OpenRaiser/Intern-Atlas huggingface dataset:
Discovering Dynamic Functional Brain Networks via Spatial and Channel-wise Attention
Venue: arXiv cs.CV 2022
Year: 2022

Using deep learning models to recognize functional brain networks (FBNs) in functional magnetic resonance imaging (fMRI) has been attracting increasing interest recently. However, most existing work focuses on detecting static FBNs from entire fMRI signals, such as correlation-based functional connectivity. Sliding-window is a widely used strategy to capture the dynamics of FBNs, but it is still limited in representing intrinsic functional interactive dynamics at each time step. And the number of FBNs usually need to be set manually. More over, due to the complexity of dynamic interactions in brain, traditional linear and shallow models are insufficient in identifying complex and spatially overlapped FBNs across each time step. In this paper, we propose a novel Spatial and Channel-wise Attention Autoencoder (SCAAE) for discovering FBNs dynamically. The core idea of SCAAE is to apply attention mechanism to FBNs construction. Specifically, we designed two attention modules: 1) spatial-wise attention (SA) module to discover FBNs in the spatial domain and 2) a channel-wise attention (CA) module to weigh the channels for selecting the FBNs automatically. We evaluated our approach on ADHD200 dataset and our results indicate that the proposed SCAAE method can effectively recover the dynamic changes of the FBNs at each fMRI time step, without using sliding windows. More importantly, our proposed hybrid attention modules (SA and CA) do not enforce assumptions of linearity and independence as previous methods, and thus provide a novel approach to better understanding dynamic functional brain networks.
TRT-ViT: TensorRT-oriented Vision Transformer
Venue: arXiv cs.CV 2022
Year: 2022

We revisit the existing excellent Transformers from the perspective of practical application. Most of them are not even as efficient as the basic ResNets series and deviate from the realistic deployment scenario. It may be due to the current criterion to measure computation efficiency, such as FLOPs or parameters is one-sided, sub-optimal, and hardware-insensitive. Thus, this paper directly treats the TensorRT latency on the specific hardware as an efficiency metric, which provides more comprehensive feedback involving computational capacity, memory cost, and bandwidth. Based on a series of controlled experiments, this work derives four practical guidelines for TensorRT-oriented and deployment-friendly network design, e.g., early CNN and late Transformer at stage-level, early Transformer and late CNN at block-level. Accordingly, a family of TensortRT-oriented Transformers is presented, abbreviated as TRT-ViT. Extensive experiments demonstrate that TRT-ViT significantly outperforms existing ConvNets and vision Transformers with respect to the latency/accuracy trade-off across diverse visual tasks, e.g., image classification, object detection and semantic segmentation. For example, at 82.7% ImageNet-1k top-1 accuracy, TRT-ViT is 2.7$\times$ faster than CSWin and 2.0$\times$ faster than Twins. On the MS-COCO object detection task, TRT-ViT achieves comparable performance with Twins, while the inference speed is increased by 2.8$\times$.
Evonne: Interactive Proof Visualization for Description Logics (System Description) -- Extended Version
Venue: arXiv cs.LO 2022
Year: 2022

Explanations for description logic (DL) entailments provide important support for the maintenance of large ontologies. The "justifications" usually employed for this purpose in ontology editors pinpoint the parts of the ontology responsible for a given entailment. Proofs for entailments make the intermediate reasoning steps explicit, and thus explain how a consequence can actually be derived. We present an interactive system for exploring description logic proofs, called Evonne, which visualizes proofs of consequences for ontologies written in expressive DLs. We describe the methods used for computing those proofs, together with a feature called signature-based proof condensation. Moreover, we evaluate the quality of generated proofs using real ontologies.
Breathing Life into Models: The Next Generation of Enterprise Modeling
Venue: arXiv cs.SE 2022
Year: 2022

Edsger W. Dijkstra has frequently suggested building a "firewall" between the technology- and application-side of computer science. His justification: The methods to attack the computer scientists' formal, mathematical "correctness problem" differ fundamentally from the methods to attack the applicants' informal "pleasantness problem". In this setting, a model is always confined to one side or the other of this wall. This keynote shows that a seamless transition between both sides can be achieved by a framework with architecture, statics, and dynamics as the three pillars of modeling computer-integrated systems. Selected examples justify this framework. It allows to "breath life" into (static) models, and it implies a new understanding of the "pleasantness" of computer-integrated systems, which is well-needed in the age of "digital first".
A Topological Approach for Semi-Supervised Learning
Venue: arXiv cs.CV 2022
Year: 2022

Nowadays, Machine Learning and Deep Learning methods have become the state-of-the-art approach to solve data classification tasks. In order to use those methods, it is necessary to acquire and label a considerable amount of data; however, this is not straightforward in some fields, since data annotation is time consuming and might require expert knowledge. This challenge can be tackled by means of semi-supervised learning methods that take advantage of both labelled and unlabelled data. In this work, we present new semi-supervised learning methods based on techniques from Topological Data Analysis (TDA), a field that is gaining importance for analysing large amounts of data with high variety and dimensionality. In particular, we have created two semi-supervised learning methods following two different topological approaches. In the former, we have used a homological approach that consists in studying the persistence diagrams associated with the data using the Bottleneck and Wasserstein distances. In the latter, we have taken into account the connectivity of the data. In addition, we have carried out a thorough analysis of the developed methods using 3 synthetic datasets, 5 structured datasets, and 2 datasets of images. The results show that the semi-supervised methods developed in this work outperform both the results obtained with models trained with only manually labelled data, and those obtained with classical semi-supervised learning methods, reaching improvements of up to a 16%.
Towards a Theory of Faithfulness: Faithful Explanations of Differentiable Classifiers over Continuous Data
Venue: arXiv cs.LG 2022
Year: 2022

There is broad agreement in the literature that explanation methods should be faithful to the model that they explain, but faithfulness remains a rather vague term. We revisit faithfulness in the context of continuous data and propose two formal definitions of faithfulness for feature attribution methods. Qualitative faithfulness demands that scores reflect the true qualitative effect (positive vs. negative) of the feature on the model and quanitative faithfulness that the magnitude of scores reflect the true quantitative effect. We discuss under which conditions these requirements can be satisfied to which extent (local vs global). As an application of the conceptual idea, we look at differentiable classifiers over continuous data and characterize Gradient-scores as follows: every qualitatively faithful feature attribution method is qualitatively equivalent to Gradient-scores. Furthermore, if an attribution method is quantitatively faithful in the sense that changes of the output of the classifier are proportional to the scores of features, then it is either equivalent to gradient-scoring or it is based on an inferior approximation of the classifier. To illustrate the practical relevance of the theory, we experimentally demonstrate that popular attribution methods can fail to give faithful explanations in the setting where the data is continuous and the classifier differentiable.
What killed the Convex Booster ?
Venue: arXiv cs.LG 2022
Year: 2022

A landmark negative result of Long and Servedio established a worst-case spectacular failure of a supervised learning trio (loss, algorithm, model) otherwise praised for its high precision machinery. Hundreds of papers followed up on the two suspected culprits: the loss (for being convex) and/or the algorithm (for fitting a classical boosting blueprint). Here, we call to the half-century+ founding theory of losses for class probability estimation (properness), an extension of Long and Servedio's results and a new general boosting algorithm to demonstrate that the real culprit in their specific context was in fact the (linear) model class. We advocate for a more general stanpoint on the problem as we argue that the source of the negative result lies in the dark side of a pervasive -- and otherwise prized -- aspect of ML: \textit{parameterisation}.
Acceptability Judgements via Examining the Topology of Attention Maps
Venue: arXiv cs.CL 2022
Year: 2022

The role of the attention mechanism in encoding linguistic knowledge has received special interest in NLP. However, the ability of the attention heads to judge the grammatical acceptability of a sentence has been underexplored. This paper approaches the paradigm of acceptability judgments with topological data analysis (TDA), showing that the geometric properties of the attention graph can be efficiently exploited for two standard practices in linguistics: binary judgments and linguistic minimal pairs. Topological features enhance the BERT-based acceptability classifier scores by $8$%-$24$% on CoLA in three languages (English, Italian, and Swedish). By revealing the topological discrepancy between attention maps of minimal pairs, we achieve the human-level performance on the BLiMP benchmark, outperforming nine statistical and Transformer LM baselines. At the same time, TDA provides the foundation for analyzing the linguistic functions of attention heads and interpreting the correspondence between the graph features and grammatical phenomena.
The Arabic Ontology -- An Arabic Wordnet with Ontologically Clean Content
Venue: arXiv cs.CL 2022
Year: 2022

We present a formal Arabic wordnet built on the basis of a carefully designed ontology hereby referred to as the Arabic Ontology. The ontology provides a formal representation of the concepts that the Arabic terms convey, and its content was built with ontological analysis in mind, and benchmarked to scientific advances and rigorous knowledge sources as much as this is possible, rather than to only speakers' beliefs as lexicons typically are. A comprehensive evaluation was conducted thereby demonstrating that the current version of the top-levels of the ontology can top the majority of the Arabic meanings. The ontology consists currently of about 1,300 well-investigated concepts in addition to 11,000 concepts that are partially validated. The ontology is accessible and searchable through a lexicographic search engine (https://ontology.birzeit.edu) that also includes about 150 Arabic-multilingual lexicons, and which are being mapped and enriched using the ontology. The ontology is fully mapped with Princeton WordNet, Wikidata, and other resources.
A graph-transformer for whole slide image classification
Venue: arXiv cs.CV 2022
Year: 2022

Deep learning is a powerful tool for whole slide image (WSI) analysis. Typically, when performing supervised deep learning, a WSI is divided into small patches, trained and the outcomes are aggregated to estimate disease grade. However, patch-based methods introduce label noise during training by assuming that each patch is independent with the same label as the WSI and neglect overall WSI-level information that is significant in disease grading. Here we present a Graph-Transformer (GT) that fuses a graph-based representation of an WSI and a vision transformer for processing pathology images, called GTP, to predict disease grade. We selected $4,818$ WSIs from the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the National Lung Screening Trial (NLST), and The Cancer Genome Atlas (TCGA), and used GTP to distinguish adenocarcinoma (LUAD) and squamous cell carcinoma (LSCC) from adjacent non-cancerous tissue (normal). First, using NLST data, we developed a contrastive learning framework to generate a feature extractor. This allowed us to compute feature vectors of individual WSI patches, which were used to represent the nodes of the graph followed by construction of the GTP framework. Our model trained on the CPTAC data achieved consistently high performance on three-label classification (normal versus LUAD versus LSCC: mean accuracy$= 91.2$ $\pm$ $2.5\%$) based on five-fold cross-validation, and mean accuracy $= 82.3$ $\pm$ $1.0\%$ on external test data (TCGA). We also introduced a graph-based saliency mapping technique, called GraphCAM, that can identify regions that are highly associated with the class label. Our findings demonstrate GTP as an interpretable and effective deep learning framework for WSI-level classification.
Local dynamic mode of Cognitive Behavioral Therapy
Venue: arXiv cs.AI 2022
Year: 2022

In order to increase mental health equity among the most vulnerable and marginalized communities, it is important to increase access to high-quality therapists. One facet of addressing these needs, is to provide timely feedback to clinicians as they interact with their clients, in a way that is also contextualized to specific clients and interactions they have had. Dynamical systems provide a framework through which to analyze interactions. The present work applies these methods to the domain of automated psychotherapist evaluation for Cognitive Behavioral Therapy (CBT). Our methods extract local dynamic modes from short windows of conversation and learns to correlate the observed dynamics to CBT competence. The results demonstrate the value of this paradigm and outlines the way in which these methods can be used to study and improve therapeutic strategies.
Towards Understanding Gender-Seniority Compound Bias in Natural Language Generation
Venue: arXiv cs.CL 2022
Year: 2022

Women are often perceived as junior to their male counterparts, even within the same job titles. While there has been significant progress in the evaluation of gender bias in natural language processing (NLP), existing studies seldom investigate how biases toward gender groups change when compounded with other societal biases. In this work, we investigate how seniority impacts the degree of gender bias exhibited in pretrained neural generation models by introducing a novel framework for probing compound bias. We contribute a benchmark robustness-testing dataset spanning two domains, U.S. senatorship and professorship, created using a distant-supervision method. Our dataset includes human-written text with underlying ground truth and paired counterfactuals. We then examine GPT-2 perplexity and the frequency of gendered language in generated text. Our results show that GPT-2 amplifies bias by considering women as junior and men as senior more often than the ground truth in both domains. These results suggest that NLP applications built using GPT-2 may harm women in professional capacities.
Single-cell Subcellular Protein Localisation Using Novel Ensembles of Diverse Deep Architectures
Venue: arXiv cs.CV 2022
Year: 2022

Unravelling protein distributions within individual cells is key to understanding their function and state and indispensable to developing new treatments. Here we present the Hybrid subCellular Protein Localiser (HCPL), which learns from weakly labelled data to robustly localise single-cell subcellular protein patterns. It comprises innovative DNN architectures exploiting wavelet filters and learnt parametric activations that successfully tackle drastic cell variability. HCPL features correlation-based ensembling of novel architectures that boosts performance and aids generalisation. Large-scale data annotation is made feasible by our "AI-trains-AI" approach, which determines the visual integrity of cells and emphasises reliable labels for efficient training. In the Human Protein Atlas context, we demonstrate that HCPL defines state-of-the-art in the single-cell classification of protein localisation patterns. To better understand the inner workings of HCPL and assess its biological relevance, we analyse the contributions of each system component and dissect the emergent features from which the localisation predictions are derived.
Gender Bias in Meta-Embeddings
Venue: arXiv cs.CL 2022
Year: 2022

Different methods have been proposed to develop meta-embeddings from a given set of source embeddings. However, the source embeddings can contain unfair gender-related biases, and how these influence the meta-embeddings has not been studied yet. We study the gender bias in meta-embeddings created under three different settings: (1) meta-embedding multiple sources without performing any debiasing (Multi-Source No-Debiasing), (2) meta-embedding multiple sources debiased by a single method (Multi-Source Single-Debiasing), and (3) meta-embedding a single source debiased by different methods (Single-Source Multi-Debiasing). Our experimental results show that meta-embedding amplifies the gender biases compared to input source embeddings. We find that debiasing not only the sources but also their meta-embedding is needed to mitigate those biases. Moreover, we propose a novel debiasing method based on meta-embedding learning where we use multiple debiasing methods on a single source embedding and then create a single unbiased meta-embedding.
Service Delay Minimization for Federated Learning over Mobile Devices
Venue: arXiv cs.LG 2022
Year: 2022

Federated learning (FL) over mobile devices has fostered numerous intriguing applications/services, many of which are delay-sensitive. In this paper, we propose a service delay efficient FL (SDEFL) scheme over mobile devices. Unlike traditional communication efficient FL, which regards wireless communications as the bottleneck, we find that under many situations, the local computing delay is comparable to the communication delay during the FL training process, given the development of high-speed wireless transmission techniques. Thus, the service delay in FL should be computing delay + communication delay over training rounds. To minimize the service delay of FL, simply reducing local computing/communication delay independently is not enough. The delay trade-off between local computing and wireless communications must be considered. Besides, we empirically study the impacts of local computing control and compression strategies (i.e., the number of local updates, weight quantization, and gradient quantization) on computing, communication and service delays. Based on those trade-off observation and empirical studies, we develop an optimization scheme to minimize the service delay of FL over heterogeneous devices. We establish testbeds and conduct extensive emulations/experiments to verify our theoretical analysis. The results show that SDEFL reduces notable service delay with a small accuracy drop compared to peer designs.
Incremental Learning with Differentiable Architecture and Forgetting Search
Venue: arXiv cs.LG 2022
Year: 2022

As progress is made on training machine learning models on incrementally expanding classification tasks (i.e., incremental learning), a next step is to translate this progress to industry expectations. One technique missing from incremental learning is automatic architecture design via Neural Architecture Search (NAS). In this paper, we show that leveraging NAS for incremental learning results in strong performance gains for classification tasks. Specifically, we contribute the following: first, we create a strong baseline approach for incremental learning based on Differentiable Architecture Search (DARTS) and state-of-the-art incremental learning strategies, outperforming many existing strategies trained with similar-sized popular architectures; second, we extend the idea of architecture search to regularize architecture forgetting, boosting performance past our proposed baseline. We evaluate our method on both RF signal and image classification tasks, and demonstrate we can achieve up to a 10% performance increase over state-of-the-art methods. Most importantly, our contribution enables learning from continuous distributions on real-world application data for which the complexity of the data distribution is unknown, or the modality less explored (such as RF signal classification).
Beyond Labels: Visual Representations for Bone Marrow Cell Morphology Recognition
Venue: arXiv cs.CV 2022
Year: 2022

Analyzing and inspecting bone marrow cell cytomorphology is a critical but highly complex and time-consuming component of hematopathology diagnosis. Recent advancements in artificial intelligence have paved the way for the application of deep learning algorithms to complex medical tasks. Nevertheless, there are many challenges in applying effective learning algorithms to medical image analysis, such as the lack of sufficient and reliably annotated training datasets and the highly class-imbalanced nature of most medical data. Here, we improve on the state-of-the-art methodologies of bone marrow cell recognition by deviating from sole reliance on labeled data and leveraging self-supervision in training our learning models. We investigate our approach's effectiveness in identifying bone marrow cell types. Our experiments demonstrate significant performance improvements in conducting different bone marrow cell recognition tasks compared to the current state-of-the-art methodologies.
Structured Attention Composition for Temporal Action Localization
Venue: arXiv cs.CV 2022
Year: 2022

Temporal action localization aims at localizing action instances from untrimmed videos. Existing works have designed various effective modules to precisely localize action instances based on appearance and motion features. However, by treating these two kinds of features with equal importance, previous works cannot take full advantage of each modality feature, making the learned model still sub-optimal. To tackle this issue, we make an early effort to study temporal action localization from the perspective of multi-modality feature learning, based on the observation that different actions exhibit specific preferences to appearance or motion modality. Specifically, we build a novel structured attention composition module. Unlike conventional attention, the proposed module would not infer frame attention and modality attention independently. Instead, by casting the relationship between the modality attention and the frame attention as an attention assignment process, the structured attention composition module learns to encode the frame-modality structure and uses it to regularize the inferred frame attention and modality attention, respectively, upon the optimal transport theory. The final frame-modality attention is obtained by the composition of the two individual attentions. The proposed structured attention composition module can be deployed as a plug-and-play module into existing action localization frameworks. Extensive experiments on two widely used benchmarks show that the proposed structured attention composition consistently improves four state-of-the-art temporal action localization methods and builds new state-of-the-art performance on THUMOS14. Code is availabel at https://github.com/VividLe/Structured-Attention-Composition.