Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new Bio-ML track at OAEI 2022.

Applying deep learning techniques, particularly language models (LMs), in ontology engineering has raised widespread attention. However, deep learning frameworks like PyTorch and Tensorflow are predominantly developed for Python programming, while widely-used ontology APIs, such as the OWL API and Jena, are primarily Java-based. To facilitate seamless integration of these frameworks and APIs, we present Deeponto, a Python package designed for ontology engineering. The package encompasses a core ontology processing module founded on the widely-recognised and reliable OWL API, encapsulating its fundamental features in a more "Pythonic" manner and extending its capabilities to include other essential components including reasoning, verbalisation, normalisation, projection, and more. Building on this module, Deeponto offers a suite of tools, resources, and algorithms that support various ontology engineering tasks, such as ontology alignment and completion, by harnessing deep learning methodologies, primarily pre-trained LMs. In this paper, we also demonstrate the practical utility of Deeponto through two use-cases: the Digital Health Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment Evaluation Initiative (OAEI).

The superconducting linear accelerator is a highly flexiable facility for modern scientific discoveries, necessitating weekly reconfiguration and tuning. Accordingly, minimizing setup time proves essential in affording users with ample experimental time. We propose a trend-based soft actor-critic(TBSAC) beam control method with strong robustness, allowing the agents to be trained in a simulated environment and applied to the real accelerator directly with zero-shot. To validate the effectiveness of our method, two different typical beam control tasks were performed on China Accelerator Facility for Superheavy Elements (CAFe II) and a light particle injector(LPI) respectively. The orbit correction tasks were performed in three cryomodules in CAFe II seperately, the time required for tuning has been reduced to one-tenth of that needed by human experts, and the RMS values of the corrected orbit were all less than 1mm. The other transmission efficiency optimization task was conducted in the LPI, our agent successfully optimized the transmission efficiency of radio-frequency quadrupole(RFQ) to over $85\%$ within 2 minutes. The outcomes of these two experiments offer substantiation that our proposed TBSAC approach can efficiently and effectively accomplish beam commissioning tasks while upholding the same standard as skilled human experts. As such, our method exhibits potential for future applications in other accelerator commissioning fields.

DNNs are one of the most widely used Deep Learning models. The matrix multiplication operations for DNNs incur significant computational costs and are bottlenecked by data movement between the memory and the processing elements. Many specialized accelerators have been proposed to optimize matrix multiplication operations. One popular idea is to use Processing-in-Memory where computations are performed by the memory storage element, thereby reducing the overhead of data movement between processor and memory. However, most PIM solutions rely either on novel memory technologies that have yet to mature or bit-serial computations which have significant performance overhead and scalability issues. In this work, an in-SRAM digital multiplier is proposed to take the best of both worlds, i.e. performing GEMM in memory but using only conventional SRAMs without the drawbacks of bit-serial computations. This allows the user to design systems with significant performance gains using existing technologies with little to no modifications. We first design a novel approximate bit-parallel multiplier that approximates multiplications with bitwise OR operations by leveraging multiple wordlines activation in the SRAM. We then propose DAISM - Digital Approximate In-SRAM Multiplier architecture, an accelerator for convolutional neural networks, based on our novel multiplier. This is followed by a comprehensive analysis of trade-offs in area, accuracy, and performance. We show that under similar design constraints, DAISM reduces energy consumption by 25\% and the number of cycles by 43\% compared to state-of-the-art baselines.

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Language (OWL). In this paper, we present a new subsumption prediction method named BERTSubs for classes of OWL ontology. It exploits the pre-trained language model BERT to compute contextual embeddings of a class, where customized templates are proposed to incorporate the class context (e.g., neighbouring classes) and the logical existential restriction. BERTSubs is able to predict multiple kinds of subsumers including named classes from the same ontology or another ontology, and existential restrictions from the same ontology. Extensive evaluation on five real-world ontologies for three different subsumption tasks has shown the effectiveness of the templates and that BERTSubs can dramatically outperform the baselines that use (literal-aware) knowledge graph embeddings, non-contextual word embeddings and the state-of-the-art OWL ontology embeddings.

Traditional machine learning follows a close-set assumption that the training and test set share the same label space. While in many practical scenarios, it is inevitable that some test samples belong to unknown classes (open-set). To fix this issue, Open-Set Recognition (OSR), whose goal is to make correct predictions on both close-set samples and open-set samples, has attracted rising attention. In this direction, the vast majority of literature focuses on the pattern of open-set samples. However, how to evaluate model performance in this challenging task is still unsolved. In this paper, a systematic analysis reveals that most existing metrics are essentially inconsistent with the aforementioned goal of OSR: (1) For metrics extended from close-set classification, such as Open-set F-score, Youden's index, and Normalized Accuracy, a poor open-set prediction can escape from a low performance score with a superior close-set prediction. (2) Novelty detection AUC, which measures the ranking performance between close-set and open-set samples, ignores the close-set performance. To fix these issues, we propose a novel metric named OpenAUC. Compared with existing metrics, OpenAUC enjoys a concise pairwise formulation that evaluates open-set performance and close-set performance in a coupling manner. Further analysis shows that OpenAUC is free from the aforementioned inconsistency properties. Finally, an end-to-end learning method is proposed to minimize the OpenAUC risk, and the experimental results on popular benchmark datasets speak to its effectiveness. Project Page: https://github.com/wang22ti/OpenAUC.

Detecting 3D objects from multi-view images is a fundamental problem in 3D computer vision. Recently, significant breakthrough has been made in multi-view 3D detection tasks. However, the unprecedented detection performance of these vision BEV (bird's-eye-view) detection models is accompanied with enormous parameters and computation, which make them unaffordable on edge devices. To address this problem, in this paper, we propose a structured knowledge distillation framework, aiming to improve the efficiency of modern vision-only BEV detection models. The proposed framework mainly includes: (a) spatial-temporal distillation which distills teacher knowledge of information fusion from different timestamps and views, (b) BEV response distillation which distills teacher response to different pillars, and (c) weight-inheriting which solves the problem of inconsistent inputs between students and teacher in modern transformer architectures. Experimental results show that our method leads to an average improvement of 2.16 mAP and 2.27 NDS on the nuScenes benchmark, outperforming multiple baselines by a large margin.

This paper aims for the task of text-to-video retrieval, where given a query in the form of a natural-language sentence, it is asked to retrieve videos which are semantically relevant to the given query, from a great number of unlabeled videos. The success of this task depends on cross-modal representation learning that projects both videos and sentences into common spaces for semantic similarity computation. In this work, we concentrate on video representation learning, an essential component for text-to-video retrieval. Inspired by the reading strategy of humans, we propose a Reading-strategy Inspired Visual Representation Learning (RIVRL) to represent videos, which consists of two branches: a previewing branch and an intensive-reading branch. The previewing branch is designed to briefly capture the overview information of videos, while the intensive-reading branch is designed to obtain more in-depth information. Moreover, the intensive-reading branch is aware of the video overview captured by the previewing branch. Such holistic information is found to be useful for the intensive-reading branch to extract more fine-grained features. Extensive experiments on three datasets are conducted, where our model RIVRL achieves a new state-of-the-art on TGIF and VATEX. Moreover, on MSR-VTT, our model using two video features shows comparable performance to the state-of-the-art using seven video features and even outperforms models pre-trained on the large-scale HowTo100M dataset.