arXiv subjects

Hamid Eghbal-zadeh

Publications and source records attributed to Hamid Eghbal-zadeh.

23 records · Page 2Linked to original sources

arXiv2018

Deep SNP: An End-to-end Deep Neural Network with Attention-based Localization for Break-point Detection in SNP Array Genomic data

Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming manual curation. As deep-learning methods outperformed classical state-of-the-art algorithms in various domains and have also been successfully applied to life science problems including medicine and biology, we here propose Deep SNP, a novel Deep Neural Network to learn from genomic data. Specifically, we used a manually curated dataset from 12 genomic single nucleotide polymorphism array (SNPa) profiles as truth-set and aimed at predicting the presence or absence of genomic breakpoints, an indicator of structural chromosomal variations, in windows of 40,000 probes. We compare our results with well-known neural network models as well as Rawcopy though this tool is designed to predict breakpoints and in addition genomic segments with high sensitivity. We show, that Deep SNP is capable of successfully predicting the presence or absence of a breakpoint in large genomic windows and outperforms state-of-the-art neural network models. Qualitative examples suggest that integration of a localization unit may enable breakpoint detection and prediction of genomic segments, even if the breakpoint coordinates were not provided for network training. These results warrant further evaluation of DeepSNP for breakpoint localization and subsequent calling of genomic segments.

q-bio.GN↗

arXiv2017

Music Playlist Continuation by Learning from Hand-Curated Examples and Song Features: Alleviating the Cold-Start Problem for Rare and Out-of-Set Songs

Automated music playlist generation is a specific form of music recommendation. Generally stated, the user receives a set of song suggestions defining a coherent listening session. We hypothesize that the best way to convey such playlist coherence to new recommendations is by learning it from actual curated examples, in contrast to imposing ad hoc constraints. Collaborative filtering methods can be used to capture underlying patterns in hand-curated playlists. However, the scarcity of thoroughly curated playlists and the bias towards popular songs result in the vast majority of songs occurring in very few playlists and thus being poorly recommended. To overcome this issue, we propose an alternative model based on a song-to-playlist classifier, which learns the underlying structure from actual playlists while leveraging song features derived from audio, social tags and independent listening logs. Experiments on two datasets of hand-curated playlists show competitive performance compared to collaborative filtering when sufficient training data is available and more robust performance when recommending rare and out-of-set songs. For example, both approaches achieve a recall@100 of roughly 35% for songs occurring in 5 or more training playists, whereas the proposed model achieves a recall@100 of roughly 15% for songs occurring in 4 or less training playlists, compared to the 3% achieved by collaborative filtering.

cs.IR↗

arXiv2017

Probabilistic Generative Adversarial Networks

We introduce the Probabilistic Generative Adversarial Network (PGAN), a new GAN variant based on a new kind of objective function. The central idea is to integrate a probabilistic model (a Gaussian Mixture Model, in our case) into the GAN framework which supports a new kind of loss function (based on likelihood rather than classification loss), and at the same time gives a meaningful measure of the quality of the outputs generated by the network. Experiments with MNIST show that the model learns to generate realistic images, and at the same time computes likelihoods that are correlated with the quality of the generated images. We show that PGAN is better able to cope with instability problems that are usually observed in the GAN training procedure. We investigate this from three aspects: the probability landscape of the discriminator, gradients of the generator, and the perfect discriminator problem.

cs.LG↗

arXiv2017

Likelihood Estimation for Generative Adversarial Networks

We present a simple method for assessing the quality of generated images in Generative Adversarial Networks (GANs). The method can be applied in any kind of GAN without interfering with the learning procedure or affecting the learning objective. The central idea is to define a likelihood function that correlates with the quality of the generated images. In particular, we derive a Gaussian likelihood function from the distribution of the embeddings (hidden activations) of the real images in the discriminator, and based on this, define two simple measures of how likely it is that the embeddings of generated images are from the distribution of the embeddings of the real images. This yields a simple measure of fitness for generated images, for all varieties of GANs. Empirical results on CIFAR-10 demonstrate a strong correlation between the proposed measures and the perceived quality of the generated images.

cs.LG↗

arXiv2017

A Hybrid Approach with Multi-channel I-Vectors and Convolutional Neural Networks for Acoustic Scene Classification

In Acoustic Scene Classification (ASC) two major approaches have been followed . While one utilizes engineered features such as mel-frequency-cepstral-coefficients (MFCCs), the other uses learned features that are the outcome of an optimization algorithm. I-vectors are the result of a modeling technique that usually takes engineered features as input. It has been shown that standard MFCCs extracted from monaural audio signals lead to i-vectors that exhibit poor performance, especially on indoor acoustic scenes. At the same time, Convolutional Neural Networks (CNNs) are well known for their ability to learn features by optimizing their filters. They have been applied on ASC and have shown promising results. In this paper, we first propose a novel multi-channel i-vector extraction and scoring scheme for ASC, improving their performance on indoor and outdoor scenes. Second, we propose a CNN architecture that achieves promising ASC results. Further, we show that i-vectors and CNNs capture complementary information from acoustic scenes. Finally, we propose a hybrid system for ASC using multi-channel i-vectors and CNNs by utilizing a score fusion technique. Using our method, we participated in the ASC task of the DCASE-2016 challenge. Our hybrid approach achieved 1 st rank among 49 submissions, substantially improving the previous state of the art.

cs.SD↗