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This technical report introduces the EXAONE 3.5 instruction-tuned language models, developed and released by LG AI Research. The EXAONE 3.5 language models are offered in three configurations: 32B, 7.8B, and 2.4B. These models feature several standout capabilities: 1) exceptional instruction following capabilities in real-world scenarios, achieving the highest scores across seven benchmarks, 2) outstanding long-context comprehension, attaining the top performance in four benchmarks, and 3) competitive results compared to state-of-the-art open models of similar sizes across nine general benchmarks. The EXAONE 3.5 language models are open to anyone for research purposes and can be downloaded from https://huggingface.co/LGAI-EXAONE. For commercial use, please reach out to the official contact point of LG AI Research: contact_us@lgresearch.ai., Comment: arXiv admin note: text overlap with arXiv:2408.03541

Image generation today can produce somewhat realistic images from text prompts. However, if one asks the generator to synthesize a particular camera setting such as creating different fields of view using a 24mm lens versus a 70mm lens, the generator will not be able to interpret and generate scene-consistent images. This limitation not only hinders the adoption of generative tools in photography applications but also exemplifies a broader issue of bridging the gap between the data-driven models and the physical world. In this paper, we introduce the concept of Generative Photography, a framework designed to control camera intrinsic settings during content generation. The core innovation of this work are the concepts of Dimensionality Lifting and Contrastive Camera Learning, which achieve continuous and consistent transitions for different camera settings. Experimental results show that our method produces significantly more scene-consistent photorealistic images than state-of-the-art models such as Stable Diffusion 3 and FLUX., Comment: Project page: https://generative-photography.github.io/project/

In this paper, we introduce SailCompass, a reproducible and robust evaluation benchmark for assessing Large Language Models (LLMs) on Southeast Asian Languages (SEA). SailCompass encompasses three main SEA languages, eight primary tasks including 14 datasets covering three task types (generation, multiple-choice questions, and classification). To improve the robustness of the evaluation approach, we explore different prompt configurations for multiple-choice questions and leverage calibrations to improve the faithfulness of classification tasks. With SailCompass, we derive the following findings: (1) SEA-specialized LLMs still outperform general LLMs, although the gap has narrowed; (2) A balanced language distribution is important for developing better SEA-specialized LLMs; (3) Advanced prompting techniques (e.g., calibration, perplexity-based ranking) are necessary to better utilize LLMs. All datasets and evaluation scripts are public., Comment: code: https://github.com/sail-sg/sailcompass

We introduce a general-purpose, human-in-the-loop dual dialogue system to support mental health care professionals. The system, co-designed with care providers, is conceptualized to assist them in interacting with care seekers rather than functioning as a fully automated dialogue system solution. The AI assistant within the system reduces the cognitive load of mental health care providers by proposing responses, analyzing conversations to extract pertinent themes, summarizing dialogues, and recommending localized relevant content and internet-based cognitive behavioral therapy exercises. These functionalities are achieved through a multi-agent system design, where each specialized, supportive agent is characterized by a large language model. In evaluating the multi-agent system, we focused specifically on the proposal of responses to emotionally distressed care seekers. We found that the proposed responses matched a reasonable human quality in demonstrating empathy, showing its appropriateness for augmenting the work of mental health care providers., Comment: Update: Render figures properly and update title

In-Context Operator Networks (ICONs) are models that learn operators across different types of PDEs using a few-shot, in-context approach. Although they show successful generalization to various PDEs, existing methods treat each data point as a single token, and suffer from computational inefficiency when processing dense data, limiting their application in higher spatial dimensions. In this work, we propose Vision In-Context Operator Networks (VICON), incorporating a vision transformer architecture that efficiently processes 2D functions through patch-wise operations. We evaluated our method on three fluid dynamics datasets, demonstrating both superior performance (reducing scaled $L^2$ error by $40\%$ and $61.6\%$ for two benchmark datasets for compressible flows, respectively) and computational efficiency (requiring only one-third of the inference time per frame) in long-term rollout predictions compared to the current state-of-the-art sequence-to-sequence model with fixed timestep prediction: Multiple Physics Pretraining (MPP). Compared to MPP, our method preserves the benefits of in-context operator learning, enabling flexible context formation when dealing with insufficient frame counts or varying timestep values.

In a criminal investigation, an inferential error occurs when the probability that a suspect is the source of some evidence -- such as a fingerprint -- is taken as the probability of guilt. This is known as the ultimate issue error, and the same error occurs in statistical inference when the probability that a parameter equals some value is incorrectly taken to be the probability of a hypothesis. Almost all statistical inference in the social and biological sciences is subject to this error, and replacing every instance of "hypothesis testing" with "parameter testing" in these fields would more accurately describe the target of inference. The relationship between parameter values and quantities derived from them, such as p-values or Bayes factors, have no direct quantitative relationship with scientific hypotheses. Here, we describe the problem, its consequences, and suggest options for improving scientific inference.

In this Technical Design Report (TDR) we describe the SABRE South detector to be built at the Stawell Underground Physics Laboratory (SUPL). The SABRE South detector is designed to test the long-standing DAMA/LIBRA signal of an annually modulating rate consistent with dark matter by using the same target material. SABRE South uses seven ultra-high purity NaI(Tl) crystals (with a total target mass of either 35 kg or 50 kg), hermetically sealed in copper enclosures that are suspended within a liquid scintillator active veto. High quantum efficiency and low background Hamamatsu R11065 photomultiplier tubes are directly coupled to both ends of the crystal, and enclosed with the crystal in an oxygen free high thermal conductivity copper enclosure. The active veto system consists of 11.6 kL of linear alkylbenzene (LAB) doped with a mixture of fluorophores and contained in a steel vessel, which is instrumented with at least 18 Hamamatsu R5912 photomultipliers. The active veto tags key radiogenic backgrounds intrinsic to the crystals, such as ${^{40}}$K, and is expected to suppress the total background by 27% in the 1-6 keV region of interest. In addition to the liquid scintillator veto, a muon veto is positioned above the detector shielding. This muon veto consists of eight EJ-200 scintillator modules, with Hamamatsu R13089 photomultipliers coupled to both ends. With an expected total background of 0.72 cpd/kg/keV, SABRE South can test the DAMA/LIBRA signal with 5$\sigma$ discovery or 3$\sigma$ exclusion after two years of data taking.

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research., Comment: 98 pages

In quantum mechanics courses, students often solve the Schr\"odinger equation for the harmonic oscillator with time-independent parameters. However, time-dependent quantum harmonic oscillators are relevant in modeling several problems as, for instance, the description of quantum motion of particles in traps, shortcuts to adiabaticity, as well as quantum scalar fields evolving in expanding universes. In the present paper, we discuss, with a pedagogical approach, the quantum harmonic oscillator with time-dependent frequency via the Lewis-Riesenfeld dynamical invariant method, revisiting the main steps to obtain the wave function associated with this model, and briefly discussing the relation between this oscillator and the generation of squeezed states. As examples of didactic applications of time-dependent harmonic oscillators and the Lewis-Riesenfeld method in quantum mechanics courses, we solve the following problems: the calculation of the transition probability associated with a harmonic oscillator which undergoes jumps in its frequency, and the analysis of the dynamics of a quantum particle in a Paul trap., Comment: 21 pages, 4 figures

Machine unlearning algorithms are increasingly important as legal concerns arise around the provenance of training data, but verifying the success of unlearning is often difficult. Provable guarantees for unlearning are often limited to supervised learning settings. In this paper, we provide the first theoretical guarantees for unlearning in the pre-training and fine-tuning paradigm by studying topic models, simple bag-of-words language models that can be adapted to solve downstream tasks like retrieval and classification. First, we design a provably effective unlearning algorithm for topic models that incurs a computational overhead independent of the size of the original dataset. Our analysis additionally quantifies the deletion capacity of the model -- i.e., the number of examples that can be unlearned without incurring a significant cost in model performance. Finally, we formally extend our analyses to account for adaptation to a given downstream task. In particular, we design an efficient algorithm to perform unlearning after fine-tuning the topic model via a linear head. Notably, we show that it is easier to unlearn pre-training data from models that have been fine-tuned to a particular task, and one can unlearn this data without modifying the base model.

Vision Transformers (ViTs) have shown exceptional performance in vehicle re-identification (ReID) tasks. However, non-square aspect ratios of image or video inputs can negatively impact re-identification accuracy. To address this challenge, we propose a novel, human perception driven, and general ViT-based ReID framework that fuses models trained on various aspect ratios. Our key contributions are threefold: (i) We analyze the impact of aspect ratios on performance using the VeRi-776 and VehicleID datasets, providing guidance for input settings based on the distribution of original image aspect ratios. (ii) We introduce patch-wise mixup strategy during ViT patchification (guided by spatial attention scores) and implement uneven stride for better alignment with object aspect ratios. (iii) We propose a dynamic feature fusion ReID network to enhance model robustness. Our method outperforms state-of-the-art transformer-based approaches on both datasets, with only a minimal increase in inference time per image.

We propose a scalable preconditioned primal-dual hybrid gradient algorithm for solving partial differential equations (PDEs). We multiply the PDE with a dual test function to obtain an inf-sup problem whose loss functional involves lower-order differential operators. The Primal-Dual Hybrid Gradient (PDHG) algorithm is then leveraged for this saddle point problem. By introducing suitable precondition operators to the proximal steps in the PDHG algorithm, we obtain an alternative natural gradient ascent-descent optimization scheme for updating the neural network parameters. We apply the Krylov subspace method (MINRES) to evaluate the natural gradients efficiently. Such treatment readily handles the inversion of precondition matrices via matrix-vector multiplication. A posterior convergence analysis is established for the time-continuous version of the proposed method. The algorithm is tested on various types of PDEs with dimensions ranging from $1$ to $50$, including linear and nonlinear elliptic equations, reaction-diffusion equations, and Monge-Amp\`ere equations stemming from the $L^2$ optimal transport problems. We compare the performance of the proposed method with several commonly used deep learning algorithms such as physics-informed neural networks (PINNs), the DeepRitz method, weak adversarial networks (WANs), etc, for solving PDEs using the Adam and L-BFGS optimizers. The numerical results suggest that the proposed method performs efficiently and robustly and converges more stably.

The healthcare sector has experienced a rapid accumulation of digital data recently, especially in the form of electronic health records (EHRs). EHRs constitute a precious resource that IS researchers could utilize for clinical applications (e.g., morbidity prediction). Deep learning seems like the obvious choice to exploit this surfeit of data. However, numerous studies have shown that deep learning does not enjoy the same kind of success on EHR data as it has in other domains; simple models like logistic regression are frequently as good as sophisticated deep learning ones. Inspired by this observation, we develop a novel model called rational logistic regression (RLR) that has standard logistic regression (LR) as its special case (and thus inherits LR's inductive bias that aligns with EHR data). RLR has rational series as its theoretical underpinnings, works on longitudinal time-series data, and learns interpretable patterns. Empirical comparisons on real-world clinical tasks demonstrate RLR's efficacy., Comment: ICIS 2021 Proceedings ( see https://aisel.aisnet.org/icis2021/is_health/is_health/18 )

In this paper we present a new approach to deblur the effect of atmospheric turbulence in the case of long range imaging. Our method is based on an analytical formulation, the Fried kernel, of the atmosphere modulation transfer function (MTF) and a framelet based deconvolution algorithm. An important parameter is the refractive index structure which requires specific measurements to be known. Then we propose a method which provides a good estimation of this parameter from the input blurred image. The final algorithms are very easy to implement and show very good results on both simulated blur and real images.

Since the seminal work of Andrey Kolmogorov in the early 1940's, imaging through atmospheric turbulence has grown from a pure scientific pursuit to an important subject across a multitude of civilian, space-mission, and national security applications. Fueled by the recent advancement of deep learning, the field is further experiencing a new wave of momentum. However, for these deep learning methods to perform well, new efforts are needed to build faster and more accurate computational models while at the same time maximizing the performance of image reconstruction. The book is written primarily for image processing engineers, computer vision scientists, and engineering students who are interested in the field of atmospheric turbulence, statistical optics, and image processing. The book can be used as a graduate text, or advanced topic classes for undergraduates.

A recently developed new approach, called ``Empirical Wavelet Transform'', aims to build 1D adaptive wavelet frames accordingly to the analyzed signal. In this paper, we present several extensions of this approach to 2D signals (images). We revisit some well-known transforms (tensor wavelets, Littlewood-Paley wavelets, ridgelets and curvelets) and show that it is possible to build their empirical counterpart. We prove that such constructions lead to different adaptive frames which show some promising properties for image analysis and processing.

In this paper, we investigate the extension of the recently proposed weighted Fourier burst accumulation (FBA) method into the wavelet domain. The purpose of FBA is to reconstruct a clean and sharp image from a sequence of blurred frames. This concept lies in the construction of weights to amplify dominant frequencies in the Fourier spectrum of each frame. The reconstructed image is then obtained by taking the inverse Fourier transform of the average of all processed spectra. In this paper, we first suggest to replace the rigid registration step used in the original algorithm by a non-rigid registration in order to be able to process sequences acquired through atmospheric turbulence. Second, we propose to work in a wavelet domain instead of the Fourier one. This leads us to the construction of two types of algorithms. Finally, we propose an alternative approach to replace the weighting idea by an approach promoting the sparsity in the used space. Several experiments are provided to illustrate the efficiency of the proposed methods.

In this paper, we design a very simple algorithm based on Split Bregman iterations to numerically solve the cartoon + textures decomposition model of Meyer. This results in a significant gain in speed compared to Chambolle's nonlinear projectors.

Large language model advancements have enabled the development of multi-agent frameworks to tackle complex, real-world problems such as to automate tasks that require interactions with diverse tools, reasoning, and human collaboration. We present MARCO, a Multi-Agent Real-time Chat Orchestration framework for automating tasks using LLMs. MARCO addresses key challenges in utilizing LLMs for complex, multi-step task execution. It incorporates robust guardrails to steer LLM behavior, validate outputs, and recover from errors that stem from inconsistent output formatting, function and parameter hallucination, and lack of domain knowledge. Through extensive experiments we demonstrate MARCO's superior performance with 94.48% and 92.74% accuracy on task execution for Digital Restaurant Service Platform conversations and Retail conversations datasets respectively along with 44.91% improved latency and 33.71% cost reduction. We also report effects of guardrails in performance gain along with comparisons of various LLM models, both open-source and proprietary. The modular and generic design of MARCO allows it to be adapted for automating tasks across domains and to execute complex usecases through multi-turn interactions., Comment: EMNLP 2024 Industry Track

The XLZD collaboration is developing a two-phase xenon time projection chamber with an active mass of 60 to 80 t capable of probing the remaining WIMP-nucleon interaction parameter space down to the so-called neutrino fog. In this work we show that, based on the performance of currently operating detectors using the same technology and a realistic reduction of radioactivity in detector materials, such an experiment will also be able to competitively search for neutrinoless double beta decay in $^{136}$Xe using a natural-abundance xenon target. XLZD can reach a 3$\sigma$ discovery potential half-life of 5.7$\times$10$^{27}$ yr (and a 90% CL exclusion of 1.3$\times$10$^{28}$ yr) with 10 years of data taking, corresponding to a Majorana mass range of 7.3-31.3 meV (4.8-20.5 meV). XLZD will thus exclude the inverted neutrino mass ordering parameter space and will start to probe the normal ordering region for most of the nuclear matrix elements commonly considered by the community., Comment: 29 pages, 7 figures

The streaming instability (SI) is a leading mechanism for concentrating solid particles into regions dense enough to form planetesimals. Its efficiency in clumping particles depends primarily on the dimensionless stopping time ($\tau_s$, a proxy for particle size) and dust-to-gas surface density ratio ($Z$). Previous simulations identified a critical $Z$ ($Z_{\rm{crit}}$) above which strong clumping occurs, where particle densities exceed the Hill density (thus satisfying a condition for gravitational collapse), over a wide range of $\tau_s$. These works found that for $\tau_s \leq 0.01$, $Z_{\rm{crit}}$ was above the ISM value $(\sim 0.01)$. In this work, we reexamine the clumping threshold using 2D axisymmetric, stratified simulations at high resolution and with relatively large (compared to many previous simulations) domain sizes. Our main results are as follows: First, when $\tau_s = 0.01$, strong clumping occurs even at $Z \lesssim 0.01$, lower than $Z_{\rm{crit}}$ found in all previous studies. Consequently, we revise a previously published fit to the $Z_{\rm{crit}}$ curve to account for this updated $Z_{\rm{crit}}$. Second, higher resolution results in a thicker dust layer, which may result from other instabilities manifesting, such as the vertical shearing streaming instability. Third, despite this thicker layer, higher resolution can lead to strong clumping even with lower midplane dust-to-gas density ratios (which results from the thicker particle layer) so long as $Z \gtrsim Z_{\rm{crit}}$. Our results demonstrate the efficiency of the SI in clumping small particles at $Z \sim 0.01$, which is a significant refinement of the conditions for planetesimal formation by the SI., Comment: 25 pages, 12 figures, submitted to the Astrophysical Journal

This report describes the experimental strategy and technologies for a next-generation xenon observatory sensitive to dark matter and neutrino physics. The detector will have an active liquid xenon target mass of 60-80 tonnes and is proposed by the XENON-LUX-ZEPLIN-DARWIN (XLZD) collaboration. The design is based on the mature liquid xenon time projection chamber technology of the current-generation experiments, LZ and XENONnT. A baseline design and opportunities for further optimization of the individual detector components are discussed. The experiment envisaged here has the capability to explore parameter space for Weakly Interacting Massive Particle (WIMP) dark matter down to the neutrino fog, with a 3$\sigma$ evidence potential for the spin-independent WIMP-nucleon cross sections as low as $3\times10^{-49}\rm cm^2$ (at 40 GeV/c$^2$ WIMP mass). The observatory is also projected to have a 3$\sigma$ observation potential of neutrinoless double-beta decay of $^{136}$Xe at a half-life of up to $5.7\times 10^{27}$ years. Additionally, it is sensitive to astrophysical neutrinos from the atmosphere, sun, and galactic supernovae., Comment: 32 pages, 14 figures

Chicken swarm optimization is a new meta-heuristic algorithm which mimics the foraging hierarchical behavior of chicken. In this paper, we describe the preprocessing of handwritten document by contrast enhancement while preserving detail with an improved chicken swarm optimization algorithm.The results of the algorithm are compared with other existing meta heuristic algorithms like Cuckoo Search, Firefly Algorithm and the Artificial bee colony. The proposed algorithm considerably outperforms all the above by giving good results., Comment: 6 pages, 2 figures, conference

This research proposes a framework for modeling and comparing two electricity scenarios for Nigeria by 2050, focusing on the inclusion and exclusion of electricity storage technologies. A Central Composite Design (CCD) was used to generate a design matrix for data collection, with EnergyPLAN software used to create energy system simulations on the CCD data for four outputs: total annual cost, CO2 emissions, critical excess electricity production (CEEP), and electricity import. Three machine learning algorithms, support vector regression (SVR), extreme gradient boosting (XGBoost), and multi-layer perceptron (MLP), were tuned using Bayesian optimization to develop models mapping the inputs to outputs. A genetic algorithm was employed for multi-objective optimization to determine the optimal input capacities that minimize the outputs. Results indicated that incorporating electricity storage technologies (EST) leads to a 37% increase in renewable electricity sources (RES) share, resulting in a 19.14% reduction in CO2 emissions. EST such as battery energy storage systems (BESS), pumped hydro storage (PHS), and vehicle-to-grid (V2G) storage allow for the storage of the critical excess electricity that comes with increasing RES share. Integrating EST in Nigeria's 2050 energy landscape is crucial for incorporating more renewable electricity sources into the energy system, thereby reducing CO2 emissions and managing excess electricity production. This study outlines a plan for optimal electricity production to meet Nigeria's 2050 demand, highlighting the need for a balanced approach that combines fossil fuels, renewable energy, nuclear power, and advanced storage solutions to achieve a sustainable and efficient electricity system., Comment: 41 Pages

The proliferation of single-photon image sensors has opened the door to a plethora of high-speed and low-light imaging applications. However, data collected by these sensors are often 1-bit or few-bit, and corrupted by noise and strong motion. Conventional video restoration methods are not designed to handle this situation, while specialized quanta burst algorithms have limited performance when the number of input frames is low. In this paper, we introduce Quanta Video Restoration (QUIVER), an end-to-end trainable network built on the core ideas of classical quanta restoration methods, i.e., pre-filtering, flow estimation, fusion, and refinement. We also collect and publish I2-2000FPS, a high-speed video dataset with the highest temporal resolution of 2000 frames-per-second, for training and testing. On simulated and real data, QUIVER outperforms existing quanta restoration methods by a significant margin. Code and dataset available at https://github.com/chennuriprateek/Quanta_Video_Restoration-QUIVER-, Comment: Accepted at European Conference on Computer Vision (ECCV) 2024, Milano, Italy, Sept 29 - Oct 4, 2024, Part XL, LNCS 15098

Bayesian optimization (BO) has become an indispensable tool for autonomous decision-making across diverse applications from autonomous vehicle control to accelerated drug and materials discovery. With the growing interest in self-driving laboratories, BO of chemical systems is crucial for machine learning (ML) guided experimental planning. Typically, BO employs a regression surrogate model to predict the distribution of unseen parts of the search space. However, for the selection of molecules, picking the top candidates with respect to a distribution, the relative ordering of their properties may be more important than their exact values. In this paper, we introduce Rank-based Bayesian Optimization (RBO), which utilizes a ranking model as the surrogate. We present a comprehensive investigation of RBO's optimization performance compared to conventional BO on various chemical datasets. Our results demonstrate similar or improved optimization performance using ranking models, particularly for datasets with rough structure-property landscapes and activity cliffs. Furthermore, we observe a high correlation between the surrogate ranking ability and BO performance, and this ability is maintained even at early iterations of BO optimization when using ranking surrogate models. We conclude that RBO is an effective alternative to regression-based BO, especially for optimizing novel chemical compounds., Comment: 14 + 4 pages, 5 + 3 figures

Sampling from a target distribution is a fundamental problem. Traditional Markov chain Monte Carlo (MCMC) algorithms, such as the unadjusted Langevin algorithm (ULA), derived from the overdamped Langevin dynamics, have been extensively studied. From an optimization perspective, the Kolmogorov forward equation of the overdamped Langevin dynamics can be treated as the gradient flow of the relative entropy in the space of probability densities embedded with Wassrstein-2 metrics. Several efforts have also been devoted to including momentum-based methods, such as underdamped Langevin dynamics for faster convergence of sampling algorithms. Recent advances in optimizations have demonstrated the effectiveness of primal-dual damping and Hessian-driven damping dynamics for achieving faster convergence in solving optimization problems. Motivated by these developments, we introduce a class of stochastic differential equations (SDEs) called gradient-adjusted underdamped Langevin dynamics (GAUL), which add stochastic perturbations in primal-dual damping dynamics and Hessian-driven damping dynamics from optimization. We prove that GAUL admits the correct stationary distribution, whose marginal is the target distribution. The proposed method outperforms overdamped and underdamped Langevin dynamics regarding convergence speed in the total variation distance for Gaussian target distributions. Moreover, using the Euler-Maruyama discretization, we show that the mixing time towards a biased target distribution only depends on the square root of the condition number of the target covariance matrix. Numerical experiments for non-Gaussian target distributions, such as Bayesian regression problems and Bayesian neural networks, further illustrate the advantages of our approach., Comment: added references, discussion on preconditioner

DNA-Encoded Libraries (DEL) are combinatorial small molecule libraries that offer an efficient way to characterize diverse chemical spaces. Selection experiments using DELs are pivotal to drug discovery efforts, enabling high-throughput screens for hit finding. However, limited availability of public DEL datasets hinders the advancement of computational techniques designed to process such data. To bridge this gap, we present KinDEL, one of the first large, publicly available DEL datasets on two kinases: Mitogen-Activated Protein Kinase 14 (MAPK14) and Discoidin Domain Receptor Tyrosine Kinase 1 (DDR1). Interest in this data modality is growing due to its ability to generate extensive supervised chemical data that densely samples around select molecular structures. Demonstrating one such application of the data, we benchmark different machine learning techniques to develop predictive models for hit identification; in particular, we highlight recent structure-based probabilistic approaches. Finally, we provide biophysical assay data, both on- and off-DNA, to validate our models on a smaller subset of molecules. Data and code for our benchmarks can be found at: https://github.com/insitro/kindel.

Independent Component Analysis (ICA) is commonly-used in electroencephalogram (EEG) signal processing to remove non-cerebral artifacts from cerebral data. Despite the ubiquity of ICA, the effect of measurement uncertainty on the artifact removal process has not been thoroughly investigated. We first characterize the measurement uncertainty distribution of a common ADC and show that it quantitatively conforms to a Gaussian distribution. We then evaluate the effect of measurement uncertainty on the artifact identification process through several computer simulations. These computer simulations evaluate the performance of two different ICA algorithms, FastICA and Infomax, in removing eyeblink artifacts from five different electrode configurations with varying levels of measurement uncertainty. FastICA and Infomax show similar performance in identifying the eyeblink artifacts for a given uncertainty level and electrode configuration. We quantify the correlation performance degradation with respect to SNR and show that in general, an SNR of greater than 15 dB results in less than a 5% degradation in performance. The biggest difference in performance between the two algorithms is in their execution time. FastICA's execution time is dependent on the amount of measurement uncertainty, with a 50% to 85% reduction in execution time over an SNR range of 20 dB. This contrasts with Infomax's execution time, which is unaffected by measurement uncertainty., Comment: 8 pages, 9 figures

We present a novel deep learning pipeline to perform a model-independent, likelihood-free search for anomalous (i.e., non-background) events in the proposed next generation multi-ton scale liquid Xenon-based direct detection experiment, DARWIN. We train an anomaly detector comprising a variational autoencoder and a classifier on extensive, high-dimensional simulated detector response data and construct a one-dimensional anomaly score optimised to reject the background only hypothesis in the presence of an excess of non-background-like events. We benchmark the procedure with a sensitivity study that determines its power to reject the background-only hypothesis in the presence of an injected WIMP dark matter signal, outperforming the classical, likelihood-based background rejection test. We show that our neural networks learn relevant energy features of the events from low-level, high-dimensional detector outputs, without the need to compress this data into lower-dimensional observables, thus reducing computational effort and information loss. For the future, our approach lays the foundation for an efficient end-to-end pipeline that eliminates the need for many of the corrections and cuts that are traditionally part of the analysis chain, with the potential of achieving higher accuracy and significant reduction of analysis time., Comment: 10 Figures, 3 Tables, 23 Pages (incl. references)

OBJECTIVE: To evaluate the efficacy of different forms of virtual reality (VR) treatments as either immersive virtual reality (IVR) or non-immersive virtual reality (NIVR) in comparison to conventional therapy (CT) in improving physical and psychological status among stroke patients. METHODS: The literature search was conducted on seven databases. ACM Digital Library, Medline (via PubMed), Cochrane, IEEE Xplore, Web of Science, and Scopus. The effect sizes of the main outcomes were calculated using Cohen's d. Pooled results were used to present an overall estimate of the treatment effect using a random-effects model. RESULTS: A total of 22 randomized controlled trials were evaluated. 3 trials demonstrated that immersive virtual reality improved upper limb activity, function and activity of daily life in a way comparable to CT. 18 trials showed that NIVR had similar benefits to CT for upper limb activity and function, balance and mobility, activities of daily living and participation. A comparison between the different forms of VR showed that IVR may be more beneficial than NIVR for upper limb training and activities of daily life. CONCLUSIONS: This study found out that IVR therapies may be more effective than NIVR but not CT to improve upper limb activity, function, and daily life activities. However, there is no evidence of the durability of IVR treatment. More research involving studies with larger samples is needed to assess the long-term effects and promising benefits of immersive virtual reality technology., Comment: 32 pages

Knowledge graphs (KGs) represent connections and relationships between real-world entities. We propose a link prediction framework for KGs named Enrichment-Driven GrAph Reasoner (EDGAR), which infers new edges by mining entity-local rules. This approach leverages enrichment analysis, a well-established statistical method used to identify mechanisms common to sets of differentially expressed genes. EDGAR's inference results are inherently explainable and rankable, with p-values indicating the statistical significance of each enrichment-based rule. We demonstrate the framework's effectiveness on a large-scale biomedical KG, ROBOKOP, focusing on drug repurposing for Alzheimer disease (AD) as a case study. Initially, we extracted 14 known drugs from the KG and identified 20 contextual biomarkers through enrichment analysis, revealing functional pathways relevant to shared drug efficacy for AD. Subsequently, using the top 1000 enrichment results, our system identified 1246 additional drug candidates for AD treatment. The top 10 candidates were validated using evidence from medical literature. EDGAR is deployed within ROBOKOP, complete with a web user interface. This is the first study to apply enrichment analysis to large graph completion and drug repurposing., Comment: 10 pages, 5 figures, 4 tables

Classical neural ordinary differential equations (ODEs) are powerful tools for approximating the log-density functions in high-dimensional spaces along trajectories, where neural networks parameterize the velocity fields. This paper proposes a system of neural differential equations representing first- and second-order score functions along trajectories based on deep neural networks. We reformulate the mean field control (MFC) problem with individual noises into an unconstrained optimization problem framed by the proposed neural ODE system. Additionally, we introduce a novel regularization term to enforce characteristics of viscous Hamilton--Jacobi--Bellman (HJB) equations to be satisfied based on the evolution of the second-order score function. Examples include regularized Wasserstein proximal operators (RWPOs), probability flow matching of Fokker--Planck (FP) equations, and linear quadratic (LQ) MFC problems, which demonstrate the effectiveness and accuracy of the proposed method.

Many fMRI analyses examine functional connectivity, or statistical dependencies among remote brain regions. Yet popular methods for studying whole-brain functional connectivity often yield results that are difficult to interpret. Factor analysis offers a natural framework in which to study such dependencies, particularly given its emphasis on interpretability. However, multivariate factor models break down when applied to functional and spatiotemporal data, like fMRI. We present a factor model for discretely-observed multidimensional functional data that is well-suited to the study of functional connectivity. Unlike classical factor models which decompose a multivariate observation into a "common" term that captures covariance between observed variables and an uncorrelated "idiosyncratic" term that captures variance unique to each observed variable, our model decomposes a functional observation into two uncorrelated components: a "global" term that captures long-range dependencies and a "local" term that captures short-range dependencies. We show that if the global covariance is smooth with finite rank and the local covariance is banded with potentially infinite rank, then this decomposition is identifiable. Under these conditions, recovery of the global covariance amounts to rank-constrained matrix completion, which we exploit to formulate consistent loading estimators. We study these estimators, and their more interpretable post-processed counterparts, through simulations, then use our approach to uncover a rich covariance structure in a collection of resting-state fMRI scans.

Stance detection is a crucial NLP task with numerous applications in social science, from analyzing online discussions to assessing political campaigns. This paper investigates the optimal way to incorporate metadata into a political stance detection task. We demonstrate that previous methods combining metadata with language-based data for political stance detection have not fully utilized the metadata information; our simple baseline, using only party membership information, surpasses the current state-of-the-art. We then show that prepending metadata (e.g., party and policy) to political speeches performs best, outperforming all baselines, indicating that complex metadata inclusion systems may not learn the task optimally.

Articulated objects and their representations pose a difficult problem for robots. These objects require not only representations of geometry and texture, but also of the various connections and joint parameters that make up each articulation. We propose a method that learns a common Neural Radiance Field (NeRF) representation across a small number of collected scenes. This representation is combined with a parts-based image segmentation to produce an implicit space part localization, from which the connectivity and joint parameters of the articulated object can be estimated, thus enabling configuration-conditioned rendering., Comment: extended abstract as submitted to ICRA@40 anniversary conference

The Radar Echo Telescope for Cosmic Rays (RET-CR), a pathfinder instrument for the radar echo method of ultrahigh energy (UHE) neutrino detection, was initially deployed near Summit Station, Greenland, in May 2023. After a 4 week commissioning period, 9 days of data were taken before the instrument went offline. In this article, we describe the instrument as it was deployed, and the initial performance of the detector. We show that the technical aspects of running a radar based particle cascade detector in the ice have been demonstrated. Analysis of the 2023 data informed improvements that were incorporated into the May-August 2024 deployment, which has just concluded at time of writing. Results from the 2024 run will be presented in forthcoming publications., Comment: To be submitted to PRD

This paper introduces SO(2)-Equivariant Gaussian Sculpting Networks (GSNs) as an approach for SO(2)-Equivariant 3D object reconstruction from single-view image observations. GSNs take a single observation as input to generate a Gaussian splat representation describing the observed object's geometry and texture. By using a shared feature extractor before decoding Gaussian colors, covariances, positions, and opacities, GSNs achieve extremely high throughput (>150FPS). Experiments demonstrate that GSNs can be trained efficiently using a multi-view rendering loss and are competitive, in quality, with expensive diffusion-based reconstruction algorithms. The GSN model is validated on multiple benchmark experiments. Moreover, we demonstrate the potential for GSNs to be used within a robotic manipulation pipeline for object-centric grasping., Comment: Accepted to RSS 2024 Workshop on Geometric and Algebraic Structure in Robot Learning

Large Language Models (LLMs) have rapidly increased in size and apparent capabilities in the last three years, but their training data is largely English text. There is growing interest in multilingual LLMs, and various efforts are striving for models to accommodate languages of communities outside of the Global North, which include many languages that have been historically underrepresented in digital realms. These languages have been coined as "low resource languages" or "long-tail languages", and LLMs performance on these languages is generally poor. While expanding the use of LLMs to more languages may bring many potential benefits, such as assisting cross-community communication and language preservation, great care must be taken to ensure that data collection on these languages is not extractive and that it does not reproduce exploitative practices of the past. Collecting data from languages spoken by previously colonized people, indigenous people, and non-Western languages raises many complex sociopolitical and ethical questions, e.g., around consent, cultural safety, and data sovereignty. Furthermore, linguistic complexity and cultural nuances are often lost in LLMs. This position paper builds on recent scholarship, and our own work, and outlines several relevant social, cultural, and ethical considerations and potential ways to mitigate them through qualitative research, community partnerships, and participatory design approaches. We provide twelve recommendations for consideration when collecting language data on underrepresented language communities outside of the Global North.

In this work, we investigate the convergence properties of the backward regularized Wasserstein proximal (BRWP) method for sampling a target distribution. The BRWP approach can be shown as a semi-implicit time discretization for a probability flow ODE with the score function whose density satisfies the Fokker-Planck equation of the overdamped Langevin dynamics. Specifically, the evolution of the score function is computed using a kernel formula derived from the regularized Wasserstein proximal operator. By applying the Laplace method to obtain the asymptotic expansion of this kernel formula, we establish guaranteed convergence in terms of the Kullback-Leibler divergence for the BRWP method towards a strongly log-concave target distribution. Our analysis also identifies the optimal and maximum step sizes for convergence. Furthermore, we demonstrate that the deterministic and semi-implicit BRWP scheme outperforms many classical Langevin Monte Carlo methods, such as the Unadjusted Langevin Algorithm (ULA), by offering faster convergence and reduced bias. Numerical experiments further validate the convergence analysis of the BRWP method.

Artificial Intelligence (AI) has paved the way for revolutionary decision-making processes, which if harnessed appropriately, can contribute to advancements in various sectors, from healthcare to economics. However, its black box nature presents significant ethical challenges related to bias and transparency. AI applications are hugely impacted by biases, presenting inconsistent and unreliable findings, leading to significant costs and consequences, highlighting and perpetuating inequalities and unequal access to resources. Hence, developing safe, reliable, ethical, and Trustworthy AI systems is essential. Our team of researchers working with Trustworthy and Responsible AI, part of the Transdisciplinary Scholarship Initiative within the University of Calgary, conducts research on Trustworthy and Responsible AI, including fairness, bias mitigation, reproducibility, generalization, interpretability, and authenticity. In this paper, we review and discuss the intricacies of AI biases, definitions, methods of detection and mitigation, and metrics for evaluating bias. We also discuss open challenges with regard to the trustworthiness and widespread application of AI across diverse domains of human-centric decision making, as well as guidelines to foster Responsible and Trustworthy AI models., Comment: 44 pages, 2 figures

This study investigates the application of machine/deep learning to classify snoring sounds excited at different levels of the upper airway in patients with obstructive sleep apnea (OSA) using data from drug-induced sleep endoscopy (DISE). The snoring sounds of 39 subjects were analyzed and labeled according to the Velum, Oropharynx, Tongue Base, and Epiglottis (VOTE) classification system. The dataset, comprising 5,173 one-second segments, was used to train and test models, including Support Vector Machine (SVM), Bidirectional Long Short-Term Memory (BiLSTM), and ResNet-50. The ResNet-50, a convolutional neural network (CNN), showed the best overall performance in classifying snoring acoustics, particularly in identifying multi-level obstructions. The study emphasizes the potential of integrating snoring acoustics with deep learning to improve the diagnosis and treatment of OSA. However, challenges such as limited sample size, data imbalance, and differences between pharmacologically induced and natural snoring sounds were noted, suggesting further research to enhance model accuracy and generalizability.