Identifying where quantum models may offer practical benefits in near term quantum machine learning (QML) requires moving beyond isolated algorithmic proposals toward systematic and empirical exploration across models, datasets, and hardware constraints. We introduce MerLin, an open-source framework designed as a discovery engine for photonic and hybrid quantum machine learning. MerLin integrates optimized strong simulation of linear optical circuits into standard PyTorch and scikit learn workflows, enabling end-to-end differentiable training of quantum layers. MerLin is designed around systematic benchmarking and reproducibility. As an initial contribution, we reproduce eighteen state-of-the-art photonic and hybrid QML works spanning kernel methods, reservoir computing, convolutional and recurrent architectures, generative models, and modern training paradigms. These reproductions are released as reusable, modular experiments that can be directly extended and adapted, establishing a shared experimental baseline consistent with empirical benchmarking methodologies widely adopted in modern artificial intelligence. By embedding photonic quantum models within established machine learning ecosystems, MerLin allows practitioners to leverage existing tooling for ablation studies, cross-modality comparisons, and hybrid classical-quantum workflows. The framework already implements hardware-aware features, allowing tests on available quantum hardware while enabling exploration beyond its current capabilities, positioning MerLin as a forward-looking co-design tool linking algorithms, benchmarks, and hardware.

This article provides the first survey of computational models of emotion in reinforcement learning (RL) agents. The survey focuses on agent/robot emotions, and mostly ignores human user emotions. Emotions are recognized as functional in decision-making by influencing motivation and action selection. Therefore, computational emotion models are usually grounded in the agent's decision making architecture, of which RL is an important subclass. Studying emotions in RL-based agents is useful for three research fields. For machine learning (ML) researchers, emotion models may improve learning efficiency. For the interactive ML and human-robot interaction (HRI) community, emotions can communicate state and enhance user investment. Lastly, it allows affective modelling (AM) researchers to investigate their emotion theories in a successful AI agent class. This survey provides background on emotion theory and RL. It systematically addresses 1) from what underlying dimensions (e.g., homeostasis, appraisal) emotions can be derived and how these can be modelled in RL-agents, 2) what types of emotions have been derived from these dimensions, and 3) how these emotions may either influence the learning efficiency of the agent or be useful as social signals. We also systematically compare evaluation criteria, and draw connections to important RL sub-domains like (intrinsic) motivation and model-based RL. In short, this survey provides both a practical overview for engineers wanting to implement emotions in their RL agents, and identifies challenges and directions for future emotion-RL research.

We seek to enable classic processing of continuous ultra-sparse spatiotemporal data generated by event-based sensors with dense machine learning models. We propose a novel hybrid pipeline composed of asynchronous sensing and synchronous processing that combines several ideas: (1) an embedding based on PointNet models -- the ALERT module -- that can continuously integrate new and dismiss old events thanks to a leakage mechanism, (2) a flexible readout of the embedded data that allows to feed any downstream model with always up-to-date features at any sampling rate, (3) exploiting the input sparsity in a patch-based approach inspired by Vision Transformer to optimize the efficiency of the method. These embeddings are then processed by a transformer model trained for object and gesture recognition. Using this approach, we achieve performances at the state-of-the-art with a lower latency than competitors. We also demonstrate that our asynchronous model can operate at any desired sampling rate.

Automatic machine learning is an important problem in the forefront of machine learning. The strongest AutoML systems are based on neural networks, evolutionary algorithms, and Bayesian optimization. Recently AlphaD3M reached state-of-the-art results with an order of magnitude speedup using reinforcement learning with self-play. In this work we extend AlphaD3M by using a pipeline grammar and a pre-trained model which generalizes from many different datasets and similar tasks. Our results demonstrate improved performance compared with our earlier work and existing methods on AutoML benchmark datasets for classification and regression tasks. In the spirit of reproducible research we make our data, models, and code publicly available.

We present the results of processing the effects of the powerful Gamma Ray Burst GRB221009A captured by the charged particle detectors (electrostatic analyzers and solid-state detectors) onboard spacecraft at different points in the heliosphere on October 9, 2022. To follow the GRB221009A propagation through the heliosphere we used the electron and proton flux measurements from solar missions Solar Orbiter and STEREO-A; Earth magnetosphere and the solar wind missions THEMIS and Wind; meteorological satellites POES15, POES19, MetOp3; and MAVEN - a NASA mission orbiting Mars. GRB221009A had a structure of four bursts: less intense Pulse 1 - the triggering impulse - was detected by gamma-ray observatories at 131659 UT (near the Earth); the most intense Pulses 2 and 3 were detected on board all the spacecraft from the list, and Pulse 4 detected in more than 500 s after Pulse 1. Due to their different scientific objectives, the spacecraft, which data was used in this study, were separated by more than 1 AU (Solar Orbiter and MAVEN). This enabled tracking GRB221009A as it was propagating across the heliosphere. STEREO-A was the first to register Pulse 2 and 3 of the GRB, almost 100 seconds before their detection by spacecraft in the vicinity of Earth. MAVEN detected GRB221009A Pulses 2, 3, and 4 at the orbit of Mars about 237 seconds after their detection near Earth. By processing the time delays observed we show that the source location of the GRB221009A was at RA 288.5 degrees, Dec 18.5 degrees (J2000) with an error cone of 2 degrees

We argue that the fundamental Theory of Everything is a conventional field theory defined in the flat multidimensional bulk. Our Universe should be obtained as a 3-brane classical solution in this theory. The renormalizability of the fundamental theory implies that it involves higher derivatives (HD). It should be supersymmetric (otherwise one cannot get rid of the huge induced cosmological term) and probably conformal (otherwise one can hardly cope with the problem of ghosts) . We present arguments that in conformal HD theories the ghosts (which are inherent for HD theories) might be not so malignant. In particular, we present a nontrivial QM HD model where ghosts are absent and the spectrum has a well defined ground state. The requirement of superconformal invariance restricts the dimension of the bulk to be D < 7. We suggest that the TOE lives in six dimensions and enjoys the maximum N = (2,0) superconformal symmetry. Unfortunately, no renormalizable field theory with this symmetry is presently known. We construct and discuss an N = (1,0) 6D supersymmetric gauge theory with four derivatives in the action. This theory involves a dimensionless coupling constant and is renormalizable. At the tree level, the theory enjoys conformal symmetry, but the latter is broken by quantum anomaly. The sign of the beta function corresponds to the Landau zero situation.

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.

The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this implies, and the rapid kinetics it engenders, arises due to the extraordinary thermodynamic cooperativity of protein folding. Studying Miyazawa-Jernigan lattice polymers we find that, even under conditions where the folding energy landscape is relatively optimized (designed sequences folding at their temperature of maximum folding rate), the folding of protein-like heteropolymers is accelerated when their thermodynamic cooperativity enhanced by enhancing the non-additivity of their energy potentials. At lower temperatures, where kinetic traps presumably play a more significant role in defining folding rates, we observe still greater cooperativity-induced acceleration. Consistent with these observations, we find that the folding kinetics of our computational models more closely approximate single-exponential behavior as their cooperativity approaches optimal levels. These observations suggest that the rapid folding of naturally occurring proteins is, at least in part, consequences of their remarkably cooperative folding.

This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid positions. These conformations are forwarded to the second phase, where an accurate search is performed with the aim of locating conformations with the best energy value. The optimization process switches between these two phases until the stopping condition is satisfied. An auxiliary fitness function was designed for the first phase, while the original fitness function is used in the second phase. The auxiliary fitness function includes an expression about the quality of the hydrophobic core. This expression is crucial for leading the search process to the promising solutions that have a good hydrophobic core and, consequently, improves the efficiency of the whole optimization process. Our differential evolution algorithm was used for demonstrating the efficiency of two-phase optimization. It was analyzed on well-known amino acid sequences that are used frequently in the literature. The obtained experimental results show that the employed two-phase optimization improves the efficiency of our algorithm significantly and that the proposed algorithm is superior to other state-of-the-art algorithms.

Determination of binding affinity of proteins in the formation of protein complexes requires sophisticated, expensive and time-consuming experimentation which can be replaced with computational methods. Most computational prediction techniques require protein structures which limit their applicability to protein complexes with known structures. In this work, we explore sequence based protein binding affinity prediction using machine learning. Our paper highlights the fact that the generalization performance of even the state of the art sequence-only predictor of binding affinity is far from satisfactory and that the development of effective and practical methods in this domain is still an open problem. We also propose a novel sequence-only predictor of binding affinity called ISLAND which gives better accuracy than existing methods over the same validation set as well as on external independent test dataset. A cloud-based webserver implementation of ISLAND and its Python code are available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#island.