With the advent of Bitcoin, a cryptographically-enabled peer-to-peer digital payment system, blockchain together with a whole package of distributed ledger technologies, which serve as the underlying foundation of all the crypto-currencies, have been gaining attention from both academia and industry in the last fifteen years. The recent years have witnessed tremendous momentum in the development of blockchain and distributed ledger technologies, largely due to the impressive rise in the market capital of these digital tokens. More and more industries, from banking and insurance, to supply chain and e-commerce, are quickly realizing the great potential in blockchain technology in efficiency boost, process automation and secure data sharing across otherwise isolated data silos. Furthermore, as the recognition of the data value began to sink in, data assets has become an essential part of the development of enterprises and countries. Blockchain technology is regarded as the foundation of digital economy and provides an effective approach for data ownership, pricing and transactions, which are the core issues of data asset management. However, the potential implications of Blockchain technologies go far beyond their application as the technological backbone for cryptocurrencies. Web3.0, using blockchain as underlying technology, allow for various novel application scenarios, which are built upon distributed consensus and thus are hard to block or censor while providing public verifiability of peer-to-peer transactions without a trusted central party. Web3.0 are expected to become the main front for a plethora of highly expressive applications. To more thoroughly explore the potential of blockchain and web3.0 and promote their progress, SDBD'24 will provide a forum for the most recent blockchain and web3.0 research, innovations, and applications, bridging the gap between theory and practice in the design.

In recent years, there have been exciting and accelerated developments in AI with novel developments in foundation models, deep learning, new AI applications across numerous verticals, and more. In addition, the pace of adoption of these innovations driven by both academic and industry research labs has sped up with both big tech companies and startups looking to deliver value-differentiated products and services. With Generative AI (GenAI) garnering significant attention, the second edition of the I2S workshop focuses on two aspects: First, bringing together AI thought leaders from academia, big tech, and startups to discuss the opportunities, use-case themes, challenges, and risks of GenAI in various business verticals; and Second, bringing together startup founders to share experiences and lessons learned in commercializing GenAI innovations into successful enterprises highlighting challenges through the entire commercial journey - from productization to acquiring customers, building a team, and securing funding.

In recent years, the AI community has witnessed an exciting acceleration in innovation across foundation models, deep learning, new AI applications across numerous verticals, and more. In addition, AI innovations driven by both academic and industry research labs have rapidly been adopted by big tech companies and startups to deliver value-differentiated products and services.

MOTIVATION: Circadian oscillations have been observed in animals, plants, fungi and cyanobacteria and play a fundamental role in coordinating the homeostasis and behavior of biological systems. Genetically encoded molecular clocks found in nearly every cell, based on negative transcription/translation feedback loops and involving only a dozen genes, play a central role in maintaining these oscillations. However, high-throughput gene expression experiments reveal that in a typical tissue, a much larger fraction ([Formula: see text]) of all transcripts oscillate with the day-night cycle and the oscillating species vary with tissue type suggesting that perhaps a much larger fraction of all transcripts, and perhaps also other molecular species, may bear the potential for circadian oscillations. RESULTS: To better quantify the pervasiveness and plasticity of circadian oscillations, we conduct the first large-scale analysis aggregating the results of 18 circadian transcriptomic studies and 10 circadian metabolomic studies conducted in mice using different tissues and under different conditions. We find that over half of protein coding genes in the cell can produce transcripts that are circadian in at least one set of conditions and similarly for measured metabolites. Genetic or environmental perturbations can disrupt existing oscillations by changing their amplitudes and phases, suppressing them or giving rise to novel circadian oscillations. The oscillating species and their oscillations provide a characteristic signature of the physiological state of the corresponding cell/tissue. Molecular networks comprise many oscillator loops that have been sculpted by evolution over two trillion day-night cycles to have intrinsic circadian frequency. These oscillating loops are coupled by shared nodes in a large network of coupled circadian oscillators where the clock genes form a major hub. Cells can program and re-program their circadian repertoire through epigenetic and other mechanisms. AVAILABILITY AND IMPLEMENTATION: High-resolution and tissue/condition specific circadian data and networks available at http://circadiomics.igb.uci.edu. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We present a cancer genomic analysis pipeline which takes as input sequencing reads for both germline and tumor genomes and outputs filtered lists of all genetic mutations in the form of short ranked list of the most affected genes in the tumor, using either the Complete Genomics or Illumina platforms. A novel reporting and ranking system has been developed that makes use of publicly available datasets and literature specific to each patient, including new methods for using publicly available expression data in the absence of proper control data. Previously implicated small and large variations (including gene fusions) are reported in addition to probable driver mutations. Relationships between cancer and the sequenced tumor genome are highlighted using a network-based approach that integrates known and predicted protein-protein, protein-TF, and protein-drug interaction data. By using an integrative approach, effects of genetic variations on gene expression are used to provide further evidence of driver mutations. This pipeline has been developed with the aim to be used in assisting in the analysis of pediatric tumors, as an unbiased and automated method for interpreting sequencing results along with identifying potentially therapeutic drugs and their targets. We present results that agree with previous literature and highlight specific findings in a few patients.

MOTIVATION: Discovery of novel protective antigens is fundamental to the development of vaccines for existing and emerging pathogens. Most computational methods for predicting protein antigenicity rely directly on homology with previously characterized protective antigens; however, homology-based methods will fail to discover truly novel protective antigens. Thus, there is a significant need for homology-free methods capable of screening entire proteomes for the antigens most likely to generate a protective humoral immune response. RESULTS: Here we begin by curating two types of positive data: (i) antigens that elicit a strong antibody response in protected individuals but not in unprotected individuals, using human immunoglobulin reactivity data obtained from protein microarray analyses; and (ii) known protective antigens from the literature. The resulting datasets are used to train a sequence-based prediction model, ANTIGENpro, to predict the likelihood that a protein is a protective antigen. ANTIGENpro correctly classifies 82% of the known protective antigens when trained using only the protein microarray datasets. The accuracy on the combined dataset is estimated at 76% by cross-validation experiments. Finally, ANTIGENpro performs well when evaluated on an external pathogen proteome for which protein microarray data were obtained after the initial development of ANTIGENpro. AVAILABILITY: ANTIGENpro is integrated in the SCRATCH suite of predictors available at http://scratch.proteomics.ics.uci.edu. CONTACT: [email protected]

At KDD-2009 in Paris, a panel on open standards and cloud computing addressed emerging trends for data mining applications in science and industry. This report summarizes the answers from a distinguished group of thought leaders representing key software vendors in the data mining industry.

Integration of visual sensing and motion planning can play a critical role in autonomous robot operation. We present a framework for vision-based robot motion planning that uses learning to handle arbitrarily configured cameras and robots. The theoretical basis of this approach is the concept of the perceptual control manifold (PCM) that extends the notion of the robot configuration space to include sensor space. This allows the inclusion of visual constraints in the motion planning. However, the analytical derivation of PCM is difficult in most cases and also depends on calibration of the camera. To overcome this modeling uncertainly, we propose the use of a topology representing network (TRN) to learn a suitable representation of the PCM. By exploiting the topology preserving features of the neural network, path planning strategies defined on the TRN lead to flexible obstacle avoidance. The practical feasibility of the approach is demonstrated by the results of simulation with a PUMA robot and experiments with a Mitsubishi robot.

Knowledge of the complex molecular structures of living cells is being accumulated at a tremendous rate. Key technologies enabling this success have been, high performance computing and powerful molecular graphics applications, but the technology is beginning to seriously lag behind challenges posed by the size and number of new structures and by the emerging opportunities in drug design and genetic engineering. A visual computing environment is being developed which permits interactive modeling of biopolymers by linking a 3D molecular graphics program with an efficient molecular dynamics simulation program executed on remote high-performance parallel computers. The system will be ideally suited for distributed computing environments, by utilizing both local 3D graphics facilities and the peak capacity of high-performance computers for the purpose of interactive biomolecular modeling. To create an interactive 3D environment three input methods will be explored: (1) a six degree of freedom "mouse" for controlling the space shared by the model and the user; (2) voice commands monitored through a microphone and recognized by a speech recognition interface; (3) hand gestures, detected through cameras and interpreted using computer vision techniques. Controlling 3D graphics connected to real time simulations and the use of voice with suitable language semantics, as well as hand gestures, promise great benefits for many types of problem solving environments. Our focus on structural biology takes advantage of existing sophisticated software, provides concrete objectives, defines a well-posed domain of tasks and offers a well-developed vocabulary for spoken communication.