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Vlado Menkovski

Publications and source records attributed to Vlado Menkovski.

At least 37 records · Page 2Linked to original sources
arXiv2024

Equivariant Neural Simulators for Stochastic Spatiotemporal Dynamics

Neural networks are emerging as a tool for scalable data-driven simulation of high-dimensional dynamical systems, especially in settings where numerical methods are infeasible or computationally expensive. Notably, it has been shown that incorporating domain symmetries in deterministic neural simulators can substantially improve their accuracy, sample efficiency, and parameter efficiency. However, to incorporate symmetries in probabilistic neural simulators that can simulate stochastic phenomena, we need a model that produces equivariant distributions over trajectories, rather than equivariant function approximations. In this paper, we propose Equivariant Probabilistic Neural Simulation (EPNS), a framework for autoregressive probabilistic modeling of equivariant distributions over system evolutions. We use EPNS to design models for a stochastic n-body system and stochastic cellular dynamics. Our results show that EPNS considerably outperforms existing neural network-based methods for probabilistic simulation. More specifically, we demonstrate that incorporating equivariance in EPNS improves simulation quality, data efficiency, rollout stability, and uncertainty quantification. We conclude that EPNS is a promising method for efficient and effective data-driven probabilistic simulation in a diverse range of domains.

cs.LG↗
arXiv2024

Topological degree as a discrete diagnostic for disentanglement, with applications to the $Δ$VAE

We investigate the ability of Diffusion Variational Autoencoder ($Δ$VAE) with unit sphere $\mathcal{S}^2$ as latent space to capture topological and geometrical structure and disentangle latent factors in datasets. For this, we introduce a new diagnostic of disentanglement: namely the topological degree of the encoder, which is a map from the data manifold to the latent space. By using tools from homology theory, we derive and implement an algorithm that computes this degree. We use the algorithm to compute the degree of the encoder of models that result from the training procedure. Our experimental results show that the $Δ$VAE achieves relatively small LSBD scores, and that regardless of the degree after initialization, the degree of the encoder after training becomes $-1$ or $+1$, which implies that the resulting encoder is at least homotopic to a homeomorphism.

cs.LG↗
arXiv2024

Accelerating Simulation of Two-Phase Flows with Neural PDE Surrogates

Simulation is a powerful tool to better understand physical systems, but generally requires computationally expensive numerical methods. Downstream applications of such simulations can become computationally infeasible if they require many forward solves, for example in the case of inverse design with many degrees of freedom. In this work, we investigate and extend neural PDE solvers as a tool to aid in scaling simulations for two-phase flow problems, and simulations of oil expulsion from a pore specifically. We extend existing numerical methods for this problem to a more complex setting involving varying geometries of the domain to generate a challenging dataset. Further, we investigate three prominent neural PDE solver methods, namely the UNet, DRN, and U-FNO, and extend them for characteristics of the oil-expulsion problem: (1) spatial conditioning on the geometry; (2) periodicity in the boundary; (3) approximate mass conservation. We scale all methods and benchmark their speed-accuracy trade-off, evaluate qualitative properties, and perform an ablation study. We find that the investigated methods can accurately model the droplet dynamics with up to three orders of magnitude speed-up, that our extensions improve performance over the baselines, and that the introduced varying geometries constitute a significantly more challenging setting over the previously considered oil expulsion problem.

cs.LG↗
arXiv2024

VADA: a Data-Driven Simulator for Nanopore Sequencing

Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of obtaining ground truth datasets, there is a need for nanopore simulators. Existing simulators rely on handcrafted rules and parameters and do not learn an internal representation that would allow for analysing underlying biological factors of interest. Instead, we propose VADA, a purely data-driven method for simulating nanopores based on an autoregressive latent variable model. We embed subsequences of DNA and introduce a conditional prior to address the challenge of a collapsing conditioning. We introduce an auxiliary regressor on the latent variable to encourage our model to learn an informative latent representation. We empirically demonstrate that our model achieves competitive simulation performance on experimental nanopore data. Moreover, we show we have learned an informative latent representation that is predictive of the DNA labels. We hypothesize that other biological factors of interest, beyond the DNA labels, can potentially be extracted from such a learned latent representation.

q-bio.QM↗
arXiv2024

Efficient Probabilistic Modeling of Crystallization at Mesoscopic Scale

Crystallization processes at the mesoscopic scale, where faceted, dendritic growth, and multigrain formation can be observed, are of particular interest within materials science and metallurgy. These processes are highly nonlinear, stochastic, and sensitive to small perturbations of system parameters and initial conditions. Methods for the simulation of these processes have been developed using discrete numerical models, but these are computationally expensive. This work aims to scale crystal growth simulation with a machine learning emulator. Specifically, autoregressive latent variable models are well suited for modeling the joint distribution over system parameters and the crystallization trajectories. However, successfully training such models is challenging due to the stochasticity and sensitivity of the system. Existing approaches consequently fail to produce diverse and faithful crystallization trajectories. In this paper, we introduce the Crystal Growth Neural Emulator (CGNE), a probabilistic model for efficient crystal growth emulation at the mesoscopic scale that overcomes these challenges. We validate CGNE results using the morphological properties of the crystals produced by numerical simulation. CGNE delivers a factor of 11 improvement in inference time and performance gains compared with recent state-of-the-art probabilistic models for dynamical systems.

cs.LG↗
arXiv2024

Node Classification in Random Trees

We propose a method for the classification of objects that are structured as random trees. Our aim is to model a distribution over the node label assignments in settings where the tree data structure is associated with node attributes (typically high dimensional embeddings). The tree topology is not predetermined and none of the label assignments are present during inference. Other methods that produce a distribution over node label assignment in trees (or more generally in graphs) either assume conditional independence of the label assignment, operate on a fixed graph topology, or require part of the node labels to be observed. Our method defines a Markov Network with the corresponding topology of the random tree and an associated Gibbs distribution. We parameterize the Gibbs distribution with a Graph Neural Network that operates on the random tree and the node embeddings. This allows us to estimate the likelihood of node assignments for a given random tree and use MCMC to sample from the distribution of node assignments. We evaluate our method on the tasks of node classification in trees on the Stanford Sentiment Treebank dataset. Our method outperforms the baselines on this dataset, demonstrating its effectiveness for modeling joint distributions of node labels in random trees.

cs.LG↗
arXiv2024

Graph Neural Networks for Carbon Dioxide Adsorption Prediction in Aluminium-Exchanged Zeolites

The ability to efficiently predict adsorption properties of zeolites can be of large benefit in accelerating the design process of novel materials. The existing configuration space for these materials is wide, while existing molecular simulation methods are computationally expensive. In this work, we propose a model which is 4 to 5 orders of magnitude faster at adsorption properties compared to molecular simulations. To validate the model, we generated datasets containing various aluminium configurations for the MOR, MFI, RHO and ITW zeolites along with their heat of adsorptions and Henry coefficients for CO$_2$, obtained from Monte Carlo simulations. The predictions obtained from the Machine Learning model are in agreement with the values obtained from the Monte Carlo simulations, confirming that the model can be used for property prediction. Furthermore, we show that the model can be used for identifying adsorption sites. Finally, we evaluate the capability of our model for generating novel zeolite configurations by using it in combination with a genetic algorithm.

cond-mat.mtrl-sci↗
arXiv2024

You Can Have Better Graph Neural Networks by Not Training Weights at All: Finding Untrained GNNs Tickets

Recent works have impressively demonstrated that there exists a subnetwork in randomly initialized convolutional neural networks (CNNs) that can match the performance of the fully trained dense networks at initialization, without any optimization of the weights of the network (i.e., untrained networks). However, the presence of such untrained subnetworks in graph neural networks (GNNs) still remains mysterious. In this paper we carry out the first-of-its-kind exploration of discovering matching untrained GNNs. With sparsity as the core tool, we can find \textit{untrained sparse subnetworks} at the initialization, that can match the performance of \textit{fully trained dense} GNNs. Besides this already encouraging finding of comparable performance, we show that the found untrained subnetworks can substantially mitigate the GNN over-smoothing problem, hence becoming a powerful tool to enable deeper GNNs without bells and whistles. We also observe that such sparse untrained subnetworks have appealing performance in out-of-distribution detection and robustness of input perturbations. We evaluate our method across widely-used GNN architectures on various popular datasets including the Open Graph Benchmark (OGB).

cs.LG↗
arXiv2023

Equivariant Parameter Sharing for Porous Crystalline Materials

Efficiently predicting properties of porous crystalline materials has great potential to accelerate the high throughput screening process for developing new materials, as simulations carried out using first principles model are often computationally expensive. To effectively make use of Deep Learning methods to model these materials, we need to utilize the symmetries present in the crystals, which are defined by their space group. Existing methods for crystal property prediction either have symmetry constraints that are too restrictive or only incorporate symmetries between unit cells. In addition, these models do not explicitly model the porous structure of the crystal. In this paper, we develop a model which incorporates the symmetries of the unit cell of a crystal in its architecture and explicitly models the porous structure. We evaluate our model by predicting the heat of adsorption of CO$_2$ for different configurations of the mordenite zeolite. Our results confirm that our method performs better than existing methods for crystal property prediction and that the inclusion of pores results in a more efficient model.

cs.LG↗
arXiv2023

Description Generation using Variational Auto-Encoders for precursor microRNA

Micro RNAs (miRNA) are a type of non-coding RNA, which are involved in gene regulation and can be associated with diseases such as cancer, cardiovascular and neurological diseases. As such, identifying the entire genome of miRNA can be of great relevance. Since experimental methods for novel precursor miRNA (pre-miRNA) detection are complex and expensive, computational detection using ML could be useful. Existing ML methods are often complex black boxes, which do not create an interpretable structural description of pre-miRNA. In this paper, we propose a novel framework, which makes use of generative modeling through Variational Auto-Encoders to uncover the generative factors of pre-miRNA. After training the VAE, the pre-miRNA description is developed using a decision tree on the lower dimensional latent space. Applying the framework to miRNA classification, we obtain a high reconstruction and classification performance, while also developing an accurate miRNA description.

q-bio.QM↗
arXiv2023

Dynamic Sparsity Is Channel-Level Sparsity Learner

Sparse training has received an upsurging interest in machine learning due to its tantalizing saving potential for the entire training process as well as inference. Dynamic sparse training (DST), as a leading sparse training approach, can train deep neural networks at high sparsity from scratch to match the performance of their dense counterparts. However, most if not all DST prior arts demonstrate their effectiveness on unstructured sparsity with highly irregular sparse patterns, which receives limited support in common hardware. This limitation hinders the usage of DST in practice. In this paper, we propose Channel-aware dynamic sparse (Chase), which for the first time seamlessly translates the promise of unstructured dynamic sparsity to GPU-friendly channel-level sparsity (not fine-grained N:M or group sparsity) during one end-to-end training process, without any ad-hoc operations. The resulting small sparse networks can be directly accelerated by commodity hardware, without using any particularly sparsity-aware hardware accelerators. This appealing outcome is partially motivated by a hidden phenomenon of dynamic sparsity: off-the-shelf unstructured DST implicitly involves biased parameter reallocation across channels, with a large fraction of channels (up to 60%) being sparser than others. By progressively identifying and removing these channels during training, our approach translates unstructured sparsity to channel-wise sparsity. Our experimental results demonstrate that Chase achieves 1.7 X inference throughput speedup on common GPU devices without compromising accuracy with ResNet-50 on ImageNet. We release our codes in https://github.com/luuyin/chase.

cs.LG↗
arXiv2023

BSDAR: Beam Search Decoding with Attention Reward in Neural Keyphrase Generation

This study mainly investigates two common decoding problems in neural keyphrase generation: sequence length bias and beam diversity. To tackle the problems, we introduce a beam search decoding strategy based on word-level and ngram-level reward function to constrain and refine Seq2Seq inference at test time. Results show that our simple proposal can overcome the algorithm bias to shorter and nearly identical sequences, resulting in a significant improvement of the decoding performance on generating keyphrases that are present and absent in source text.

cs.CL↗
arXiv2023

KeyGen2Vec: Learning Document Embedding via Multi-label Keyword Generation in Question-Answering

Representing documents into high dimensional embedding space while preserving the structural similarity between document sources has been an ultimate goal for many works on text representation learning. Current embedding models, however, mainly rely on the availability of label supervision to increase the expressiveness of the resulting embeddings. In contrast, unsupervised embeddings are cheap, but they often cannot capture implicit structure in target corpus, particularly for samples that come from different distribution with the pretraining source. Our study aims to loosen up the dependency on label supervision by learning document embeddings via Sequence-to-Sequence (Seq2Seq) text generator. Specifically, we reformulate keyphrase generation task into multi-label keyword generation in community-based Question Answering (cQA). Our empirical results show that KeyGen2Vec in general is superior than multi-label keyword classifier by up to 14.7% based on Purity, Normalized Mutual Information (NMI), and F1-Score metrics. Interestingly, although in general the absolute advantage of learning embeddings through label supervision is highly positive across evaluation datasets, KeyGen2Vec is shown to be competitive with classifier that exploits topic label supervision in Yahoo! cQA with larger number of latent topic labels.

cs.CL↗
arXiv2023

Fast Dynamic 1D Simulation of Divertor Plasmas with Neural PDE Surrogates

Managing divertor plasmas is crucial for operating reactor scale tokamak devices due to heat and particle flux constraints on the divertor target. Simulation is an important tool to understand and control these plasmas, however, for real-time applications or exhaustive parameter scans only simple approximations are currently fast enough. We address this lack of fast simulators using neural PDE surrogates, data-driven neural network-based surrogate models trained using solutions generated with a classical numerical method. The surrogate approximates a time-stepping operator that evolves the full spatial solution of a reference physics-based model over time. We use DIV1D, a 1D dynamic model of the divertor plasma, as reference model to generate data. DIV1D's domain covers a 1D heat flux tube from the X-point (upstream) to the target. We simulate a realistic TCV divertor plasma with dynamics induced by upstream density ramps and provide an exploratory outlook towards fast transients. State-of-the-art neural PDE surrogates are evaluated in a common framework and extended for properties of the DIV1D data. We evaluate (1) the speed-accuracy trade-off; (2) recreating non-linear behavior; (3) data efficiency; and (4) parameter inter- and extrapolation. Once trained, neural PDE surrogates can faithfully approximate DIV1D's divertor plasma dynamics at sub real-time computation speeds: In the proposed configuration, 2ms of plasma dynamics can be computed in $\approx$0.63ms of wall-clock time, several orders of magnitude faster than DIV1D.

physics.plasm-ph↗
arXiv2023

NLG Evaluation Metrics Beyond Correlation Analysis: An Empirical Metric Preference Checklist

In this study, we analyze automatic evaluation metrics for Natural Language Generation (NLG), specifically task-agnostic metrics and human-aligned metrics. Task-agnostic metrics, such as Perplexity, BLEU, BERTScore, are cost-effective and highly adaptable to diverse NLG tasks, yet they have a weak correlation with human. Human-aligned metrics (CTC, CtrlEval, UniEval) improves correlation level by incorporating desirable human-like qualities as training objective. However, their effectiveness at discerning system-level performance and quality of system outputs remain unclear. We present metric preference checklist as a framework to assess the effectiveness of automatic metrics in three NLG tasks: Text Summarization, Dialogue Response Generation, and Controlled Generation. Our proposed framework provides access: (i) for verifying whether automatic metrics are faithful to human preference, regardless of their correlation level to human; and (ii) for inspecting the strengths and limitations of NLG systems via pairwise evaluation. We show that automatic metrics provide a better guidance than human on discriminating system-level performance in Text Summarization and Controlled Generation tasks. We also show that multi-aspect human-aligned metric (UniEval) is not necessarily dominant over single-aspect human-aligned metrics (CTC, CtrlEval) and task-agnostic metrics (BLEU, BERTScore), particularly in Controlled Generation tasks.

cs.CL↗
arXiv2023

Comparison of neural closure models for discretised PDEs

Neural closure models have recently been proposed as a method for efficiently approximating small scales in multiscale systems with neural networks. The choice of loss function and associated training procedure has a large effect on the accuracy and stability of the resulting neural closure model. In this work, we systematically compare three distinct procedures: "derivative fitting", "trajectory fitting" with discretise-then-optimise, and "trajectory fitting" with optimise-then-discretise. Derivative fitting is conceptually the simplest and computationally the most efficient approach and is found to perform reasonably well on one of the test problems (Kuramoto-Sivashinsky) but poorly on the other (Burgers). Trajectory fitting is computationally more expensive but is more robust and is therefore the preferred approach. Of the two trajectory fitting procedures, the discretise-then-optimise approach produces more accurate models than the optimise-then-discretise approach. While the optimise-then-discretise approach can still produce accurate models, care must be taken in choosing the length of the trajectories used for training, in order to train the models on long-term behaviour while still producing reasonably accurate gradients during training. Two existing theorems are interpreted in a novel way that gives insight into the long-term accuracy of a neural closure model based on how accurate it is in the short term.

cs.LG↗
arXiv2023

Lottery Pools: Winning More by Interpolating Tickets without Increasing Training or Inference Cost

Lottery tickets (LTs) is able to discover accurate and sparse subnetworks that could be trained in isolation to match the performance of dense networks. Ensemble, in parallel, is one of the oldest time-proven tricks in machine learning to improve performance by combining the output of multiple independent models. However, the benefits of ensemble in the context of LTs will be diluted since ensemble does not directly lead to stronger sparse subnetworks, but leverages their predictions for a better decision. In this work, we first observe that directly averaging the weights of the adjacent learned subnetworks significantly boosts the performance of LTs. Encouraged by this observation, we further propose an alternative way to perform an 'ensemble' over the subnetworks identified by iterative magnitude pruning via a simple interpolating strategy. We call our method Lottery Pools. In contrast to the naive ensemble which brings no performance gains to each single subnetwork, Lottery Pools yields much stronger sparse subnetworks than the original LTs without requiring any extra training or inference cost. Across various modern architectures on CIFAR-10/100 and ImageNet, we show that our method achieves significant performance gains in both, in-distribution and out-of-distribution scenarios. Impressively, evaluated with VGG-16 and ResNet-18, the produced sparse subnetworks outperform the original LTs by up to 1.88% on CIFAR-100 and 2.36% on CIFAR-100-C; the resulting dense network surpasses the pre-trained dense-model up to 2.22% on CIFAR-100 and 2.38% on CIFAR-100-C.

cs.LG↗
arXiv2022

Neural Langevin Dynamics: towards interpretable Neural Stochastic Differential Equations

Neural Stochastic Differential Equations (NSDE) have been trained as both Variational Autoencoders, and as GANs. However, the resulting Stochastic Differential Equations can be hard to interpret or analyse due to the generic nature of the drift and diffusion fields. By restricting our NSDE to be of the form of Langevin dynamics, and training it as a VAE, we obtain NSDEs that lend themselves to more elaborate analysis and to a wider range of visualisation techniques than a generic NSDE. More specifically, we obtain an energy landscape, the minima of which are in one-to-one correspondence with latent states underlying the used data. This not only allows us to detect states underlying the data dynamics in an unsupervised manner, but also to infer the distribution of time spent in each state according to the learned SDE. More in general, restricting an NSDE to Langevin dynamics enables the use of a large set of tools from computational molecular dynamics for the analysis of the obtained results.

cs.LG↗