BioModels—15 years of sharing computational models in life science

Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world’s largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse

Summarizing Dialogic Arguments from Social Media

Online argumentative dialog is a rich source of information on popular beliefs and opinions that could be useful to companies as well as governmental or public policy agencies. Compact, easy to read, summaries of these dialogues would thus be highly valuable. A priori, it is not even clear what form such a summary should take. Previous work on summarization has primarily focused on summarizing written texts, where the notion of an abstract of the text is well defined. We collect gold standard training data consisting of five human summaries for each of 161 dialogues on the topics of Gay Marriage, Gun Control and Abortion. We present several different computational models aimed at identifying segments of the dialogues whose content should be used for the summary, using linguistic features and Word2vec features with both SVMs and Bidirectional LSTMs. We show that we can identify the most important arguments by using the dialog context with a best F-measure of 0.74 for gun control, 0.71 for gay marriage, and 0.67 for abortion.Comment: Proceedings of the 21th Workshop on the Semantics and Pragmatics of Dialogue (SemDial 2017

Algorithms and methods for video transcoding.

Video transcoding is the process of dynamic video adaptation. Dynamic video adaptation can be defined as the process of converting video from one format to another, changing the bit rate, frame rate or resolution of the encoded video, which is mainly necessitated by the end user requirements. H.264 has been the predominantly used video compression standard for the last 15 years. HEVC (High Efficiency Video Coding) is the latest video compression standard finalised in 2013, which is an improvement over H.264 video compression standard. HEVC performs significantly better than H.264 in terms of the Rate-Distortion performance. As H.264 has been widely used in the last decade, a large amount of video content exists in H.264 format. There is a need to convert H.264 video content to HEVC format to achieve better Rate-Distortion performance and to support legacy video formats on newer devices. However, the computational complexity of HEVC encoder is 2-10 times higher than that of H.264 encoder. This makes it necessary to develop low complexity video transcoding algorithms to transcode from H.264 to HEVC format. This research work proposes low complexity algorithms for H.264 to HEVC video transcoding. The proposed algorithms reduce the computational complexity of H.264 to HEVC video transcoding significantly, with negligible loss in Rate-Distortion performance. This work proposes three different video transcoding algorithms. The MV-based mode merge algorithm uses the block mode and MV variances to estimate the split/non-split decision as part of the HEVC block prediction process. The conditional probability-based mode mapping algorithm models HEVC blocks of sizes 16×16 and lower as a function of H.264 block modes, H.264 and HEVC Quantisation Parameters (QP). The motion-compensated MB residual-based mode mapping algorithm makes the split/non-split decision based on content-adaptive classification models. With a combination of the proposed set of algorithms, the computational complexity of the HEVC encoder is reduced by around 60%, with negligible loss in Rate-Distortion performance, outperforming existing state-of-art algorithms by 20-25% in terms of computational complexity. The proposed algorithms can be used in computation-constrained video transcoding applications, to support video format conversion in smart devices, migration of large-scale H.264 video content from host servers to HEVC, cloud computing-based transcoding applications, and also to support high quality videos over bandwidth-constrained networks

Tailoring Semantic Communication at Network Edge: A Novel Approach Using Dynamic Knowledge Distillation

Semantic Communication (SemCom) systems, empowered by deep learning (DL), represent a paradigm shift in data transmission. These systems prioritize the significance of content over sheer data volume. However, existing SemCom designs face challenges when applied to diverse computational capabilities and network conditions, particularly in time-sensitive applications. A key challenge is the assumption that diverse devices can uniformly benefit from a standard, large DL model in SemCom systems. This assumption becomes increasingly impractical, especially in high-speed, high-reliability applications such as industrial automation or critical healthcare. Therefore, this paper introduces a novel SemCom framework tailored for heterogeneous, resource-constrained edge devices and computation-intensive servers. Our approach employs dynamic knowledge distillation (KD) to customize semantic models for each device, balancing computational and communication constraints while ensuring Quality of Service (QoS). We formulate an optimization problem and develop an adaptive algorithm that iteratively refines semantic knowledge on edge devices, resulting in better models tailored to their resource profiles. This algorithm strategically adjusts the granularity of distilled knowledge, enabling devices to maintain high semantic accuracy for precise inference tasks, even under unstable network conditions. Extensive simulations demonstrate that our approach significantly reduces model complexity for edge devices, leading to better semantic extraction and achieving the desired QoS.Comment: Accepted for the International Conference on Communications (ICC) 202