OpenRaiser/Intern-Atlas huggingface dataset:
Artificial Intelligence in Drug Discovery: Applications and Techniques
Venue: arXiv cs.LG 2021
Year: 2021

Artificial intelligence (AI) has been transforming the practice of drug discovery in the past decade. Various AI techniques have been used in a wide range of applications, such as virtual screening and drug design. In this survey, we first give an overview on drug discovery and discuss related applications, which can be reduced to two major tasks, i.e., molecular property prediction and molecule generation. We then discuss common data resources, molecule representations and benchmark platforms. Furthermore, to summarize the progress of AI in drug discovery, we present the relevant AI techniques including model architectures and learning paradigms in the papers surveyed. We expect that this survey will serve as a guide for researchers who are interested in working at the interface of artificial intelligence and drug discovery. We also provide a GitHub repository (https://github.com/dengjianyuan/Survey_AI_Drug_Discovery) with the collection of papers and codes, if applicable, as a learning resource, which is regularly updated.
Deep Direct Volume Rendering: Learning Visual Feature Mappings From Exemplary Images
Venue: arXiv cs.GR 2021
Year: 2021

Volume Rendering is an important technique for visualizing three-dimensional scalar data grids and is commonly employed for scientific and medical image data. Direct Volume Rendering (DVR) is a well established and efficient rendering algorithm for volumetric data. Neural rendering uses deep neural networks to solve inverse rendering tasks and applies techniques similar to DVR. However, it has not been demonstrated successfully for the rendering of scientific volume data. In this work, we introduce Deep Direct Volume Rendering (DeepDVR), a generalization of DVR that allows for the integration of deep neural networks into the DVR algorithm. We conceptualize the rendering in a latent color space, thus enabling the use of deep architectures to learn implicit mappings for feature extraction and classification, replacing explicit feature design and hand-crafted transfer functions. Our generalization serves to derive novel volume rendering architectures that can be trained end-to-end directly from examples in image space, obviating the need to manually define and fine-tune multidimensional transfer functions while providing superior classification strength. We further introduce a novel stepsize annealing scheme to accelerate the training of DeepDVR models and validate its effectiveness in a set of experiments. We validate our architectures on two example use cases: (1) learning an optimized rendering from manually adjusted reference images for a single volume and (2) learning advanced visualization concepts like shading and semantic colorization that generalize to unseen volume data. We find that deep volume rendering architectures with explicit modeling of the DVR pipeline effectively enable end-to-end learning of scientific volume rendering tasks from target images.
Data augmentation to improve robustness of image captioning solutions
Venue: arXiv cs.CL 2021
Year: 2021

In this paper, we study the impact of motion blur, a common quality flaw in real world images, on a state-of-the-art two-stage image captioning solution, and notice a degradation in solution performance as blur intensity increases. We investigate techniques to improve the robustness of the solution to motion blur using training data augmentation at each or both stages of the solution, i.e., object detection and captioning, and observe improved results. In particular, augmenting both the stages reduces the CIDEr-D degradation for high motion blur intensity from 68.7 to 11.7 on MS COCO dataset, and from 22.4 to 6.8 on Vizwiz dataset.
Unsupervised Video Person Re-identification via Noise and Hard frame Aware Clustering
Venue: arXiv cs.CV 2021
Year: 2021

Unsupervised video-based person re-identification (re-ID) methods extract richer features from video tracklets than image-based ones. The state-of-the-art methods utilize clustering to obtain pseudo-labels and train the models iteratively. However, they underestimate the influence of two kinds of frames in the tracklet: 1) noise frames caused by detection errors or heavy occlusions exist in the tracklet, which may be allocated with unreliable labels during clustering; 2) the tracklet also contains hard frames caused by pose changes or partial occlusions, which are difficult to distinguish but informative. This paper proposes a Noise and Hard frame Aware Clustering (NHAC) method. NHAC consists of a graph trimming module and a node re-sampling module. The graph trimming module obtains stable graphs by removing noise frame nodes to improve the clustering accuracy. The node re-sampling module enhances the training of hard frame nodes to learn rich tracklet information. Experiments conducted on two video-based datasets demonstrate the effectiveness of the proposed NHAC under the unsupervised re-ID setting.
Multi-VFL: A Vertical Federated Learning System for Multiple Data and Label Owners
Venue: arXiv cs.LG 2021
Year: 2021

Vertical Federated Learning (VFL) refers to the collaborative training of a model on a dataset where the features of the dataset are split among multiple data owners, while label information is owned by a single data owner. In this paper, we propose a novel method, Multi Vertical Federated Learning (Multi-VFL), to train VFL models when there are multiple data and label owners. Our approach is the first to consider the setting where $D$-data owners (across which features are distributed) and $K$-label owners (across which labels are distributed) exist. This proposed configuration allows different entities to train and learn optimal models without having to share their data. Our framework makes use of split learning and adaptive federated optimizers to solve this problem. For empirical evaluation, we run experiments on the MNIST and FashionMNIST datasets. Our results show that using adaptive optimizers for model aggregation fastens convergence and improves accuracy.
A Unified Framework for Task-Driven Data Quality Management
Venue: arXiv cs.LG 2021
Year: 2021

High-quality data is critical to train performant Machine Learning (ML) models, highlighting the importance of Data Quality Management (DQM). Existing DQM schemes often cannot satisfactorily improve ML performance because, by design, they are oblivious to downstream ML tasks. Besides, they cannot handle various data quality issues (especially those caused by adversarial attacks) and have limited applications to only certain types of ML models. Recently, data valuation approaches (e.g., based on the Shapley value) have been leveraged to perform DQM; yet, empirical studies have observed that their performance varies considerably based on the underlying data and training process. In this paper, we propose a task-driven, multi-purpose, model-agnostic DQM framework, DataSifter, which is optimized towards a given downstream ML task, capable of effectively removing data points with various defects, and applicable to diverse models. Specifically, we formulate DQM as an optimization problem and devise a scalable algorithm to solve it. Furthermore, we propose a theoretical framework for comparing the worst-case performance of different DQM strategies. Remarkably, our results show that the popular strategy based on the Shapley value may end up choosing the worst data subset in certain practical scenarios. Our evaluation shows that DataSifter achieves and most often significantly improves the state-of-the-art performance over a wide range of DQM tasks, including backdoor, poison, noisy/mislabel data detection, data summarization, and data debiasing.
DUET: Detection Utilizing Enhancement for Text in Scanned or Captured Documents
Venue: arXiv cs.CV 2021
Year: 2021

We present a novel deep neural model for text detection in document images. For robust text detection in noisy scanned documents, the advantages of multi-task learning are adopted by adding an auxiliary task of text enhancement. Namely, our proposed model is designed to perform noise reduction and text region enhancement as well as text detection. Moreover, we enrich the training data for the model with synthesized document images that are fully labeled for text detection and enhancement, thus overcome the insufficiency of labeled document image data. For the effective exploitation of the synthetic and real data, the training process is separated in two phases. The first phase is training only synthetic data in a fully-supervised manner. Then real data with only detection labels are added in the second phase. The enhancement task for the real data is weakly-supervised with information from their detection labels. Our methods are demonstrated in a real document dataset with performances exceeding those of other text detection methods. Moreover, ablations are conducted and the results confirm the effectiveness of the synthetic data, auxiliary task, and weak-supervision. Whereas the existing text detection studies mostly focus on the text in scenes, our proposed method is optimized to the applications for the text in scanned documents.
Validation of Simulation-Based Testing: Bypassing Domain Shift with Label-to-Image Synthesis
Venue: arXiv cs.CV 2021
Year: 2021

Many machine learning applications can benefit from simulated data for systematic validation - in particular if real-life data is difficult to obtain or annotate. However, since simulations are prone to domain shift w.r.t. real-life data, it is crucial to verify the transferability of the obtained results. We propose a novel framework consisting of a generative label-to-image synthesis model together with different transferability measures to inspect to what extent we can transfer testing results of semantic segmentation models from synthetic data to equivalent real-life data. With slight modifications, our approach is extendable to, e.g., general multi-class classification tasks. Grounded on the transferability analysis, our approach additionally allows for extensive testing by incorporating controlled simulations. We validate our approach empirically on a semantic segmentation task on driving scenes. Transferability is tested using correlation analysis of IoU and a learned discriminator. Although the latter can distinguish between real-life and synthetic tests, in the former we observe surprisingly strong correlations of 0.7 for both cars and pedestrians.
Studying the characteristics of scientific communities using individual-level bibliometrics: the case of Big Data research
Venue: arXiv cs.DL 2021
Year: 2021

Unlike most bibliometric studies focusing on publications, taking Big Data research as a case study, we introduce a novel bibliometric approach to unfold the status of a given scientific community from an individual level perspective. We study the academic age, production, and research focus of the community of authors active in Big Data research. Artificial Intelligence (AI) is selected as a reference area for comparative purposes. Results show that the academic realm of "Big Data" is a growing topic with an expanding community of authors, particularly of new authors every year. Compared to AI, Big Data attracts authors with a longer academic age, who can be regarded to have accumulated some publishing experience before entering the community. Despite the highly skewed distribution of productivity amongst researchers in both communities, Big Data authors have higher values of both research focus and production than those of AI. Considering the community size, overall academic age, and persistence of publishing on the topic, our results support the idea of Big Data as a research topic with attractiveness for researchers. We argue that the community-focused indicators proposed in this study could be generalized to investigate the development and dynamics of other research fields and topics.
Multi-Dataset Benchmarks for Masked Identification using Contrastive Representation Learning
Venue: arXiv cs.CV 2021
Year: 2021

The COVID-19 pandemic has drastically changed accepted norms globally. Within the past year, masks have been used as a public health response to limit the spread of the virus. This sudden change has rendered many face recognition based access control, authentication and surveillance systems ineffective. Official documents such as passports, driving license and national identity cards are enrolled with fully uncovered face images. However, in the current global situation, face matching systems should be able to match these reference images with masked face images. As an example, in an airport or security checkpoint it is safer to match the unmasked image of the identifying document to the masked person rather than asking them to remove the mask. We find that current facial recognition techniques are not robust to this form of occlusion. To address this unique requirement presented due to the current circumstance, we propose a set of re-purposed datasets and a benchmark for researchers to use. We also propose a contrastive visual representation learning based pre-training workflow which is specialized to masked vs unmasked face matching. We ensure that our method learns robust features to differentiate people across varying data collection scenarios. We achieve this by training over many different datasets and validating our result by testing on various holdout datasets. The specialized weights trained by our method outperform standard face recognition features for masked to unmasked face matching. We believe the provided synthetic mask generating code, our novel training approach and the trained weights from the masked face models will help in adopting existing face recognition systems to operate in the current global environment. We open-source all contributions for broader use by the research community.
Context-Free TextSpotter for Real-Time and Mobile End-to-End Text Detection and Recognition
Venue: arXiv cs.CV 2021
Year: 2021

In the deployment of scene-text spotting systems on mobile platforms, lightweight models with low computation are preferable. In concept, end-to-end (E2E) text spotting is suitable for such purposes because it performs text detection and recognition in a single model. However, current state-of-the-art E2E methods rely on heavy feature extractors, recurrent sequence modellings, and complex shape aligners to pursue accuracy, which means their computations are still heavy. We explore the opposite direction: How far can we go without bells and whistles in E2E text spotting? To this end, we propose a text-spotting method that consists of simple convolutions and a few post-processes, named Context-Free TextSpotter. Experiments using standard benchmarks show that Context-Free TextSpotter achieves real-time text spotting on a GPU with only three million parameters, which is the smallest and fastest among existing deep text spotters, with an acceptable transcription quality degradation compared to heavier ones. Further, we demonstrate that our text spotter can run on a smartphone with affordable latency, which is valuable for building stand-alone OCR applications.
Date Estimation in the Wild of Scanned Historical Photos: An Image Retrieval Approach
Venue: arXiv cs.CV 2021
Year: 2021

This paper presents a novel method for date estimation of historical photographs from archival sources. The main contribution is to formulate the date estimation as a retrieval task, where given a query, the retrieved images are ranked in terms of the estimated date similarity. The closer are their embedded representations the closer are their dates. Contrary to the traditional models that design a neural network that learns a classifier or a regressor, we propose a learning objective based on the nDCG ranking metric. We have experimentally evaluated the performance of the method in two different tasks: date estimation and date-sensitive image retrieval, using the DEW public database, overcoming the baseline methods.
A Comparison and Combination of Unsupervised Blind Source Separation Techniques
Venue: arXiv cs.SD 2021
Year: 2021

Unsupervised blind source separation methods do not require a training phase and thus cannot suffer from a train-test mismatch, which is a common concern in neural network based source separation. The unsupervised techniques can be categorized in two classes, those building upon the sparsity of speech in the Short-Time Fourier transform domain and those exploiting non-Gaussianity or non-stationarity of the source signals. In this contribution, spatial mixture models which fall in the first category and independent vector analysis (IVA) as a representative of the second category are compared w.r.t. their separation performance and the performance of a downstream speech recognizer on a reverberant dataset of reasonable size. Furthermore, we introduce a serial concatenation of the two, where the result of the mixture model serves as initialization of IVA, which achieves significantly better WER performance than each algorithm individually and even approaches the performance of a much more complex neural network based technique.
Blockchain and 6G: The Future of Secure and Ubiquitous Communication
Venue: arXiv cs.CR 2021
Year: 2021

The future communication will be characterized by ubiquitous connectivity and security. These features will be essential requirements for the efficient functioning of the futuristic applications. In this paper, in order to highlight the impact of blockchain and 6G on the future communication systems, we categorize these application requirements into two broad groups. In the first category, called Requirement Group I \mbox{(RG-I)}, we include the performance-related needs on data rates, latency, reliability and massive connectivity, while in the second category, called Requirement Group II \mbox{(RG-II)}, we include the security-related needs on data integrity, non-repudiability, and auditability. With blockchain and 6G, the network decentralization and resource sharing would minimize resource under-utilization thereby facilitating RG-I targets. Furthermore, through appropriate selection of blockchain type and consensus algorithms, RG-II needs of 6G applications can also be readily addressed. Through this study, the combination of blockchain and 6G emerges as an elegant solution for secure and ubiquitous future communication.
Parallel Deep Learning-Driven Sarcasm Detection from Pop Culture Text and English Humor Literature
Venue: arXiv cs.CL 2021
Year: 2021

Sarcasm is a sophisticated way of wrapping any immanent truth, mes-sage, or even mockery within a hilarious manner. The advent of communications using social networks has mass-produced new avenues of socialization. It can be further said that humor, irony, sarcasm, and wit are the four chariots of being socially funny in the modern days. In this paper, we manually extract the sarcastic word distribution features of a benchmark pop culture sarcasm corpus, containing sarcastic dialogues and monologues. We generate input sequences formed of the weighted vectors from such words. We further propose an amalgamation of four parallel deep long-short term networks (pLSTM), each with distinctive activation classifier. These modules are primarily aimed at successfully detecting sarcasm from the text corpus. Our proposed model for detecting sarcasm peaks a training accuracy of 98.95% when trained with the discussed dataset. Consecutively, it obtains the highest of 98.31% overall validation accuracy on two handpicked Project Gutenberg English humor literature among all the test cases. Our approach transcends previous state-of-the-art works on several sarcasm corpora and results in a new gold standard performance for sarcasm detection.
Linguistically Informed Masking for Representation Learning in the Patent Domain
Venue: arXiv cs.CL 2021
Year: 2021

Domain-specific contextualized language models have demonstrated substantial effectiveness gains for domain-specific downstream tasks, like similarity matching, entity recognition or information retrieval. However successfully applying such models in highly specific language domains requires domain adaptation of the pre-trained models. In this paper we propose the empirically motivated Linguistically Informed Masking (LIM) method to focus domain-adaptative pre-training on the linguistic patterns of patents, which use a highly technical sublanguage. We quantify the relevant differences between patent, scientific and general-purpose language and demonstrate for two different language models (BERT and SciBERT) that domain adaptation with LIM leads to systematically improved representations by evaluating the performance of the domain-adapted representations of patent language on two independent downstream tasks, the IPC classification and similarity matching. We demonstrate the impact of balancing the learning from different information sources during domain adaptation for the patent domain. We make the source code as well as the domain-adaptive pre-trained patent language models publicly available at https://github.com/sophiaalthammer/patent-lim.
On the overlooked issue of defining explanation objectives for local-surrogate explainers
Venue: arXiv cs.LG 2021
Year: 2021

Local surrogate approaches for explaining machine learning model predictions have appealing properties, such as being model-agnostic and flexible in their modelling. Several methods exist that fit this description and share this goal. However, despite their shared overall procedure, they set out different objectives, extract different information from the black-box, and consequently produce diverse explanations, that are -- in general -- incomparable. In this work we review the similarities and differences amongst multiple methods, with a particular focus on what information they extract from the model, as this has large impact on the output: the explanation. We discuss the implications of the lack of agreement, and clarity, amongst the methods' objectives on the research and practice of explainability.
Enforcing Morphological Information in Fully Convolutional Networks to Improve Cell Instance Segmentation in Fluorescence Microscopy Images
Venue: arXiv cs.CV 2021
Year: 2021

Cell instance segmentation in fluorescence microscopy images is becoming essential for cancer dynamics and prognosis. Data extracted from cancer dynamics allows to understand and accurately model different metabolic processes such as proliferation. This enables customized and more precise cancer treatments. However, accurate cell instance segmentation, necessary for further cell tracking and behavior analysis, is still challenging in scenarios with high cell concentration and overlapping edges. Within this framework, we propose a novel cell instance segmentation approach based on the well-known U-Net architecture. To enforce the learning of morphological information per pixel, a deep distance transformer (DDT) acts as a back-bone model. The DDT output is subsequently used to train a top-model. The following top-models are considered: a three-class (\emph{e.g.,} foreground, background and cell border) U-net, and a watershed transform. The obtained results suggest a performance boost over traditional U-Net architectures. This opens an interesting research line around the idea of injecting morphological information into a fully convolutional model.