Amir Joudaki,

"happy to be proven wrong"

PhD Student

E-Mail
amir.joudaki@get-your-addresses-elsewhere.inf.ethz.ch
Phone
+41 44 632 65 24
Address
ETH Zürich
Department of Computer Science
Biomedical Informatics Group Universitätsstrasse 6
CAB F52.1
8092 Zürich
Room
CAB F39

I am currently a direct PhD student in biomedical informatics (BMI) group led by Prof. Gunnar Ratsch, working in theoretical machine learning and algorithm design for bio-medicine.

My lifelong passion is to work on the biggest challenges facing us with leveraging recent scientific and technical advances in computer science. I am lucky to be a member of the BMI group, where I can work on a wide range of problems that arise in machine learning for biomedical applications. In particular, I am highly interested in the theoretical understanding of deep neural networks, which could lead to more robust models for the pharmaceutical and medical industries. I also work on designing more scalable genomics and medical methods, using techniques from high-dimensional statistics and randomized algorithms, which will be essential for their adoption beyond academic fields. 

Before joining BMI, I did a BSc in computer engineering at Sharif University, Iran, an MPhil in cognitive neuroscience in SISSA, Italy, and an MSc in computer scienc eat ETH Zurich as part of the direct Ph.D program. During these studies I took theoretical and hands-on topics that are invaluable to my research.

Abstract This paper underlines an elegant property of batch-normalization (BN): Successive batch normalizations with random linear updates make samples increasingly orthogonal. We establish a non-asymptotic characterization of the interplay between depth, width, and the orthogonality of deep representations. More precisely, we prove, under a mild assumption, the deviation of the representations from orthogonality rapidly decays with depth up to a term inversely proportional to the network width. This result has two main theoretical and practical implications: 1) Theoretically, as the depth grows, the distribution of the outputs contracts to a Wasserstein-2 ball around an isotropic normal distribution. Furthermore, the radius of this Wasserstein ball shrinks with the width of the network. 2) Practically, the orthogonality of the representations directly influences the performance of stochastic gradient descent (SGD). When representations are initially aligned, we observe SGD wastes many iterations to disentangle representations before the classification. Nevertheless, we experimentally show that starting optimization from orthogonal representations is sufficient to accelerate SGD, with no need for BN.

Authors Hadi Daneshmand, Amir Joudaki, Francis Bach

Submitted NeurIPS 2021 (Spotlight)

Link

Abstract To understand the essential role of depth in neural networks, we investigate a variational principle for depth: Does increasing depth perform an implicit optimization for the representations in neural networks? We prove that random neural networks equipped with batch normalization maximize the differential entropy of representations with depth up to constant factors, assuming that the representations are contractive. Thus, representations inherently obey the \textit{principle of maximum entropy} at initialization, in the absence of information about the learning task. Our variational formulation for neural representations characterizes the interplay between representation entropy and architectural components, including depth, width, and non-linear activations, thereby potentially inspiring the design of neural architectures.

Authors Amir Joudaki, Hadi Daneshmand, Francis Bach

Submitted arXiv preprint

Link

Abstract This paper underlines an elegant property of batch-normalization (BN): Successive batch normalizations with random linear updates make samples increasingly orthogonal. We establish a non-asymptotic characterization of the interplay between depth, width, and the orthogonality of deep representations. More precisely, we prove, under a mild assumption, the deviation of the representations from orthogonality rapidly decays with depth up to a term inversely proportional to the network width. This result has two main theoretical and practical implications: 1) Theoretically, as the depth grows, the distribution of the outputs contracts to a Wasserstein-2 ball around an isotropic normal distribution. Furthermore, the radius of this Wasserstein ball shrinks with the width of the network. 2) Practically, the orthogonality of the representations directly influences the performance of stochastic gradient descent (SGD). When representations are initially aligned, we observe SGD wastes many iterations to disentangle representations before the classification. Nevertheless, we experimentally show that starting optimization from orthogonal representations is sufficient to accelerate SGD, with no need for BN.

Authors Hadi Daneshmand, Amir Joudaki, Francis Bach

Submitted NeurIPS 2021 (Spotlight)

Link

Abstract The sharp increase in next-generation sequencing technologies’ capacity has created a demand for algorithms capable of quickly searching a large corpus of biological sequences. The complexity of biological variability and the magnitude of existing data sets have impeded finding algorithms with guaranteed accuracy that efficiently run in practice. Our main contribution is the Tensor Sketch method that efficiently and accurately estimates edit distances. In our experiments, Tensor Sketch had 0.88 Spearman’s rank correlation with the exact edit distance, almost doubling the 0.466 correlation of the closest competitor while running 8.8 times faster. Finally, all sketches can be updated dynamically if the input is a sequence stream, making it appealing for large-scale applications where data cannot fit into memory. Conceptually, our approach has three steps: 1) represent sequences as tensors over their sub-sequences, 2) apply tensor sketching that preserves tensor inner products, 3) implicitly compute the sketch. The sub-sequences, which are not necessarily contiguous pieces of the sequence, allow us to outperform fc-mer-based methods, such as min-hash sketching over a set of k-mers. Typically, the number of sub-sequences grows exponentially with the sub-sequence length, introducing both memory and time overheads. We directly address this problem in steps 2 and 3 of our method. While the sketching of rank-1 or super-symmetric tensors is known to admit efficient sketching, the sub-sequence tensor does not satisfy either of these properties. Hence, we propose a new sketching scheme that completely avoids the need for constructing the ambient space. Our tensor-sketching technique’s main advantages are three-fold: 1) Tensor Sketch has higher accuracy than any of the other assessed sketching methods used in practice. 2) All sketches can be computed in a streaming fashion, leading to significant time and memory savings when there is overlap between input sequences. 3) It is straightforward to extend tensor sketching to different settings leading to efficient methods for related sequence analysis tasks. We view tensor sketching as a framework to tackle a wide range of relevant bioinformatics problems, and we are confident that it can bring significant improvements for applications based on edit distance estimation.

Authors Amir Joudaki, Gunnar Rätsch, André Kahles

Submitted RECOMB 2021

Link

Abstract High-throughput DNA sequencing data are accumulating in public repositories, and efficient approaches for storing and indexing such data are in high demand. In recent research, several graph data structures have been proposed to represent large sets of sequencing data and to allow for efficient querying of sequences. In particular, the concept of labeled de Bruijn graphs has been explored by several groups. Although there has been good progress toward representing the sequence graph in small space, methods for storing a set of labels on top of such graphs are still not sufficiently explored. It is also currently not clear how characteristics of the input data, such as the sparsity and correlations of labels, can help to inform the choice of method to compress the graph labeling. In this study, we present a new compression approach, Multi-binary relation wavelet tree (BRWT), which is adaptive to different kinds of input data. We show an up to 29% improvement in compression performance over the basic BRWT method, and up to a 68% improvement over the current state-of-the-art for de Bruijn graph label compression. To put our results into perspective, we present a systematic analysis of five different state-of-the-art annotation compression schemes, evaluate key metrics on both artificial and real-world data, and discuss how different data characteristics influence the compression performance. We show that the improvements of our new method can be robustly reproduced for different representative real-world data sets.

Authors Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles

Submitted Journal of Computational Biology

Link DOI

Abstract High-throughput DNA sequencing data is accumulating in public repositories, and efficient approaches for storing and indexing such data are in high demand. In recent research, several graph data structures have been proposed to represent large sets of sequencing data and to allow for efficient querying of sequences. In particular, the concept of labeled de Bruijn graphs has been explored by several groups. While there has been good progress towards representing the sequence graph in small space, methods for storing a set of labels on top of such graphs are still not sufficiently explored. It is also currently not clear how characteristics of the input data, such as the sparsity and correlations of labels, can help to inform the choice of method to compress the graph labeling. In this work, we present a new compression approach, Multi-BRWT, which is adaptive to different kinds of input data. We show an up to 29% improvement in compression performance over the basic BRWT method, and up to a 68% improvement over the current state-of-the-art for de Bruijn graph label compression. To put our results into perspective, we present a systematic analysis of five different state-of-the-art annotation compression schemes, evaluate key metrics on both artificial and real-world data and discuss how different data characteristics influence the compression performance. We show that the improvements of our new method can be robustly reproduced for different representative real-world datasets.

Authors Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, Andre Kahles

Submitted RECOMB 2019

Link DOI