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Self-supervised learning has proved to be a powerful approach to learn image representations without the need of large labeled datasets. For underwater robotics, it is of great interest to design computer vision algorithms to improve perception capabilities such as sonar image classification. Due to the confidential nature of sonar imaging and the difficulty to interpret sonar images, it is challenging to create public large labeled sonar datasets to train supervised learning algorithms. In this work, we investigate the potential of three self-supervised learning methods (RotNet, Denoising Autoencoders, and Jigsaw) to learn high-quality sonar image representation without the need of human labels. We present pre-training and transfer learning results on real-life sonar image datasets. Our results indicate that self-supervised pre-training yields classification performance comparable to supervised pre-training in a few-shot transfer learning setup across all three methods. Code and self-supervised pre-trained models are be available at https://github.com/agrija9/ssl-sonar-images
We introduce canonical weight normalization for convolutional neural networks. Inspired by the canonical tensor decomposition, we express the weight tensors in so-called canonical networks as scaled sums of outer vector products. In particular, we train network weights in the decomposed form, where scale weights are optimized separately for each mode. Additionally, similarly to weight normalization, we include a global scaling parameter. We study the initialization of the canonical form by running the power method and by drawing randomly from Gaussian or uniform distributions. Our results indicate that we can replace the power method with cheaper initializations drawn from standard distributions. The canonical re-parametrization leads to competitive normalization performance on the MNIST, CIFAR10, and SVHN data sets. Moreover, the formulation simplifies network compression. Once training has converged, the canonical form allows convenient model-compression by truncating the parameter sums.
Vietnam requires a sustainable urbanization, for which city sensing is used in planning and de-cision-making. Large cities need portable, scalable, and inexpensive digital technology for this purpose. End-to-end air quality monitoring companies such as AirVisual and Plume Air have shown their reliability with portable devices outfitted with superior air sensors. They are pricey, yet homeowners use them to get local air data without evaluating the causal effect. Our air quality inspection system is scalable, reasonably priced, and flexible. Minicomputer of the sys-tem remotely monitors PMS7003 and BME280 sensor data through a microcontroller processor. The 5-megapixel camera module enables researchers to infer the causal relationship between traffic intensity and dust concentration. The design enables inexpensive, commercial-grade hardware, with Azure Blob storing air pollution data and surrounding-area imagery and pre-venting the system from physically expanding. In addition, by including an air channel that re-plenishes and distributes temperature, the design improves ventilation and safeguards electrical components. The gadget allows for the analysis of the correlation between traffic and air quali-ty data, which might aid in the establishment of sustainable urban development plans and poli-cies.
Comparative study of 3D object detection frameworks based on LiDAR data and sensor fusion techniques
(2022)
Estimating and understanding the surroundings of the vehicle precisely forms the basic and crucial step for the autonomous vehicle. The perception system plays a significant role in providing an accurate interpretation of a vehicle's environment in real-time. Generally, the perception system involves various subsystems such as localization, obstacle (static and dynamic) detection, and avoidance, mapping systems, and others. For perceiving the environment, these vehicles will be equipped with various exteroceptive (both passive and active) sensors in particular cameras, Radars, LiDARs, and others. These systems are equipped with deep learning techniques that transform the huge amount of data from the sensors into semantic information on which the object detection and localization tasks are performed. For numerous driving tasks, to provide accurate results, the location and depth information of a particular object is necessary. 3D object detection methods, by utilizing the additional pose data from the sensors such as LiDARs, stereo cameras, provides information on the size and location of the object. Based on recent research, 3D object detection frameworks performing object detection and localization on LiDAR data and sensor fusion techniques show significant improvement in their performance. In this work, a comparative study of the effect of using LiDAR data for object detection frameworks and the performance improvement seen by using sensor fusion techniques are performed. Along with discussing various state-of-the-art methods in both the cases, performing experimental analysis, and providing future research directions.
Recent advances in Natural Language Processing have substantially improved contextualized representations of language. However, the inclusion of factual knowledge, particularly in the biomedical domain, remains challenging. Hence, many Language Models (LMs) are extended by Knowledge Graphs (KGs), but most approaches require entity linking (i.e., explicit alignment between text and KG entities). Inspired by single-stream multimodal Transformers operating on text, image and video data, this thesis proposes the Sophisticated Transformer trained on biomedical text and Knowledge Graphs (STonKGs). STonKGs incorporates a novel multimodal architecture based on a cross encoder that uses the attention mechanism on a concatenation of input sequences derived from text and KG triples, respectively. Over 13 million so-called text-triple pairs, coming from PubMed and assembled using the Integrated Network and Dynamical Reasoning Assembler (INDRA), were used in an unsupervised pre-training procedure to learn representations of biomedical knowledge in STonKGs. By comparing STonKGs to an NLP- and a KG-baseline (operating on either text or KG data) on a benchmark consisting of eight fine-tuning tasks, the proposed knowledge integration method applied in STonKGs was empirically validated. Specifically, on tasks with a comparatively small dataset size and a larger number of classes, STonKGs resulted in considerable performance gains, beating the F1-score of the best baseline by up to 0.083. Both the source code as well as the code used to implement STonKGs are made publicly available so that the proposed method of this thesis can be extended to many other biomedical applications.
Contextual information is widely considered for NLP and knowledge discovery in life sciences since it highly influences the exact meaning of natural language. The scientific challenge is not only to extract such context data, but also to store this data for further query and discovery approaches. Classical approaches use RDF triple stores, which have serious limitations. Here, we propose a multiple step knowledge graph approach using labeled property graphs based on polyglot persistence systems to utilize context data for context mining, graph queries, knowledge discovery and extraction. We introduce the graph-theoretic foundation for a general context concept within semantic networks and show a proof of concept based on biomedical literature and text mining. Our test system contains a knowledge graph derived from the entirety of PubMed and SCAIView data and is enriched with text mining data and domain-specific language data using Biological Expression Language. Here, context is a more general concept than annotations. This dense graph has more than 71M nodes and 850M relationships. We discuss the impact of this novel approach with 27 real-world use cases represented by graph queries. Storing and querying a giant knowledge graph as a labeled property graph is still a technological challenge. Here, we demonstrate how our data model is able to support the understanding and interpretation of biomedical data. We present several real-world use cases that utilize our massive, generated knowledge graph derived from PubMed data and enriched with additional contextual data. Finally, we show a working example in context of biologically relevant information using SCAIView.
State-of-the-art object detectors are treated as black boxes due to their highly non-linear internal computations. Even with unprecedented advancements in detector performance, the inability to explain how their outputs are generated limits their use in safety-critical applications. Previous work fails to produce explanations for both bounding box and classification decisions, and generally make individual explanations for various detectors. In this paper, we propose an open-source Detector Explanation Toolkit (DExT) which implements the proposed approach to generate a holistic explanation for all detector decisions using certain gradient-based explanation methods. We suggests various multi-object visualization methods to merge the explanations of multiple objects detected in an image as well as the corresponding detections in a single image. The quantitative evaluation show that the Single Shot MultiBox Detector (SSD) is more faithfully explained compared to other detectors regardless of the explanation methods. Both quantitative and human-centric evaluations identify that SmoothGrad with Guided Backpropagation (GBP) provides more trustworthy explanations among selected methods across all detectors. We expect that DExT will motivate practitioners to evaluate object detectors from the interpretability perspective by explaining both bounding box and classification decisions.
21 pages, with supplementary
ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs
(2022)
While most approaches individually exploit unstructured data from the biomedical literature or structured data from biomedical knowledge graphs, their union can better exploit the advantages of such approaches, ultimately improving representations of biology. Using multimodal transformers for such purposes can improve performance on context dependent classication tasks, as demonstrated by our previous model, the Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs (STonKGs). In this work, we introduce ProtSTonKGs, a transformer aimed at learning all-encompassing representations of protein-protein interactions. ProtSTonKGs presents an extension to our previous work by adding textual protein descriptions and amino acid sequences (i.e., structural information) to the text- and knowledge graph-based input sequence used in STonKGs. We benchmark ProtSTonKGs against STonKGs, resulting in improved F1 scores by up to 0.066 (i.e., from 0.204 to 0.270) in several tasks such as predicting protein interactions in several contexts. Our work demonstrates how multimodal transformers can be used to integrate heterogeneous sources of information, paving the foundation for future approaches that use multiple modalities for biomedical applications.
Effective Neighborhood Feature Exploitation in Graph CNNs for Point Cloud Object-Part Segmentation
(2022)
Part segmentation is the task of semantic segmentation applied on objects and carries a wide range of applications from robotic manipulation to medical imaging. This work deals with the problem of part segmentation on raw, unordered point clouds of 3D objects. While pioneering works on deep learning for point clouds typically ignore taking advantage of local geometric structure around individual points, the subsequent methods proposed to extract features by exploiting local geometry have not yielded significant improvements either. In order to investigate further, a graph convolutional network (GCN) is used in this work in an attempt to increase the effectiveness of such neighborhood feature exploitation approaches. Most of the previous works also focus only on segmenting complete point cloud data. Considering the impracticality of such approaches, taking into consideration the real world scenarios where complete point clouds are scarcely available, this work proposes approaches to deal with partial point cloud segmentation.
In the attempt to better capture neighborhood features, this work proposes a novel method to learn regional part descriptors which guide and refine the segmentation predictions. The proposed approach helps the network achieve state-of-the-art performance of 86.4% mIoU on the ShapeNetPart dataset for methods which do not use any preprocessing techniques or voting strategies. In order to better deal with partial point clouds, this work also proposes new strategies to train and test on partial data. While achieving significant improvements compared to the baseline performance, the problem of partial point cloud segmentation is also viewed through an alternate lens of semantic shape completion.
Semantic shape completion networks not only help deal with partial point cloud segmentation but also enrich the information captured by the system by predicting complete point clouds with corresponding semantic labels for each point. To this end, a new network architecture for semantic shape completion is also proposed based on point completion network (PCN) which takes advantage of a graph convolution based hierarchical decoder for completion as well as segmentation. In addition to predicting complete point clouds, results indicate that the network is capable of reaching within a margin of 5% to the mIoU performance of dedicated segmentation networks for partial point cloud segmentation.
As cameras are ubiquitous in autonomous systems, object detection is a crucial task. Object detectors are widely used in applications such as autonomous driving, healthcare, and robotics. Given an image, an object detector outputs both the bounding box coordinates as well as classification probabilities for each object detected. The state-of-the-art detectors are treated as black boxes due to their highly non-linear internal computations. Even with unprecedented advancements in detector performance, the inability to explain how their outputs are generated limits their use in safety-critical applications in particular. It is therefore crucial to explain the reason behind each detector decision in order to gain user trust, enhance detector performance, and analyze their failure.
Previous work fails to explain as well as evaluate both bounding box and classification decisions individually for various detectors. Moreover, no tools explain each detector decision, evaluate the explanations, and also identify the reasons for detector failures. This restricts the flexibility to analyze detectors. The main contribution presented here is an open-source Detector Explanation Toolkit (DExT). It is used to explain the detector decisions, evaluate the explanations, and analyze detector errors. The detector decisions are explained visually by highlighting the image pixels that most influence a particular decision. The toolkit implements the proposed approach to generate a holistic explanation for all detector decisions using certain gradient-based explanation methods. To the author’s knowledge, this is the first work to conduct extensive qualitative and novel quantitative evaluations of different explanation methods across various detectors. The qualitative evaluation incorporates a visual analysis of the explanations carried out by the author as well as a human-centric evaluation. The human-centric evaluation includes a user study to understand user trust in the explanations generated across various explanation methods for different detectors. Four multi-object visualization methods are provided to merge the explanations of multiple objects detected in an image as well as the corresponding detector outputs in a single image. Finally, DExT implements the procedure to analyze detector failures using the formulated approach.
The visual analysis illustrates that the ability to explain a model is more dependent on the model itself than the actual ability of the explanation method. In addition, the explanations are affected by the object explained, the decision explained, detector architecture, training data labels, and model parameters. The results of the quantitative evaluation show that the Single Shot MultiBox Detector (SSD) is more faithfully explained compared to other detectors regardless of the explanation methods. In addition, a single explanation method cannot generate more faithful explanations than other methods for both the bounding box and the classification decision across different detectors. Both the quantitative and human-centric evaluations identify that SmoothGrad with Guided Backpropagation (GBP) provides more trustworthy explanations among selected methods across all detectors. Finally, a convex polygon-based multi-object visualization method provides more human-understandable visualization than other methods.
The author expects that DExT will motivate practitioners to evaluate object detectors from the interpretability perspective by explaining both bounding box and classification decisions.
We describe a systematic approach for rendering time-varying simulation data produced by exa-scale simulations, using GPU workstations. The data sets we focus on use adaptive mesh refinement (AMR) to overcome memory bandwidth limitations by representing interesting regions in space with high detail. Particularly, our focus is on data sets where the AMR hierarchy is fixed and does not change over time. Our study is motivated by the NASA Exajet, a large computational fluid dynamics simulation of a civilian cargo aircraft that consists of 423 simulation time steps, each storing 2.5 GB of data per scalar field, amounting to a total of 4 TB. We present strategies for rendering this time series data set with smooth animation and at interactive rates using current generation GPUs. We start with an unoptimized baseline and step by step extend that to support fast streaming updates. Our approach demonstrates how to push current visualization workstations and modern visualization APIs to their limits to achieve interactive visualization of exa-scale time series data sets.
Trojanized software packages used in software supply chain attacks constitute an emerging threat. Unfortunately, there is still a lack of scalable approaches that allow automated and timely detection of malicious software packages and thus most detections are based on manual labor and expertise. However, it has been observed that most attack campaigns comprise multiple packages that share the same or similar malicious code. We leverage that fact to automatically reproduce manually identified clusters of known malicious packages that have been used in real world attacks, thus, reducing the need for expert knowledge and manual inspection. Our approach, AST Clustering using MCL to mimic Expertise (ACME), yields promising results with a 𝐹1 score of 0.99. Signatures are automatically generated based on characteristic code fragments from clusters and are subsequently used to scan the whole npm registry for unreported malicious packages. We are able to identify and report six malicious packages that have been removed from npm consequentially. Therefore, our approach can support the detection by reducing manual labor and hence may be employed by maintainers of package repositories to detect possible software supply chain attacks through trojanized software packages.
Graph databases employ graph structures such as nodes, attributes and edges to model and store relationships among data. To access this data, graph query languages (GQL) such as Cypher are typically used, which might be difficult to master for end-users. In the context of relational databases, sequence to SQL models, which translate natural language questions to SQL queries, have been proposed. While these Neural Machine Translation (NMT) models increase the accessibility of relational databases, NMT models for graph databases are not yet available mainly due to the lack of suitable parallel training data. In this short paper we sketch an architecture which enables the generation of synthetic training data for the graph query language Cypher.
MOTIVATION
The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models (KGEMs). However, representations based on a single modality are inherently limited.
RESULTS
To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs (KGs). This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations in a shared embedding space. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA) consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against three baseline models trained on either one of the modalities (i.e., text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.084 (i.e., from 0.881 to 0.965). Finally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications.
AVAILABILITY
We make the source code and the Python package of STonKGs available at GitHub (https://github.com/stonkgs/stonkgs) and PyPI (https://pypi.org/project/stonkgs/). The pre-trained STonKGs models and the task-specific classification models are respectively available at https://huggingface.co/stonkgs/stonkgs-150k and https://zenodo.org/communities/stonkgs.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
BACKGROUND: Humans demonstrate many physiological changes in microgravity for which long-duration head down bed rest (HDBR) is a reliable analog. However, information on how HDBR affects sensory processing is lacking.
OBJECTIVE: We previously showed [25] that microgravity alters the weighting applied to visual cues in determining the perceptual upright (PU), an effect that lasts long after return. Does long-duration HDBR have comparable effects?
METHODS: We assessed static spatial orientation using the luminous line test (subjective visual vertical, SVV) and the oriented character recognition test (PU) before, during and after 21 days of 6° HDBR in 10 participants. Methods were essentially identical as previously used in orbit [25].
RESULTS: Overall, HDBR had no effect on the reliance on visual relative to body cues in determining the PU. However, when considering the three critical time points (pre-bed rest, end of bed rest, and 14 days post-bed rest) there was a significant decrease in reliance on visual relative to body cues, as found in microgravity. The ratio had an average time constant of 7.28 days and returned to pre-bed-rest levels within 14 days. The SVV was unaffected.
CONCLUSIONS: We conclude that bed rest can be a useful analog for the study of the perception of static self-orientation during long-term exposure to microgravity. More detailed work on the precise time course of our effects is needed in both bed rest and microgravity conditions.