ranging from social networks and natural language processing to bioinformatics and chemoinformatics, thanks to their ability to capture the complex relationships between concepts. At present, the vast majority of GCNs use a neighborhood aggregation framework to learn a continuous and compact vector, then performing a pooling operation to generalize graph embedding for the classification task. These approaches have two disadvantages in the graph classification task: (1)when only the largest sub-graph structure ($k$-hop neighbor) is used for neighborhood aggregation, a large amount of early-stage information is lost during the graph convolution step; (2) simple average/sum pooling or max pooling utilized, which loses the characteristics of each node and the topology between nodes. In this paper, we propose a novel framework called, dual attention graph convolutional networks (DAGCN) to address these problems. DAGCN automatically learns the importance of neighbors at different hops using a novel attention graph convolution layer, and then employs a second attention component, a self-attention pooling layer, to generalize the graph representation from the various aspects of a matrix graph embedding. The dual attention network is trained in an end-to-end manner for the graph classification task. We compare our model with state-of-the-art graph kernels and other deep learning methods. The experimental results show that our framework not only outperforms other baselines but also achieves a better rate of convergence.
This paper surveys the machine learning literature and presents machine learning as optimization models. Such models can benefit from the advancement of numerical optimization techniques which have already played a distinctive role in several machine learning settings. Particularly, mathematical optimization models are presented for commonly used machine learning approaches for regression, classification, clustering, and deep neural networks as well new emerging applications in machine teaching and empirical model learning. The strengths and the shortcomings of these models are discussed and potential research directions are highlighted.
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