Author Archives: Thijs van Ommen

Talk by Emiel Hoogeboom

You are all cordially invited to the AMLab seminar on Tuesday May 15 at 16:00 in C3.163, where Emiel Hoogeboom will give a talk titled “G-HexaConv”. Afterwards there are the usual drinks and snacks!

Abstract: The effectiveness of Convolutional Neural Networks stems in large part from their ability to exploit the translation invariance that is inherent in many learning problems. Recently, it was shown that CNNs can exploit other invariances, such as rotation invariance, by using group convolutions instead of planar convolutions. However, for reasons of performance and ease of implementation, it has been necessary to limit the group convolution to transformations that can be applied to the filters without interpolation. Thus, for images with square pixels, only integer translations, rotations by multiples of 90 degrees, and reflections are admissible.

Whereas the square tiling provides a 4-fold rotational symmetry, a hexagonal tiling of the plane has a 6-fold rotational symmetry. In this paper we show how one can efficiently implement planar convolution and group convolution over hexagonal lattices, by re-using existing highly optimized convolution routines. We find that, due to the reduced anisotropy of hexagonal filters, planar HexaConv provides better accuracy than planar convolution with square filters, given a fixed parameter budget. Furthermore, we find that the increased degree of symmetry of the hexagonal grid increases the effectiveness of group convolutions, by allowing for more parameter sharing. We show that our method significantly outperforms conventional CNNs on the AID aerial scene classification dataset, even outperforming ImageNet pre-trained models.

Talk by Zeynep Akata

You are all cordially invited to the AMLab seminar on Tuesday April 24 at 16:00 in C3.163, where Zeynep Akata will give a talk titled “Representing and Explaining Novel Concepts with Minimal Supervision”. Afterwards there are the usual drinks and snacks!

Abstract: Clearly explaining a rationale for a classification decision to an end-user can be as important as the decision itself. Existing approaches for deep visual recognition are generally opaque and do not output any justification text; contemporary vision-language models can describe image content but fail to take into account class-discriminative image aspects which justify visual predictions. In this talk, I will present my past and current work on Zero-Shot Learning, Vision and Language for Generative Modeling and Explainable Artificial Intelligence in that (1) how we can generalize the image classification models to the cases with no visual training data available, (2) how to generate images and image features using detailed visual descriptions, and (3) how our models focus on discriminating properties of the visible object, jointly predict a correct and an incorrect class label, and explain why the predicted correct label is appropriate for the image and why the predicted incorrect label is not appropriate for the image.

Talk by Tineke Blom

You are all cordially invited to the AMLab seminar on Tuesday April 17 at 16:00 in C3.163, where Tineke Blom will give a talk titled “Causal Modeling for Dynamical Systems using Generalized Structural Causal Models”. Afterwards there are the usual drinks and snacks!

Abstract: Structural causal models (SCMs) are a popular tool to describe causal relations in systems in many fields such as economy, the social sciences, and biology. Complex (cyclical) dynamical systems, such as chemical reaction networks, are often described by a set of ODEs. We show that SCMs are not flexible enough in general to give a complete causal representation of equilibrium states in these dynamical systems. Since such systems do form an important modeling class for real-world data, we extend the concept of an SCM to a generalized structural causal model. We show that this allows us to capture the essential causal semantics that characterize dynamical systems. We illustrate our approach on a basic enzymatic reaction.

Two talks: Avital Oliver and Petar Veličković

Next week Monday and Tuesday, the AMLab seminar will host two talks at FNWI, Amsterdam Science Park:

On Monday April 9 at 16:00 in room C1.112, Avital Oliver (Google Brain) will give a talk titled “Realistic Evaluation of Semi-Supervised Learning Algorithms“;

On Tuesday April 10 at 16:00 in room F1.02, Petar Veličković (University of Cambridge) will give a talk titled “Keeping our graphs attentive“.

Abstracts and bio’s are included below. Afterwards there will be the usual drinks and snacks. (Note that room F1.02 for Petar’s talk is a several minute walk away from the main entrance.)

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Talk by Karen Ullrich

You are all cordially invited to the AMLab seminar on Tuesday April 3 at 16:00 in C3.163, where Karen Ullrich will give a talk titled “Variational Bayes Wake-Sleep algorithm for expressive latent representations in 3D protein reconstruction”. Afterwards there are the usual drinks and snacks!

Abstract: Reconstructing three dimensional structures from noisy two dimensional orthographic projections is a central task in many scientific domains, examples range from medical tomography to single particle electron microscopy.
We treat this problem from a Bayesian point of view. Specifically, we regard a specimen’s structure and its pose as latent factors which are marginalized over. This allows us to express uncertainty in pose and even local uncertainty in the sample’s structure. This information can serve to detect unstable sub-structures or multiple configurations of a specimen. In particular, we apply amortized deep neural networks to encode observations into latent factors. This bears the advantage of transferability across multiple structures. To this end, we propose to train the model alternately in observation space and latent space, resulting in a generalized version of the wake-sleep algorithm.
We focus our experiments on cryogenic electron microscopy (CryoEM) single particle analysis, a technique that enables deep understanding of structural biology and chemistry by inspecting single proteins. We show our model to be competitive while predicting reasonable uncertainties. Moreover, we empirically demonstrate that the model is more data efficient than competitive methods and that it is transferable between molecules.

Talk by Wouter Kool

You are all cordially invited to the AMLab seminar on Tuesday March 27 at 16:00 in C3.163, where Wouter Kool will give a talk titled “Attention Solves Your TSP”. Afterwards there are the usual drinks and snacks!

Abstract: We propose a framework for solving combinatorial optimization problems of which the output can be represented as a sequence of input elements. As an alternative to the Pointer Network, we parameterize a policy by a model based entirely on (graph) attention layers, and train it efficiently using REINFORCE with a simple and robust baseline based on a deterministic (greedy) rollout of the best policy found during training. We significantly improve over state-of-the-art results for learning algorithms for the 2D Euclidean TSP, reducing the optimality gap for a single tour construction by more than 75% (to 0.33%) and 50% (to 2.28%) for instances with 20 and 50 nodes respectively.

Talk by Paul Baireuther

You are all cordially invited to the AMLab seminar on Tuesday March 20 at 16:00 in C3.163, where Paul Baireuther (Lorentz Institute of Leiden University) will give a talk titled “Quantum Error Correction with Recurrent Neural Networks”. Afterwards there are the usual drinks and snacks!

Abstract: In quantum computation one of the key challenges is to build fault-tolerant logical qubits. A logical qubit consists of several physical qubits. In stabilizer codes, a popular class of quantum error correction schemes, a part of the system of physical qubits is measured repeatedly, without measuring (and collapsing by the Born rule) the state of the encoded logical qubit. These repetitive measurements are called syndrome measurements, and must be interpreted by a classical decoder in order to determine what errors occurred on the underlying physical system. The decoding of these space- and time-correlated syndromes is a highly non-trivial task, and efficient decoding algorithms are known only for a few stabilizer codes. In this talk I will explain how we design and train decoders based on recurrent neural networks.

Talk by Max Welling

You are all cordially invited to the AMLab seminar on Tuesday March 13 at 16:00 in C3.163 (FNWI, Amsterdam Science Park), where prof. Max Welling will give a talk titled “Stochastic Deep Learning”. Afterwards there are the usual drinks and snacks.

Abstract: Deep learning has been very successful in many applications, but there are a number challenges that still need to be addressed:
1) DL does not provide reliable confidence intervals
2) DL is susceptible to small adversarial input perturbations
3) DL easily overfits
4) DL uses too much energy and memory
In this talk I will argue that we should be looking at stochastic DL models where the hidden units are noisy. We can train these models with variational methods.
A number of interesting connections emerge in such models:
1) The noisy hidden units form an information bottleneck
2) Through local reparameterization we can interpret these models as Bayesian
3) The noise can be used to create privacy preserving models
4) Stochastic quantization to low bit-width can make DL more power and memory efficient.
This talk will not go in great depth in these topics but rather paint the larger picture.

Talk by Thijs van Ommen

You are all cordially invited to the AMLab seminar on Tuesday March 6 at 16:00 in C3.163, where Thijs van Ommen will give a talk titled “Accurate and efficient causal discovery”. Afterwards there are the usual drinks and snacks!

Abstract: Will administering a certain chemical cause a cancer cell to stop multiplying? To answer this and other scientific “what-if” questions, we need causal models, which describe the cause-effect relations within a system of interest. Because even domain experts may not know the right causal model, we want to learn it automatically from large-scale data. This problem is called causal discovery, and is very difficult: the signals in the data that allow us to distinguish different causal models are often weak, so we need to be careful when interpreting them. Also, the number of candidate models that must be considered makes this problem computationally challenging. I will present some of my recent results which are an important step towards developing a statistically accurate and computationally efficient algorithm for causal discovery.

Talk by Bas Veeling

You are all cordially invited to the AMLab seminar on Tuesday February 20 at 16:00 in C3.163, where Bas Veeling will give a talk titled “Uncertainty in Deep Neural Networks with Stochastic Quantized Activation Variational Inference”. Afterwards there are the usual drinks and snacks!

Abstract: The successful uptake of deep neural networks in high-risk domains is contingent on the capability to ensure minimal-risk guarantees. This requires that deep neural networks provide predictive uncertainty of high quality. Amortized variational inference provides a promising direction to achieve this, but demands a flexible yet tractable approximative posterior, which is an open area of research. We propose “SQUAVI”, a novel and flexible variational inference model that imposes a multinomial distribution on quantized latent variables. The proposed method is scalable, self-normalizing and sample efficient, and we demonstrate that the model utilizes the flexible posterior to its full potential, learns interesting non-linearities, and provides predictive uncertainty of competitive quality.