RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the structural information of the RNA. Historically, this problem has been tackled by machine learning models using expert-engineered features and trained on scarce labeled datasets. Here, we find that the knowledge learned by a protein-coevolution Transformer-based deep neural network can be transferred to the RNA contact prediction task. As protein datasets are orders of magnitude larger than those for RNA contact prediction, our findings and the subsequent framework greatly reduce the data scarcity bottleneck. Experiments confirm that RNA contact prediction through transfer learning using a publicly available protein model is greatly improved. Our findings indicate that the learned structural patterns of proteins can be transferred to RNAs, opening up potential new avenues for research.
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When deploying segmentation models in practice, it is critical to evaluate their behaviors in varied and complex scenes. Different from the previous evaluation paradigms only in consideration of global attribute variations (e.g. adverse weather), we investigate both local and global attribute variations for robustness evaluation. To achieve this, we construct a mask-preserved attribute editing pipeline to edit visual attributes of real images with precise control of structural information. Therefore, the original segmentation labels can be reused for the edited images. Using our pipeline, we construct a benchmark covering both object and image attributes (e.g. color, material, pattern, style). We evaluate a broad variety of semantic segmentation models, spanning from conventional close-set models to recent open-vocabulary large models on their robustness to different types of variations. We find that both local and global attribute variations affect segmentation performances, and the sensitivity of models diverges across different variation types. We argue that local attributes have the same importance as global attributes, and should be considered in the robustness evaluation of segmentation models. Code: //github.com/PRIS-CV/Pascal-EA.
Cybersecurity, which notoriously concerns both human and technological aspects, is becoming more and more regulated by a number of textual documents spanning several pages, such as the European GDPR Regulation and the NIS Directive. This paper introduces an approach that leverages techniques of semantic representation and reasoning, hence an ontological approach, towards the compliance check with the security measures that textual documents prescribe. We choose the ontology instrument to achieve two fundamental objectives: domain modelling and resource interrogation. The formalisation of entities and relations from the directive, and the consequent improved structuring with respect to sheer prose is dramatically helpful for any organisation through the hard task of compliance verification. The semantic approach is demonstrated with two articles of the new European NIS 2 directive.
In recent years, there has been a notable surge in research on machine learning techniques for combinatorial optimization. It has been shown that learning-based methods outperform traditional heuristics and mathematical solvers on the Traveling Salesman Problem (TSP) in terms of both performance and computational efficiency. However, most learning-based TSP solvers are primarily designed for fixed-scale TSP instances, and also require a large number of training samples to achieve optimal performance. To fill this gap, this work proposes a data-driven graph representation learning method for solving TSPs with various numbers of cities. Specifically, we formulate the TSP as a link prediction task and propose an edge-aware graph autoencoder (EdgeGAE) model that can solve TSPs by learning from various-scale samples with an imbalanced distribution. A residual gated encoder is trained to learn latent edge embeddings, followed by an edge-centered decoder to output link predictions in an end-to-end manner. Furthermore, we introduce an active sampling strategy into the training process to improve the model's generalization capability in large-scale scenarios. To investigate the model's practical applicability, we generate a scale-imbalanced dataset comprising 50,000 TSP instances ranging from 50 to 500 cities. The experimental results demonstrate that the proposed edge-aware graph autoencoder model achieves a highly competitive performance among state-of-the-art graph learning-based approaches in solving TSPs with various scales, implying its remarkable potential in dealing with practical optimization challenges.
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.
Microbial communities play a key role in biological wastewater treatment processes. Activated sludge settling characteristics, for example, are affected by microbial community composition, varying by changes in operating conditions and influent characteristics of wastewater treatment plants (WWTPs). Timely assessment and prediction of changes in microbial composition leading to settling problems, such as filamentous bulking (FB), can prevent operational challenges, reductions in treatment efficiency, and adverse environmental impacts. This study presents an innovative computer vision-based approach to assess activated sludge-settling characteristics based on the morphological properties of flocs and filaments in microscopy images. Implementing the transfer learning of deep convolutional neural network (CNN) models, this approach aims to overcome the limitations of existing quantitative image analysis techniques. The offline microscopy image dataset was collected over two years, with weekly sampling at a full-scale industrial WWTP in Belgium. Multiple data augmentation techniques were employed to enhance the generalizability of the CNN models. Various CNN architectures, including Inception v3, ResNet18, ResNet152, ConvNeXt-nano, and ConvNeXt-S, were tested to evaluate their performance in predicting sludge settling characteristics. The sludge volume index was used as the final prediction variable, but the method can easily be adjusted to predict any other settling metric of choice. The results showed that the suggested CNN-based approach provides less labour-intensive, objective, and consistent assessments, while transfer learning notably minimises the training phase, resulting in a generalizable system that can be employed in real-time applications.
Deep neural networks have been shown to provide accurate function approximations in high dimensions. However, fitting network parameters requires informative training data that are often challenging to collect in science and engineering applications. This work proposes Neural Galerkin schemes based on deep learning that generate training data with active learning for numerically solving high-dimensional partial differential equations. Neural Galerkin schemes build on the Dirac-Frenkel variational principle to train networks by minimizing the residual sequentially over time, which enables adaptively collecting new training data in a self-informed manner that is guided by the dynamics described by the partial differential equations. This is in contrast to other machine learning methods that aim to fit network parameters globally in time without taking into account training data acquisition. Our finding is that the active form of gathering training data of the proposed Neural Galerkin schemes is key for numerically realizing the expressive power of networks in high dimensions. Numerical experiments demonstrate that Neural Galerkin schemes have the potential to enable simulating phenomena and processes with many variables for which traditional and other deep-learning-based solvers fail, especially when features of the solutions evolve locally such as in high-dimensional wave propagation problems and interacting particle systems described by Fokker-Planck and kinetic equations.
Pixel-aligned implicit models, such as PIFu, PIFuHD, and ICON, are used for single-view clothed human reconstruction. These models need to be trained using a sampling training scheme. Existing sampling training schemes either fail to capture thin surfaces (e.g. ears, fingers) or cause noisy artefacts in reconstructed meshes. To address these problems, we introduce Fine Structured-Aware Sampling (FSS), a new sampling training scheme to train pixel-aligned implicit models for single-view human reconstruction. FSS resolves the aforementioned problems by proactively adapting to the thickness and complexity of surfaces. In addition, unlike existing sampling training schemes, FSS shows how normals of sample points can be capitalized in the training process to improve results. Lastly, to further improve the training process, FSS proposes a mesh thickness loss signal for pixel-aligned implicit models. It becomes computationally feasible to introduce this loss once a slight reworking of the pixel-aligned implicit function framework is carried out. Our results show that our methods significantly outperform SOTA methods qualitatively and quantitatively. Our code is publicly available at //github.com/kcyt/FSS.
Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.
Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.
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