Publishes on Reinforcement Learning in Robotics, Domain Adaptation and Few-Shot Learning, Machine Learning and Data Classification. 43 papers and 33.8k citations.
Generative adversarial networks are a kind of artificial intelligence algorithm designed to solve the generative modeling problem. The goal of a generative model is to study a collection of training examples and learn the probability distribution that generated them. Generative Adversarial Networks (GANs) are then able to generate more examples from the estimated probability distribution. Generative models based on deep learning are common, but GANs are among the most successful generative models (especially in terms of their ability to generate realistic high-resolution images). GANs have been successfully applied to a wide variety of tasks (mostly in research settings) but continue to present unique challenges and research opportunities because they are based on game theory while most other approaches to generative modeling are based on optimization.
GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist.
Large Language Models (LLMS) rely on Key-Value (KV) caches to store attention context during autoregressive decoding. In long-sequence settings, the KV cache can consume large amounts of VRAM and become a practical bottleneck for throughput . We introduce KVHALO, an auxiliary reconstruction model that restores higher-fidelity KV tensors from a compressed cache state when required, reducing persistent memory footprint during inference. In our evaluation, KVHALO achieves up to 91.85% directional cosine alignment at convergence and reduces long-context degradation relative to a low-bit baseline under our stress-test workloads. We used HRM instead of other architectures, which allowed for higher-quality results in only 18,600 steps.
BACKGROUND: Most successful computational approaches for protein function prediction integrate multiple genomics and proteomics data sources to make inferences about the function of unknown proteins. The most accurate of these algorithms have long running times, making them unsuitable for real-time protein function prediction in large genomes. As a result, the predictions of these algorithms are stored in static databases that can easily become outdated. We propose a new algorithm, GeneMANIA, that is as accurate as the leading methods, while capable of predicting protein function in real-time. RESULTS: We use a fast heuristic algorithm, derived from ridge regression, to integrate multiple functional association networks and predict gene function from a single process-specific network using label propagation. Our algorithm is efficient enough to be deployed on a modern webserver and is as accurate as, or more so than, the leading methods on the MouseFunc I benchmark and a new yeast function prediction benchmark; it is robust to redundant and irrelevant data and requires, on average, less than ten seconds of computation time on tasks from these benchmarks. CONCLUSION: GeneMANIA is fast enough to predict gene function on-the-fly while achieving state-of-the-art accuracy. A prototype version of a GeneMANIA-based webserver is available at http://morrislab.med.utoronto.ca/prototype.