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Register a new userTechnical Note on Transcription Factor Motif Discovery from Importance Scores (TF-MoDISco) version 0.5.6.5
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TF-MoDISco (Transcription Factor Motif Discovery from Importance Scores) is an algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data. This technical note focuses on version v0.5.6.5. The implementation is available at https://github.com/kundajelab/tfmodisco/tree/v0.5.6.5
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In this paper, we describe novel components for extracting clinically relevant information from medical conversations which will be available as Google APIs. We describe a transformer-based Recurrent Neural Network Transducer (RNN-T) model tailored for long-form audio, which can produce rich transcriptions including speaker segmentation, speaker role labeling, punctuation and capitalization. On a representative test set, we compare performance of RNN-T models with different encoders, units and streaming constraints. Our transformer-based streaming model performs at about 20% WER on the ASR task, 6% WDER on the diarization task, 43% SER on periods, 52% SER on commas, 43% SER on question marks and 30% SER on capitalization. Our recognizer is paired with a confidence model that utilizes both acoustic and lexical features from the recognizer. The model performs at about 0.37 NCE. Finally, we describe a RNN-T based tagging model. The performance of the model depends on the ontologies, with F-scores of 0.90 for medications, 0.76 for symptoms, 0.75 for conditions, 0.76 for diagnosis, and 0.61 for treatments. While there is still room for improvement, our results suggest that these models are sufficiently accurate for practical applications.
Random features provide a practical framework for large-scale kernel approximation and supervised learning. It has been shown that data-dependent sampling of random features using leverage scores can significantly reduce the number of features required to achieve optimal learning bounds. Leverage scores introduce an optimized distribution for features based on an infinite-dimensional integral operator (depending on input distribution), which is impractical to sample from. Focusing on empirical leverage scores in this paper, we establish an out-of-sample performance bound, revealing an interesting trade-off between the approximated kernel and the eigenvalue decay of another kernel in the domain of random features defined based on data distribution. Our experiments verify that the empirical algorithm consistently outperforms vanilla Monte Carlo sampling, and with a minor modification the method is even competitive to supervised data-dependent kernel learning, without using the output (label) information.
Membership Inference Attacks exploit the vulnerabilities of exposing models trained on customer data to queries by an adversary. In a recently proposed implementation of an auditing tool for measuring privacy leakage from sensitive datasets, more refined aggregates like the Log-Loss scores are exposed for simulating inference attacks as well as to assess the total privacy leakage based on the adversarys predictions. In this paper, we prove that this additional information enables the adversary to infer the membership of any number of datapoints with full accuracy in a single query, causing complete membership privacy breach. Our approach obviates any attack model training or access to side knowledge with the adversary. Moreover, our algorithms are agnostic to the model under attack and hence, enable perfect membership inference even for models that do not memorize or overfit. In particular, our observations provide insight into the extent of information leakage from statistical aggregates and how they can be exploited.
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 golden amino acids, 7 of their complements, and 6 non-complements) are observed now together with two further possible splittings into 4 x 5 and 5 x 4 amino acids.
The genomic profile underlying an individual tumor can be highly informative in the creation of a personalized cancer treatment strategy for a given patient; a practice known as precision oncology. This involves next generation sequencing of a tumor sample and the subsequent identification of genomic aberrations, such as somatic mutations, to provide potential candidates of targeted therapy. The identification of these aberrations from sequencing noise and germline variant background poses a classic classification-style problem. This has been previously broached with many different supervised machine learning methods, including deep-learning neural networks. However, these neural networks have thus far not been tailored to give any indication of confidence in the mutation call, meaning an oncologist could be targeting a mutation with a low probability of being true. To address this, we present here a deep bayesian recurrent neural network for cancer variant calling, which shows no degradation in performance compared to standard neural networks. This approach enables greater flexibility through different priors to avoid overfitting to a single dataset. We will be incorporating this approach into software for oncologists to obtain safe, robust, and statistically confident somatic mutation calls for precision oncology treatment choices.
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