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Tomas Tokar

Publications and source records attributed to Tomas Tokar.

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Improving Set Function Approximation with Quasi-Arithmetic Neural Networks

Sets represent a fundamental abstraction across many types of data. To handle the unordered nature of set-structured data, models such as DeepSets and PointNet rely on fixed, non-learnable pooling operations (e.g., sum or max) -- a design choice that can hinder the transferability of learned embeddings and limits model expressivity. More recently, learnable aggregation functions have been proposed as more expressive alternatives. In this work, we advance this line of research by introducing the Neuralized Kolmogorov Mean (NKM) -- a novel, trainable framework for learning a generalized measure of central tendency through an invertible neural function. We further propose quasi-arithmetic neural networks (QUANNs), which incorporate the NKM as a learnable aggregation function. We provide a theoretical analysis showing that, QUANNs are universal approximators for a broad class of common set-function decompositions and, thanks to their invertible neural components, learn more structured latent representations. Empirically, QUANNs outperform state-of-the-art baselines across diverse benchmarks, while learning embeddings that transfer effectively even to tasks that do not involve sets.

cs.LG

Bcl-2 family controls mitochondrial outer membrane permeabilization by performing non-trivial pattern recognition

Interactions between individual members of the B-cell lymphoma 2 (Bcl-2) family of proteins form a regulatory network governing mitochondrial outer membrane permeabilization (MOMP). Bcl-2 family initiated MOMP causes release of the inter-membrane pro-apoptotic proteins to cytosol and creates a cytosolic environment suitable for the executionary phase of apoptosis. Using mathematical modeling and computational simulation, we have analyzed the response of this regulatory network caused by the up-/downregulation of each individual member of the Bcl-2 family. As a result, a non-linear stimulus-response emerged, the characteristics of which are associated with bistability and switch-like behavior. Using the principal component analysis (PCA) we have shown that the Bcl-2 family classifies the random combinations of inputs into two distinct classes, and responds to these by one of the two qualitatively distinct outputs. As we showed, the emergence of this behavior requires specific organization of the interactions between particular Bcl-2 proteins.

q-bio.MN

Boolean network-based model of the Bcl-2 family mediated MOMP regulation

Mitochondrial outer membrane permeabilization (MOMP) is one of the most important points, in majority of apoptotic signaling cascades. Decision mechanism controlling whether the MOMP occurs or not, is formed by an interplay between members of the Bcl-2 family. To understand the role of individual members of this family within the MOMP regulation, we constructed a boolean network-based mathematical model of interactions between the Bcl-2 proteins. Results of computational simulations reveal the existence of the potentially malign configurations of activities of the Bcl-2 proteins, blocking the occurrence of MOMP, independently of the incoming stimuli. Our results suggest role of the antiapoptotic protein Mcl-1 in relation to these configurations. We demonstrate here, the importance of the Bid and Bim according to activation of effectors Bax and Bak, and the irreversibility of this activation. The model further shows the distinct requirements for effectors activation, where the antiapoptic protein Bcl-w is seemingly a key factor preventing the Bax activation. We believe that this work may help to describe the functioning of the Bcl-2 regulation of MOMP better, and hopefully provide some contribution regarding the anti-cancer drug development research.

q-bio.MN