The Bible of AI

r0:e8a2060e33594781594577f87d876bb1

Advancing regulatory variant effect prediction with AlphaGenome

Deep learning models that predict functional genomic measurements from DNA sequences are powerful tools for deciphering the genetic regulatory code. Existing methods involve a trade-off between input sequence length and prediction resolution, thereby limiting their modality scope and performance1,2,3,4,5. We present AlphaGenome, a unified DNA sequence model, which takes as input 1 Mb of DNA sequence and predicts thousands of functional genomic tracks up to single-base-pair resolution across diverse modalities. The modalities include gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chromatin contact maps, splice site usage and splice junction coordinates and strength. Trained on human and mouse genomes, AlphaGenome matches or exceeds the strongest available external models in 25 of 26 evaluations of variant effect prediction. The ability of AlphaGenome to simultaneously score variant effects across all modalities accurately recapitulates the mechanisms of clinically relevant variants near the TAL1 oncogene6. To facilitate broader use, we provide tools for making genome track and variant effect predictions from sequence.

When AI sounds certain but should say “I do not know”

Juan Antonio Lloret DOI: https://doi.org/10.21428/39829d0b.6b61c462 In an internal review that later became public, IBM’s Watson for Oncology was shown a patient much like thousands treated every day: a 65-year-old man with lung cancer who was also suffering from severe bleeding. The system recommended bevacizumab — a drug that carries an explicit warning against use in …

When AI sounds certain but should say “I do not know” Leer más »

Sequence Feature Extraction for Malware Family Analysis via Graph Neural Network

Sequence Feature Extraction for Malware Family Analysis via Graph Neural Network

Malicious software (malware) causes much harm to our devices and life. We are eager to understand the malware behavior and the threat it made. Most of the record files of malware are variable length and text-based files with time stamps, such as event log data and dynamic analysis profiles. Using the time stamps, we can sort such data into sequence-based data for the following analysis. However, dealing with the text-based sequences with variable lengths is difficult. In addition, unlike natural language text data, most sequential data in information security have specific properties and structure, such as loop, repeated call, noise, etc. To deeply analyze the API call sequences with their structure, we use graphs to represent the sequences, which can further investigate the information and structure, such as the Markov model. Therefore, we design and implement an Attention Aware Graph Neural Network (AWGCN) to analyze the API call sequences. Through AWGCN, we can obtain the sequence embeddings to analyze the behavior of the malware. Moreover, the classification experiment result shows that AWGCN outperforms other classifiers in the call-like datasets, and the embedding can further improve the classic model’s performance.

r0:e605066113bd05bcb2ad6161c651d958- Auto Quantum Circuits

Auto Quantum Circuits

«AutoQML, self-assembling circuits, hyper-parameterized Quantum ML platform, using cirq, tensorflow and tfq. Trillions of possible qubit registries, gate combinations and moment sequences, ready to be adapted into your ML flow. Here I demonstrate climatechange, jameswebbspacetelescope and microbiology vision applications… [Thus far, a circuit with 16-Qubits and a gate sequence of [ YY ] – [ XX ] – [CNOT] has performed the best, per my blend of metrics…].

R0:507c2e7fe07ef9a317eb4c7a51869fdc-Federated Learning: Issues in Medical Application

Federated Learning: Issues in Medical Application

In this presentation, the current issues to make federated learning flawlessly useful in the real world will be briefly overviewed. They are related to data/system heterogeneity, client management, traceability, and security. Also, we introduce the modularized federated learning framework, we currently develop, to experiment various techniques and protocols to find solutions for aforementioned issues. The framework will be open to public after development completes.

R0:c4c3ffc882452ee50fea21d2c6b1486a-CNN Explainer: Learning Convolutional Neural Networks with Interactive Visualization

CNN Explainer: Learning Convolutional Neural Networks with Interactive Visualization

CNN Explainer tightly integrates a model overview that summarizes a CNN’s structure, and on-demand, dynamic visual explanation views that help users understand the underlying components of CNNs. Through smooth transitions across levels of abstraction, our tool enables users to inspect the interplay between low-level mathematical operations and high-level model structures.

R0:884a5f6297216a3c5e883ae639b13721-Between words and characters: A Brief History of Open-Vocabulary Modeling and Tokenization in NLP

Between words and characters: A Brief History of Open-Vocabulary Modeling and Tokenization in NLP

In this survey, we connect several lines of work from the pre-neural and neural era, by showing how hybrid approaches of words and characters as well as subword-based approaches based on learned segmentation have been proposed and evaluated. We conclude that there is and likely will never be a silver bullet singular solution for all applications and that thinking seriously about tokenization remains important for many applications

R0:7194c033807f71949262faf563aef58e-Scientific Visualization: Python + Matplotlib

Scientific Visualization: Python + Matplotlib

The Python scientific visualisation landscape is huge. It is composed of a myriad of tools, ranging from the most versatile and widely used down to the more specialised and confidential. Some of these tools are community based while others are developed by companies. Some are made specifically for the web, others are for the desktop only, some deal with 3D and large data, while others target flawless 2D rendering.

R0:62a6aa3b4882ad9b194a4ae5c97b4d58-Ethics-based auditing of automated decision-making systems: intervention points and policy implications

Ethics-based auditing of automated decision-making systems: intervention points and policy implications

Organisations increasingly use automated decision-making systems (ADMS) to inform decisions that affect humans and their environment. While the use of ADMS can improve the accuracy and efficiency of decision-making processes, it is also coupled with ethical challenges. Unfortunately, the governance mechanisms currently used to oversee human decision-making often fail when applied to ADMS.