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Gene Transformer: Transformers for the Gene Expression-based Classification of Cancer Subtypes

arXiv.org Artificial Intelligence

Abstract--Adenocarcinoma and squamous cell carcinoma constitute approximately 40% and 30% of all lung cancer subtypes, respectively, and display broad heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled precision medicine to overcome these challenges and provide significant biological insights to predict prognosis and improve clinical decision making. Over the past decade, conventional machine learning algorithms and DL-based CNNs have been espoused for the classification of cancer subtypes from gene expression datasets. However, these methods are potentially biased toward identification of cancer biomarkers. Recently proposed transformer-based architectures that leverage the self-attention mechanism can encode high throughput gene expressions and learn representations that are computationally complex and parametrically expensive. However, compared to the datasets for natural language processing applications, gene expression consists of several hundreds of thousands of genes from a limited number of observations, making it difficult to efficiently train transformers for bioinformatics applications. Hence, we propose an end-to-end deep learning approach, Gene Transformer, which addresses the complexity of high-dimensional gene expression with a multi-head self-attention module by identifying relevant biomarkers across multiple cancer subtypes without requiring feature selection as a prerequisite for the current classification algorithms. The proposed architecture achieved an overall improved performance for all evaluation metrics and had fewer misclassification errors than the commonly used traditional classification algorithms. The classification results show that Gene Transformer can be an efficient approach for classifying cancer subtypes, indicating that any improvement in deep learning models in computational biology can also be reflected well in this domain. I. Introduction enes, a unit of inheritance, are responsible for storing genetic information in all living organisms, and their expression in a Therefore, any type of gene mutation, single or multiple, can lead to a dysregulation in gene expression, which is broadly termed, genetic disorder.


Artificial Intelligence: The Next Generation Anti-Corruption Technology

#artificialintelligence

Artificial Intelligence (AI) can be a useful weapon in the fight against corruption. Its capacity to handle huge data is unrivaled, as is its ability to spot abnormalities or trends, such as in financial transaction data. Some of the ways AI is used in society have skeptics, who fear a society that is more monitored, putting privacy and individual freedom in danger. Let's get into the topic in more detail. Artificial intelligence (AI) refers to technologies that allow machines to simulate human intelligence in order to tackle complicated issues.


Ai Palette raises $4.4M to help companies react faster to consumer trends โ€“ TechCrunch

#artificialintelligence

Developing new packaged foods and consumer goods can take a couple years as companies research, prototype and test products. In a society that runs on social media, however, people expect to see trends land on store shelves much more quickly. Founded in 2018, Ai Palette uses machine learning to help companies spot trends in real time and get them retail-ready, often within a few months. The startup, whose clients include Danone, Kellogg's, Cargill and Dole, announced today it has raised an oversubscribed $4.4 million Series A co-led by pi Ventures and Exfinity Venture Partners. Both will join Ai Palette's board.


Multi-task learning from fixed-wing UAV images for 2D/3D city modeling

arXiv.org Artificial Intelligence

Single-task learning in artificial neural networks will be able to learn the model very well, and the benefits brought by transferring knowledge thus become limited. In this regard, when the number of tasks increases (e.g., semantic segmentation, panoptic segmentation, monocular depth estimation, and 3D point cloud), duplicate information may exist across tasks, and the improvement becomes less significant. Multi-task learning has emerged as a solution to knowledge-transfer issues and is an approach to scene understanding which involves multiple related tasks each with potentially limited training data. Multi-task learning improves generalization by leveraging the domain-specific information contained in the training data of related tasks. In urban management applications such as infrastructure development, traffic monitoring, smart 3D cities, and change detection, automated multi-task data analysis for scene understanding based on the semantic, instance, and panoptic annotation, as well as monocular depth estimation, is required to generate precise urban models. In this study, a common framework for the performance assessment of multi-task learning methods from fixed-wing UAV images for 2D/3D city modeling is presented.


From Statistical Relational to Neural Symbolic Artificial Intelligence: a Survey

arXiv.org Artificial Intelligence

The integration of learning and reasoning is one of the key challenges in artificial intelligence and machine learning today, and various communities have been addressing it. That is especially true for the field of neural-symbolic computation (NeSy) [10, 21], where the goal is to integrate symbolic reasoning and neural networks. NeSy already has a long tradition, and it has recently attracted a lot of attention from various communities (cf. the keynotes of Y. Bengio and H. Kautz on this topic at AAAI 2020, the AI Debate [9] between Y. Bengio and G. Marcus). Another domain that has a rich tradition in integrating learning and reasoning is that of statistical relational learning and artificial intelligence (StarAI) [39, 85]. But rather than focusing on integrating logic and neural networks, it is centred around the question of integrating logic with probabilistic reasoning, more specifically probabilistic graphical models. Despite the common interest in combining symbolic reasoning with a basic paradigm for learning, i.e., probabilistic graphical models or neural networks, it is surprising that there are not more interactions between these two fields.


Subgoal Search For Complex Reasoning Tasks

arXiv.org Artificial Intelligence

Humans excel in solving complex reasoning tasks through a mental process of moving from one idea to a related one. Inspired by this, we propose Subgoal Search (kSubS) method. Its key component is a learned subgoal generator that produces a diversity of subgoals that are both achievable and closer to the solution. Using subgoals reduces the search space and induces a high-level search graph suitable for efficient planning. In this paper, we implement kSubS using a transformer-based subgoal module coupled with the classical best-first search framework. We show that a simple approach of generating $k$-th step ahead subgoals is surprisingly efficient on three challenging domains: two popular puzzle games, Sokoban and the Rubik's Cube, and an inequality proving benchmark INT. kSubS achieves strong results including state-of-the-art on INT within a modest computational budget.


A "far out" take on transportation planning

MIT Technology Review

As a boy, Eric Plosky '99, MCP '00, rode the New York subway with his grandmother to every city attraction on the map. "Whenever anyone asks me how I got into transportation, I always ask them, 'How did you get out of it?'" he says. "Every little kid seems to love trains and subways and buses and cars and planes, and for some reason they'grow out of it.' Now, as chief of transportation planning at the Volpe National Transportation Systems Center in Kendall Square, Plosky and his team put their imaginations to work reenvisioning what transportation can be. It's people, it's decision-making, it's history and culture," he says.


Can Explainable AI be Automated?

#artificialintelligence

I recently fell in love with Explainable AI (XAI). XAI is a set of methods aimed at making increasingly complex machine learning (ML) models understandable by humans. XAI could help bridge the gap between AI and humans. That is very much needed as the gap is widening. Machine learning is proving incredibly successful in tackling problems from cancer diagnostics to fraud detection.


The Impact of Artificial - Issuu

#artificialintelligence

Africa has a knack for inventing and reinvigorating old technologies. To some degree, Africa has managed to sidestep this AI revolution and maintain its traditional way of life. That's because in Africa, artificial intelligence isn't really a thing yet - there are no driverless busses or pizza delivery robots that speak your local languages. Many discussions about the future of artificial intelligence in Africa, as well as why and how African countries have been slow to embrace this new technology trend have been had, so how do we move from these Conversations to implementation? The fact that Africa is so behind in artificial intelligence is a matter of concern - what are the effects of this new technology on African countries?


Drones Are Now Top Threat In Syria: US Air Force Shoots Down Iranian Drone

International Business Times

A U.S.-led coalition aircraft shot down an unmanned drone in Eastern Syria's Deir al-Zour province Saturday, months after the U.S. Central Command expressed concern over the use of weaponized drones to attack U.S. forces in the region. "Coalition aircraft successfully engaged and defeated a UAS through air to air engagement in the vicinity of Mission Support Site Green Village," Reuters quoted coalition spokesperson U.S. Army Colonel Wayne Marotto. While the coalition refused to reveal the type of aircraft used or other details citing security issues, a report by Aviation Week said a U.S. Air Force F-15E Strike Eagle used an AIM-9X Sidewinder missile to hit the UAS. The report added that Brig. Gen. Christopher Sage, commander of the 332nd Air Expeditionary Wing, was piloting the F-15E that fired the missile.