Twisting adjoint module algebras

Transformation of operator algebras under Hopf algebra twist is studied. It is shown that that adjoint module algebras are stable under the twist. Applications to vector fields on non-commutative space-time are considered.Comment: 16 page

SubTuning: Efficient Finetuning for Multi-Task Learning

Finetuning a pretrained model has become a standard approach for training neural networks on novel tasks, resulting in fast convergence and improved performance. In this work, we study an alternative finetuning method, where instead of finetuning all the weights of the network, we only train a carefully chosen subset of layers, keeping the rest of the weights frozen at their initial (pretrained) values. We demonstrate that \emph{subset finetuning} (or SubTuning) often achieves accuracy comparable to full finetuning of the model, and even surpasses the performance of full finetuning when training data is scarce. Therefore, SubTuning allows deploying new tasks at minimal computational cost, while enjoying the benefits of finetuning the entire model. This yields a simple and effective method for multi-task learning, where different tasks do not interfere with one another, and yet share most of the resources at inference time. We demonstrate the efficiency of SubTuning across multiple tasks, using different network architectures and pretraining methods

Computational analysis of gene expression space associated with metastatic cancer

<p>Abstract</p> <p>Background</p> <p>Prostate carcinoma is among the most common types of cancer affecting hundreds of thousands people every year. Once the metastatic form of prostate carcinoma is documented, the majority of patients die from their tumors as opposed to other causes. The key to successful treatment is in the earliest possible diagnosis, as well as understanding the molecular mechanisms of metastatic progression. A number of recent studies have identified multiple biomarkers for metastatic progression. However, most of the studies consider only direct comparison between metastatic and non-metastatic classes of samples.</p> <p>Results</p> <p>We propose an alternative concept of analysis that considers the entire multidimensional space of gene expression and identifies the partition of this space in which metastatic development is possible. To apply this concept in cancer gene expression studies we utilize a modification of high-dimension natural taxonomy algorithm FOREL. Our analysis of microarray data containing primary and metastatic cancer samples has revealed not only differentially expressed genes, but also relations between different groups of primary and metastatic cancer. Metastatic samples tend to occupy a distinct partition of gene expression space. Further pathway analysis suggests that this partition is delineated by a specific pattern of gene expression in cytoskeleton remodeling, cell adhesion and apoptosis/cell survival pathways. We compare our findings with both report of original analysis and recent studies in molecular mechanism of metastasis.</p> <p>Conclusion</p> <p>Our analysis indicates a single molecular mechanism of metastasis. The new approach does not contradict previously reported findings, but reveals important details unattainable with traditional methodology.</p

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe