Collaborating Authors


Six digital transformation trends to watch in 2021


One of the biggest lessons Australia and New Zealand business leaders can take from the past 12 months is that a climate of uncertainty is now the new normal. The shift in customer behaviour brought about by the COVID-19 pandemic, coupled with rapid information technology changes, has already presented significant challenges. As a result, many organisations have had to bring forward their digital transformation plans and complete projects in weeks or months rather than years. During 2021, CIOs will have to work throughout their organisations and apply digital technologies and data to unlock new business opportunities. They must also work to promote a growth mindset that will help to unlock fresh innovation and agility. Adopting such a growth mindset will require CIOs and IT teams to embrace six key trends during the coming 12 months.

Data and AI Will Drive Autonomous Future in Banking


The priorities of every financial institution have been impacted by the pandemic, with some firms believing that a greater investment needs to be made in technology, others focusing on new products and services, and still others wanting to improve components of trust and security. The foundation of each of these priorities is a combination of a need to improve customer experiences while managing operating costs in an uncertain economic environment. The reassessment of corporate priorities is being done with the backdrop of consumer standards for engagement that have moved away from one-size-fits-all transactional experiences to contextualized experiences that are personalized across multiple touchpoints and channels. At the same time, as consumers widen their scope of understanding of what can be achieved with digital engagement, more of them will be willing to pay more for services that enhance their financial lifestyle through real-time insights, proactive recommendations and simplified engagement. According to Salesforce's Trends in Financial Services report, there is an urgent need for the industry to transform data and insights into actionable outcomes that are consumer-centric.

Facebook and NYU trained an AI to estimate COVID outcomes


COVID-19 has infected more than 23 million Americans and killed 386,000 of them to date, since the global pandemic began last March. Complicating the public health response is the fact that we still know so little about how the virus operates -- such as why some patients remain asymptomatic while it ravages others. Effectively allocating resources like ICU beds and ventilators becomes a Sisyphean task when doctors can only guess as to who might recover and who might be intubated within the next 96 hours. However a trio of new machine learning algorithms developed by Facebook's AI division (FAIR) in cooperation with NYU Langone Health can help predict patient outcomes up to four days in advance using just a patient's chest x-rays. The models can, respectively, predict patient deterioration based on either a single X-ray or a sequence as well as determine how much supplemental oxygen the patient will likely need.

Banks need to strike the right balance for digital transformation

MIT Technology Review

Every financial institution is looking to digital transformation to meet rising customer expectations for speed and convenience, lower its operating cost, and fend off competition, including from tech companies moving into financial services. Some are spending over 10% of yearly revenue on technology investments, according to Bloomberg. "This is a huge investment and most financial institutions cannot support this for the long term," says Michael Fei, SME banking CEO at OneConnect Financial Technology, an associate of Ping An Insurance. The covid-19 pandemic has revealed how even financial institutions that considered themselves digitally advanced are, in reality, still wedded to analog processes along the chain of processing. "For many financial institutions, this has been a wake-up call," says Fei. "In the past, many had thought that if they have an online portal and a mobile application then that's enough. But now they've realized it's not. Some banks have online portals and mobile apps where you can apply for loans, but they still need to send items to the customer and carry out on-site inspection before they can process the loans, which hasn't been possible during covid. Banks have had to reshape and redesign the whole process of their lending products."

The Best of CES 2021: Gadgets From the All-Digital Tech Show WSJD - Technology

CES 2021 was unlike any trade show we've ever experienced. Due to Covid-19, it was "all digital," which really meant "mostly websites." To find the hot stuff this year, we didn't wander the millions of square feet of the Las Vegas Convention Center and surrounding facilities, but instead watched streamed presentations, combed through hundreds of exhibitors' "digital activations" and, of course, heard plenty of pitches from entrepreneurs and marketing folks eager to keep us in the loop--global pandemic or not. That means we weren't able to touch and feel the innovations like in years past--although we did get some stuff sent to our homes. Still, it hasn't stopped us from bringing you the craziest, coolest and kookiest gadgets we could find.

Masks, sanitizers, and social distancing gadgets: The COVID tech that dominated CES 2021


With virtual booths and digital portals taking the place of convention center halls and showcases, CES in the time of coronavirus looked different. So did some of the tech. COVID-oriented tech products stood out at this year's CES. Some brands debuted new products made for the pandemic, others found that items they'd been working on all along now have newfound applications and relevance. But is "COVID tech" really necessary? After all, the best way to slow the spread of the virus is to practice social distancing and wear a face mask, which can be as simple as a bandana or a repurposed old T-shirt -- fundamentally low-tech strategies.

Returning as Intel CEO, prodigal son Pat Gelsinger faces daunting challenges


This week, Intel announced CEO Bob Swan will be replaced by VMware CEO Pat Gelsinger. Facing stronger competitive challenges, Intel has struggled. Recently, the company has come under pressure by activist investors to make significant changes. Wednesday brought one such change. Gelsinger is no stranger to Intel.

AIs that read sentences can also spot virus mutations

MIT Technology Review

In a study published in Science today, Berger and her colleagues pull several of these strands together and use NLP to predict mutations that allow viruses to avoid being detected by antibodies in the human immune system, a process known as viral immune escape. The basic idea is that the interpretation of a virus by an immune system is analogous to the interpretation of a sentence by a human. "It's a neat paper, building off the momentum of previous work," says Ali Madani, a scientist at Salesforce, who is using NLP to predict protein sequences. Berger's team uses two different linguistic concepts: grammar and semantics (or meaning). The genetic or evolutionary fitness of a virus--characteristics such as how good it is at infecting a host--can be interpreted in terms of grammatical correctness.

The language of a virus


Uncovering connections between seemingly unrelated branches of science might accelerate research in one branch by using the methods developed in the other branch as stepping stones. On page 284 of this issue, Hie et al. ([ 1 ][1]) provide an elegant example of such unexpected connections. The authors have uncovered a parallel between the properties of a virus and its interpretation by the host immune system and the properties of a sentence in natural language and its interpretation by a human. By leveraging an extensive natural language processing (NLP) toolbox ([ 2 ][2], [ 3 ][3]) developed over the years, they have come up with a powerful new method for the identification of mutations that allow a virus to escape from recognition by neutralizing antibodies. In 1950, Alan Turing predicted that machines will eventually compete with men in “intellectual fields” and suggested that one possible way forward would be to build a machine that can be taught to understand and speak English ([ 4 ][4]). This was, and still is, an ambitious goal. It is clear that language grammar can provide a formal skeleton for building sentences, but how can machines be trained to infer the meanings? In natural language, there are many ways to express the same idea, and yet small changes in expression can often change the meaning. Linguistics developed a way of quantifying the similarity of meaning (semantics). Specifically, it was proposed that words that are used in the same context are likely to have similar meanings ([ 5 ][5], [ 6 ][6]). This distributional hypothesis became a key feature for the computational technique in NLP, known as word (semantic) embedding. The main idea is to characterize words as vectors that represent distributional properties in a large amount of language data and then embed these sparse, high-dimensional vectors into more manageable, low-dimensional space in a distance-preserving manner. By the distributional hypothesis, this technique should group words that have similar semantics together in the embedding space. Hie et al. proposed that viruses can also be thought to have a grammar and semantics. Intuitively, the grammar describes which sequences make specific viruses (or their parts). Biologically, a viral protein sequence should have all the properties needed to invade a host, multiply, and continue invading another host. Thus, in some way, the grammar represents the fitness of a virus. With enough data, current machine learning approaches can be used to learn this sequence-based fitness function. ![Figure][7] Predicting immune escape The constrained semantic change search algorithm obtains semantic embeddings of all mutated protein sequences using bidirectional long short-term memory (LSTM). The sequences are ranked according to the combined score of the semantic change (the distance of a mutation from the original sequence) and fitness (the probability that a mutation appears in viral sequences). GRAPHIC: V. ALTOUNIAN/SCIENCE But what would be the meaning (semantics) of a virus? Hie et al. suggested that the semantics of a virus should be defined in terms of its recognition by immune systems. Specifically, viruses with different semantics would require a different state of the immune system (for example, different antibodies) to be recognized. The authors hypothesized that semantic embeddings allow sequences that require different immune responses to be uncovered. In this context, words represent protein sequences (or protein fragments), and recognition of such protein fragments is the task performed by the immune system. To escape immune responses, viral genomes can become mutated so that the virus evolves to no longer be recognized by the immune system. However, a virus that acquires a mutation that compromises its function (and thus fitness) will not survive. Using the NLP analogy, immune escape will be achieved by the mutations that change the semantics of the virus while maintaining its grammaticality so that the virus will remain infectious but escape the immune system. On the basis of this idea, Hie et al. developed a new approach, called constrained semantic change search (CSCS). Computationally, the goal of CSCS is to identify mutations that confer high fitness and substantial semantic changes at the same time (see the figure). The immune escape scores are computed by combining the two quantities. The search algorithm builds on a powerful deep learning technique for language modeling, called long short-term memory (LSTM), to obtain semantic embeddings of all mutated sequences and rank the sequences according to their immune escape scores in the embedded space. The semantic changes correspond to the distance of the mutated sequences to the original sequence in the semantic embedding, and its “grammaticality” (or fitness) is estimated by the probability that the mutation appears in viral sequences. The immune escape scores can then be computed by simultaneously considering both the semantic distance and fitness probability. Hie et al. confirmed their hypothesis for the correspondence of grammaticality and semantics to fitness and immune response in three viral proteins: influenza A hemagglutinin (HA), HIV-1 envelope (Env), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike. For the analogy of semantics to immune response, they found that clusters of semantically similar viruses were in good correspondence with virus subtypes, host, or both, confirming that the language model can extract functional meanings from protein sequences. The clustering patterns also revealed interspecies transmissibility and antigenic similarity. The correspondence of grammaticality to fitness was assessed more directly by using deep mutational scans evaluated for replication fitness (for HA and Env) or binding (for Spike). The combined model was tested against experimentally verified mutations that allow for immue escape. Scoring each amino acid residue with CSCS, the authors uncovered viral protein regions that are significantly enriched with escape potential: the head of HA for influenza, the V1/V2 hypervariable regions for HIV Env, and the receptor-binding domain (RBD) and amino-terminal domain for SARS-CoV-2 Spike. The language of viral evolution and escape proposed by Hie et al. provides a powerful framework for predicting mutations that lead to viral escape. However, interesting questions remain. Further extending the natural language analogy, it is notable that individuals can interpret the same English sentence differently depending on their past experience and the fluency in the language. Similarly, immune response differs between individuals depending on factors such as past pathogenic exposures and overall “strength” of the immune system. It will be interesting to see whether the proposed approach can be adapted to provide a “personalized” view of the language of virus evolution. 1. [↵][8]1. B. Hie, 2. E. Zhong, 3. B. Berger, 4. B. Bryson , Science 371, 284 (2021). [OpenUrl][9][Abstract/FREE Full Text][10] 2. [↵][11]1. L. Yann, 2. Y. Bengio, 3. G. Hinton , Nature 521, 436 (2015). [OpenUrl][12][CrossRef][13][PubMed][14] 3. [↵][15]1. T. Young, 2. D. Hazarika, 3. S. Poria, 4. E. Cambria , IEEE Comput. Intell. Mag. 13, 55 (2018). [OpenUrl][16] 4. [↵][17]1. A. Turing , Mind LIX, 433 (1950). 5. [↵][18]1. Z. S. Harris , Word 10, 146 (1954). [OpenUrl][19][CrossRef][20][PubMed][21] 6. [↵][22]1. J. R. Firth , in Studies in Linguistic Analysis (1957), pp. 1–32. Acknowledgments: The authors are supported by the Intramural Research Programs of the National Library of Medicine at the National Institutes of Health, USA. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-4 [5]: #ref-5 [6]: #ref-6 [7]: pending:yes [8]: #xref-ref-1-1 "View reference 1 in text" [9]: {openurl}?query=rft.jtitle%253DScience%26rft.stitle%253DScience%26rft.aulast%253DHie%26rft.auinit1%253DB.%26rft.volume%253D371%26rft.issue%253D6526%26rft.spage%253D284%26rft.epage%253D288%26rft.atitle%253DLearning%2Bthe%2Blanguage%2Bof%2Bviral%2Bevolution%2Band%2Bescape%26rft_id%253Dinfo%253Adoi%252F10.1126%252Fscience.abd7331%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [10]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiQUJTVCI7czoxMToiam91cm5hbENvZGUiO3M6Mzoic2NpIjtzOjU6InJlc2lkIjtzOjEyOiIzNzEvNjUyNi8yODQiO3M6NDoiYXRvbSI7czoyMjoiL3NjaS8zNzEvNjUyNi8yMzMuYXRvbSI7fXM6ODoiZnJhZ21lbnQiO3M6MDoiIjt9 [11]: #xref-ref-2-1 "View reference 2 in text" [12]: {openurl}?query=rft.jtitle%253DNature%26rft.volume%253D521%26rft.spage%253D436%26rft_id%253Dinfo%253Adoi%252F10.1038%252Fnature14539%26rft_id%253Dinfo%253Apmid%252F26017442%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [13]: /lookup/external-ref?access_num=10.1038/nature14539&link_type=DOI [14]: /lookup/external-ref?access_num=26017442&link_type=MED&atom=%2Fsci%2F371%2F6526%2F233.atom [15]: #xref-ref-3-1 "View reference 3 in text" [16]: {openurl}?query=rft.jtitle%253DIEEE%2BComput.%2BIntell.%2BMag.%26rft.volume%253D13%26rft.spage%253D55%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [17]: #xref-ref-4-1 "View reference 4 in text" [18]: #xref-ref-5-1 "View reference 5 in text" [19]: {openurl}?query=rft.jtitle%253DWord%26rft.volume%253D10%26rft.spage%253D146%26rft_id%253Dinfo%253Adoi%252F10.1080%252F00437956.1954.11659520%26rft_id%253Dinfo%253Apmid%252F32513867%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [20]: /lookup/external-ref?access_num=10.1080/00437956.1954.11659520&link_type=DOI [21]: /lookup/external-ref?access_num=32513867&link_type=MED&atom=%2Fsci%2F371%2F6526%2F233.atom [22]: #xref-ref-6-1 "View reference 6 in text"

Phylodynamics for cell biologists


Advances in experimental approaches for single-cell analysis allow in situ sequencing, genomic barcoding, and mapping of cell lineages within tissues and organisms. Large amounts of data have thus accumulated and present an analytical challenge. Stadler et al. recognized the need for conceptual and computational approaches to fully exploit these technological advances for the understanding of normal and disease states. The authors review ideas taken from phylodynamics of infectious disease and show how similar tree-building techniques can be applied to monitoring changes in somatic cell lineages for applications ranging from development and differentiation to cancer biology. Science , this issue p. [eaah6266][1] ### BACKGROUND The birth, death, and diversification of individuals are events that drive biological processes across all scales. This is true whether the individuals in question represent nucleic acids, cells, whole organisms, populations, or species. The ancestral relationships of individuals can be visualized as branching trees or phylogenies, which are long-established representations in the fields of evolution, ecology, and epidemiology. Molecular phylogenetics is the discipline concerned with the reconstruction of such trees from gene or genome sequence data. The shape and size of such phylogenies depend on the past birth and death processes that generated them, and in phylodynamics, mathematical models are used to infer and quantify the dynamical behavior of biological populations from ancestral relationships. New technological advances in genetics and cell biology have led to a growing body of data about the molecular state and ancestry of individual cells in multicellular organisms. Ideas from phylogenetics and phylodynamics are being applied to these data to investigate many questions in tissue formation and tumorigenesis. ### ADVANCES Trees offer a valuable framework for tracing cell division and change through time, beginning with individual ancestral stem cells or fertilized eggs and resulting in complex tissues, tumors, or whole organisms (see the figure). They also provide the basis for computational and statistical methods with which to analyze data from cell biology. Our Review explains how “tree-thinking” and phylodynamics can be beneficial to the interpretation of empirical data pertaining to the individual cells of multicellular organisms. We summarize some recent research questions in developmental and cancer biology and briefly introduce the new technologies that allow us to observe the spatiotemporal histories of cell division and change. We provide an overview of the various and sometimes confusing ways in which graphical models, based on or represented by trees, have been applied in cell biology. To provide conceptual clarity, we outline four distinct graphical representations of the history of cell division and differentiation in multicellular organisms. We highlight that cells from an organism cannot be always treated as statistically independent observations but instead are often correlated because of phylogenetic history, and we explain how this can cause difficulties when attempting to infer dynamical behavior from experimental single-cell data. We introduce simple ecological null models for cell populations and illustrate some potential pitfalls in hypothesis testing and the need for quantitative phylodynamic models that explicitly incorporate the dependencies caused by shared ancestry. ### OUTLOOK We expect the rapid growth in the number of cell-level phylogenies to continue, a trend enhanced by ongoing technological advances in cell lineage tracing, genomic barcoding, and in situ sequencing. In particular, we anticipate the generation of exciting datasets that combine phenotypic measurements for individual cells (such as through transcriptome sequencing) with high-resolution reconstructions of the ancestry of the sampled cells. These developments will offer new ways to study developmental, oncogenic, and immunological processes but will require new and appropriate conceptual and computational tools. We discuss how models from phylogenetics and phylodynamics will benefit the interpretation of the data sets generated in the foreseeable future and will aid the development of statistical tests that exploit, and are robust to, cell shared ancestry. We hope that our discussion will initiate the integration of cell-level phylodynamic approaches into experimental and theoretical studies of development, cancer, and immunology. We sketch out some of the theoretical advances that will be required to analyze complex spatiotemporal cell dynamics and encourage explorations of these new directions. Powerful new statistical and computational tools are essential if we are to exploit fully the wealth of new experimental data being generated in cell biology. ![Figure][2] Multicellular organisms develop from a single fertilized egg. The division, apoptosis, and differentiation of cells can be displayed in a development tree, with the fertilized egg being the root of the tree. The development of any particular tissue within an organism can be traced as a subtree of the full developmental tree. Subtrees that represent cancer tumors or B cell clones may exhibit rapid growth and genetic change. Here, we illustrate the developmental tree of a human and expand the subtree representing haematopoiesis (blood formation) in the bone marrow. Stem cells in the bone marrow differentiate, giving rise to the numerous blood cell types in humans. The structure of the tree that underlies haematopoiesis and the formation of all tissues is unclear. Phylogenetic and phylodynamic tools can help to describe and statistically explore questions about this cell differentiation process. Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth, death, and inheritance within an organism give rise to the fundamental processes of development, differentiation, and cancer. Technical advances in molecular biology now allow us to study cellular composition, ancestry, and evolution at the resolution of individual cells within an organism or tissue. Here, we take a phylogenetic and phylodynamic approach to single-cell biology. We explain how “tree thinking” is important to the interpretation of the growing body of cell-level data and how ecological null models can benefit statistical hypothesis testing. Experimental progress in cell biology should be accompanied by theoretical developments if we are to exploit fully the dynamical information in single-cell data. [1]: /lookup/doi/10.1126/science.aah6266 [2]: pending:yes