To understand how genetic variants in human genomes manifest in phenotypes -- traits like height or diseases like asthma -- geneticists have sequenced and measured hundreds of thousands of individuals. Geneticists use this data to build models that predict how a genetic variant impacts phenotype given genomic features of the variant, like DNA accessibility or the presence of nearby DNA-bound proteins. As more data and features become available, one might expect predictive models to improve. Unfortunately, training these models is bottlenecked by the need to solve expensive linear algebra problems because variants in the genome are correlated with nearby variants, requiring inversion of large matrices. Previous methods have therefore been restricted to fitting small models, and fitting simplified summary statistics, rather than the full likelihood of the statistical model. In this paper, we leverage modern fast linear algebra techniques to develop DeepWAS (Deep genome Wide Association Studies), a method to train large and flexible neural network predictive models to optimize likelihood. Notably, we find that larger models only improve performance when using our full likelihood approach; when trained by fitting traditional summary statistics, larger models perform no better than small ones. We find larger models trained on more features make better predictions, potentially improving disease predictions and therapeutic target identification.

Communication network engineering in enterprise environments is traditionally a complex, time-consuming, and error-prone manual process. Most research on network engineering automation has concentrated on configuration synthesis, often overlooking changes in the physical network topology. This paper introduces GeNet, a multimodal co-pilot for enterprise network engineers. GeNet is a novel framework that leverages a large language model (LLM) to streamline network design workflows. It uses visual and textual modalities to interpret and update network topologies and device configurations based on user intents. GeNet was evaluated on enterprise network scenarios adapted from Cisco certification exercises. Our results demonstrate GeNet's ability to interpret network topology images accurately, potentially reducing network engineers' efforts and accelerating network design processes in enterprise environments. Furthermore, we show the importance of precise topology understanding when handling intents that require modifications to the network's topology.

To discover new drugs is to seek and to prove causality. As an emerging approach leveraging human knowledge and creativity, data, and machine intelligence, causal inference holds the promise of reducing cognitive bias and improving decision making in drug discovery. While it has been applied across the value chain, the concepts and practice of causal inference remain obscure to many practitioners. This article offers a non-technical introduction to causal inference, reviews its recent applications, and discusses opportunities and challenges of adopting the causal language in drug discovery and development.

Accurate drug response prediction (DRP) is a crucial yet challenging task in precision medicine. This paper presents a novel Attention-Guided Multi-omics Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph (MeG) for each cell line, and then aggregates multi-omics features to predict drug response using a novel structure, called Graph edge-aware Network (GeNet). For the first time, our AGMI approach explores gene constraint based multi-omics integration for DRP with the whole-genome using GNNs. Empirical experiments on the CCLE and GDSC datasets show that our AGMI largely outperforms state-of-the-art DRP methods by 8.3%--34.2% on four metrics. Our data and code are available at https://github.com/yivan-WYYGDSG/AGMI.

Artificial Moral Agents (AMA's) is a field in computer science with the purpose of creating autonomous machines that can make moral decisions akin to how humans do. Researchers have proposed theoretical means of creating such machines, while philosophers have made arguments as to how these machines ought to behave, or whether they should even exist. Of the currently theorised AMA's, all research and design has been done with either none or at most one specified normative ethical theory as basis. This is problematic because it narrows down the AMA's functional ability and versatility which in turn causes moral outcomes that a limited number of people agree with (thereby undermining an AMA's ability to be moral in a human sense). As solution we design a three-layer model for general normative ethical theories that can be used to serialise the ethical views of people and businesses for an AMA to use during reasoning. Four specific ethical norms (Kantianism, divine command theory, utilitarianism, and egoism) were modelled and evaluated as proof of concept for normative modelling. Furthermore, all models were serialised to XML/XSD as proof of support for computerisation.

We introduce GeNet, a method for shotgun metagenomic classification from raw DNA sequences that exploits the known hierarchical structure between labels for training. We provide a comparison with state-of-the-art methods Kraken and Centrifuge on datasets obtained from several sequencing technologies, in which dataset shift occurs. We show that GeNet obtains competitive precision and good recall, with orders of magnitude less memory requirements. Moreover, we show that a linear model trained on top of representations learned by GeNet achieves recall comparable to state-of-the-art methods on the aforementioned datasets, and achieves over 90% accuracy in a challenging pathogen detection problem. This provides evidence of the usefulness of the representations learned by GeNet for downstream biological tasks.