Deep learning is now widely used in drug discovery, providing significant acceleration and cost reduction. As the most fundamental building block, molecular representation is essential for predicting molecular properties to enable various downstream applications. Most existing methods attempt to incorporate more information to learn better representations. However, not all features are equally important for a specific task. Ignoring this would potentially compromise the training efficiency and predictive accuracy. To address this issue, we propose a novel approach, which treats language models as an agent and molecular pretraining models as a knowledge base. The agent accentuates task-relevant features in the molecular representation by understanding the natural language description of the task, just as a tailor customizes clothes for clients. Thus, we call this approach MolTailor. Evaluations demonstrate MolTailor's superior performance over baselines, validating the efficacy of enhancing relevance for molecular representation learning. This illustrates the potential of language model guided optimization to better exploit and unleash the capabilities of existing powerful molecular representation methods. Our codes and appendix are available at //github.com/SCIR-HI/MolTailor.
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The integration of learning and reasoning is high on the research agenda in AI. Nevertheless, there is only a little attention to use existing background knowledge for reasoning about partially observed scenes to answer questions about the scene. Yet, we as humans use such knowledge frequently to infer plausible answers to visual questions (by eliminating all inconsistent ones). Such knowledge often comes in the form of constraints about objects and it tends to be highly domain or environment-specific. We contribute a novel benchmark called CLEVR-POC for reasoning-intensive visual question answering (VQA) in partially observable environments under constraints. In CLEVR-POC, knowledge in the form of logical constraints needs to be leveraged to generate plausible answers to questions about a hidden object in a given partial scene. For instance, if one has the knowledge that all cups are colored either red, green or blue and that there is only one green cup, it becomes possible to deduce the color of an occluded cup as either red or blue, provided that all other cups, including the green one, are observed. Through experiments, we observe that the low performance of pre-trained vision language models like CLIP (~ 22%) and a large language model (LLM) like GPT-4 (~ 46%) on CLEVR-POC ascertains the necessity for frameworks that can handle reasoning-intensive tasks where environment-specific background knowledge is available and crucial. Furthermore, our demonstration illustrates that a neuro-symbolic model, which integrates an LLM like GPT-4 with a visual perception network and a formal logical reasoner, exhibits exceptional performance on CLEVR-POC.
In federated learning, the models can be trained synchronously or asynchronously. Many research works have focused on developing an aggregation method for the server to aggregate multiple local models into the global model with improved performance. They ignore the heterogeneity of the training workers, which causes the delay in the training of the local models, leading to the obsolete information issue. In this paper, we design and develop Asyn2F, an Asynchronous Federated learning Framework with bidirectional model aggregation. By bidirectional model aggregation, Asyn2F, on one hand, allows the server to asynchronously aggregate multiple local models and results in a new global model. On the other hand, it allows the training workers to aggregate the new version of the global model into the local model, which is being trained even in the middle of a training epoch. We develop Asyn2F considering the practical implementation requirements such as using cloud services for model storage and message queuing protocols for communications. Extensive experiments with different datasets show that the models trained by Asyn2F achieve higher performance compared to the state-of-the-art techniques. The experiments also demonstrate the effectiveness, practicality, and scalability of Asyn2F, making it ready for deployment in real scenarios.
Due to the advantages of fusing information from various modalities, multimodal learning is gaining increasing attention. Being a fundamental task of multimodal learning, Visual Grounding (VG), aims to locate objects in images through natural language expressions. Ensuring the quality of VG models presents significant challenges due to the complex nature of the task. In the black box scenario, existing adversarial testing techniques often fail to fully exploit the potential of both modalities of information. They typically apply perturbations based solely on either the image or text information, disregarding the crucial correlation between the two modalities, which would lead to failures in test oracles or an inability to effectively challenge VG models. To this end, we propose PEELING, a text perturbation approach via image-aware property reduction for adversarial testing of the VG model. The core idea is to reduce the property-related information in the original expression meanwhile ensuring the reduced expression can still uniquely describe the original object in the image. To achieve this, PEELING first conducts the object and properties extraction and recombination to generate candidate property reduction expressions. It then selects the satisfied expressions that accurately describe the original object while ensuring no other objects in the image fulfill the expression, through querying the image with a visual understanding technique. We evaluate PEELING on the state-of-the-art VG model, i.e. OFA-VG, involving three commonly used datasets. Results show that the adversarial tests generated by PEELING achieves 21.4% in MultiModal Impact score (MMI), and outperforms state-of-the-art baselines for images and texts by 8.2%--15.1%.
Machine learning holds tremendous promise for transforming the fundamental practice of scientific discovery by virtue of its data-driven nature. With the ever-increasing stream of research data collection, it would be appealing to autonomously explore patterns and insights from observational data for discovering novel classes of phenotypes and concepts. However, in the biomedical domain, there are several challenges inherently presented in the cumulated data which hamper the progress of novel class discovery. The non-i.i.d. data distribution accompanied by the severe imbalance among different groups of classes essentially leads to ambiguous and biased semantic representations. In this work, we present a geometry-constrained probabilistic modeling treatment to resolve the identified issues. First, we propose to parameterize the approximated posterior of instance embedding as a marginal von MisesFisher distribution to account for the interference of distributional latent bias. Then, we incorporate a suite of critical geometric properties to impose proper constraints on the layout of constructed embedding space, which in turn minimizes the uncontrollable risk for unknown class learning and structuring. Furthermore, a spectral graph-theoretic method is devised to estimate the number of potential novel classes. It inherits two intriguing merits compared to existent approaches, namely high computational efficiency and flexibility for taxonomy-adaptive estimation. Extensive experiments across various biomedical scenarios substantiate the effectiveness and general applicability of our method.
Labeled data are critical to modern machine learning applications, but obtaining labels can be expensive. To mitigate this cost, machine learning methods, such as transfer learning, semi-supervised learning and active learning, aim to be label-efficient: achieving high predictive performance from relatively few labeled examples. While obtaining the best label-efficiency in practice often requires combinations of these techniques, existing benchmark and evaluation frameworks do not capture a concerted combination of all such techniques. This paper addresses this deficiency by introducing LabelBench, a new computationally-efficient framework for joint evaluation of multiple label-efficient learning techniques. As an application of LabelBench, we introduce a novel benchmark of state-of-the-art active learning methods in combination with semi-supervised learning for fine-tuning pretrained vision transformers. Our benchmark demonstrates better label-efficiencies than previously reported in active learning. LabelBench's modular codebase is open-sourced for the broader community to contribute label-efficient learning methods and benchmarks. The repository can be found at: //github.com/EfficientTraining/LabelBench.
PRIME: Scaffolding Manipulation Tasks with Behavior Primitives for Data-Efficient Imitation Learning
Imitation learning has shown great potential for enabling robots to acquire complex manipulation behaviors. However, these algorithms suffer from high sample complexity in long-horizon tasks, where compounding errors accumulate over the task horizons. We present PRIME (PRimitive-based IMitation with data Efficiency), a behavior primitive-based framework designed for improving the data efficiency of imitation learning. PRIME scaffolds robot tasks by decomposing task demonstrations into primitive sequences, followed by learning a high-level control policy to sequence primitives through imitation learning. Our experiments demonstrate that PRIME achieves a significant performance improvement in multi-stage manipulation tasks, with 10-34% higher success rates in simulation over state-of-the-art baselines and 20-48% on physical hardware.
Deep learning has been the mainstream technique in natural language processing (NLP) area. However, the techniques require many labeled data and are less generalizable across domains. Meta-learning is an arising field in machine learning studying approaches to learn better learning algorithms. Approaches aim at improving algorithms in various aspects, including data efficiency and generalizability. Efficacy of approaches has been shown in many NLP tasks, but there is no systematic survey of these approaches in NLP, which hinders more researchers from joining the field. Our goal with this survey paper is to offer researchers pointers to relevant meta-learning works in NLP and attract more attention from the NLP community to drive future innovation. This paper first introduces the general concepts of meta-learning and the common approaches. Then we summarize task construction settings and application of meta-learning for various NLP problems and review the development of meta-learning in NLP community.
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.
Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show that our proposed SSL methods can achieve a substantial improvement of up to 17.3% over state-of-the-art supervised learning approaches with 400 unlabeled CT scans.
Convolutional Neural Networks (CNNs) have gained significant traction in the field of machine learning, particularly due to their high accuracy in visual recognition. Recent works have pushed the performance of GPU implementations of CNNs to significantly improve their classification and training times. With these improvements, many frameworks have become available for implementing CNNs on both CPUs and GPUs, with no support for FPGA implementations. In this work we present a modified version of the popular CNN framework Caffe, with FPGA support. This allows for classification using CNN models and specialized FPGA implementations with the flexibility of reprogramming the device when necessary, seamless memory transactions between host and device, simple-to-use test benches, and the ability to create pipelined layer implementations. To validate the framework, we use the Xilinx SDAccel environment to implement an FPGA-based Winograd convolution engine and show that the FPGA layer can be used alongside other layers running on a host processor to run several popular CNNs (AlexNet, GoogleNet, VGG A, Overfeat). The results show that our framework achieves 50 GFLOPS across 3x3 convolutions in the benchmarks. This is achieved within a practical framework, which will aid in future development of FPGA-based CNNs.
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