Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families. Does successful inference mainly rely on correlations from structural contacts or from phylogeny, or both? Do these two types of signal combine constructively or hinder each other? To address these questions, we generate and analyze synthetic data produced using a minimal model that allows us to control the amounts of structural constraints and phylogeny. We show that correlations from these two sources combine constructively to increase the performance of partner inference by DCA or MI. Furthermore, signal from phylogeny can rescue partner inference when signal from contacts becomes less informative, including in the realistic case where inter-protein contacts are restricted to a small subset of sites. We also demonstrate that DCA-inferred couplings between non-contact pairs of sites improve partner inference in the presence of strong phylogeny, while deteriorating it otherwise. Moreover, restricting to non-contact pairs of sites preserves inference performance in the presence of strong phylogeny. In a natural data set, as well as in realistic synthetic data based on it, we find that non-contact pairs of sites contribute positively to partner inference performance, and that restricting to them preserves performance, evidencing an important role of phylogeny. Author summary In protein sequence data, the amino acid usages at different sites of a protein or of two interacting proteins can be correlated because of functional constraints. For instance, the need to maintain physicochemical complementarity among two sites that are in contact in the three-dimensional structure of a protein complex causes such correlations. However, correlations can also arise due to shared evolutionary history, even in the absence of any functional constraint. While these phylogenetic correlations are known to obscure the inference of structural contacts, we show, using controlled synthetic data, that correlations from structure and phylogeny combine constructively to allow the inference of protein partners among paralogs using just sequences. We also show that pairs of amino acids that are not in contact in the structure have a major impact on partner inference in a natural data set and in realistic synthetic ones. These findings explain the success of methods based on pairwise maximum-entropy models or on information theory at predicting protein partners from sequences among paralogs.
Local Linearity and Double Descent in Catastrophic Overfitting

Catastrophic overfitting is a phenomenon observed during Adversarial Training (AT) with the Fast Gradient Sign Method (FGSM) where the test robustness steeply declines over just one epoch in the training stage. Prior work has attributed this loss in robustness to a sharp decrease in local linearity of the neural network with respect to the input space, and has demonstrated that introducing a local linearity measure as a regularization term prevents catastrophic overfitting. Using a simple neural network architecture, we experimentally demonstrate that maintaining high local linearity might be sufficient to prevent catastrophic overfitting but is not necessary. Further, inspired by Parseval networks, we introduce a regularization term to AT with FGSM to make the weight matrices of the network orthogonal and study the connection between orthogonality of the network weights and local linearity. Lastly, we identify the double descent phenomenon during the adversarial training process. Source code is available at https://github.com/nikilrselvam/linearity-orthogonality-dd.
Safe Multi-Task Learning

In recent years, Multi-Task Learning (MTL) attracts much attention due to its good performance in many applications. However, many existing MTL models cannot guarantee that its performance is no worse than its single-task counterpart on each task. Though this phenomenon has been empirically observed by some works, little work aims to handle the resulting problem, which is formally defined as negative sharing in this paper. To achieve safe multi-task learning where no negative sharing occurs, we propose a Safe Multi-Task Learning (SMTL) model, which consists of a public encoder shared by all the tasks, private encoders, gates, and private decoders. Specifically, each task has a private encoder, a gate, and a private decoder, where the gate is to learn how to combine the private encoder and public encoder for the downstream private decoder. To reduce the storage cost during the inference stage, a lite version of SMTL is proposed to allow the gate to choose either the public encoder or the corresponding private encoder. Moreover, we propose a variant of SMTL to place all the gates after decoders of all the tasks. Experiments on several benchmark datasets demonstrate the effectiveness of the proposed methods.
CpT: Convolutional Point Transformer for 3D Point Cloud Processing

We present CpT: Convolutional point Transformer - a novel deep learning architecture for dealing with the unstructured nature of 3D point cloud data. CpT is an improvement over existing attention-based Convolutions Neural Networks as well as previous 3D point cloud processing transformers. It achieves this feat due to its effectiveness in creating a novel and robust attention-based point set embedding through a convolutional projection layer crafted for processing dynamically local point set neighbourhoods. The resultant point set embedding is robust to the permutations of the input points. Our novel CpT block builds over local neighbourhoods of points obtained via a dynamic graph computation at each layer of the networks' structure. It is fully differentiable and can be stacked just like convolutional layers to learn global properties of the points. We evaluate our model on standard benchmark datasets such as ModelNet40, ShapeNet Part Segmentation, and the S3DIS 3D indoor scene semantic segmentation dataset to show that our model can serve as an effective backbone for various point cloud processing tasks when compared to the existing state-of-the-art approaches.
PRISM: A Hierarchical Intrusion Detection Architecture for Large-Scale Cyber Networks

The increase in scale of cyber networks and the rise in sophistication of cyber-attacks have introduced several challenges in intrusion detection. The primary challenge is the requirement to detect complex multi-stage attacks in realtime by processing the immense amount of traffic produced by present-day networks. In this paper we present PRISM, a hierarchical intrusion detection architecture that uses a novel attacker behavior model-based sampling technique to minimize the realtime traffic processing overhead. PRISM has a unique multi-layered architecture that monitors network traffic distributedly to provide efficiency in processing and modularity in design. PRISM employs a Hidden Markov Model-based prediction mechanism to identify multi-stage attacks and ascertain the attack progression for a proactive response. Furthermore, PRISM introduces a stream management procedure that rectifies the issue of alert reordering when collected from distributed alert reporting systems. To evaluate the performance of PRISM, multiple metrics have been proposed, and various experiments have been conducted on multi-stage attack datasets. The results exhibit up to 7.5x improvement in processing overhead as compared to a standard centralized IDS without the loss of prediction accuracy while demonstrating the ability to predict different attack stages promptly.
Structural Color Production in Melanin‐Based Disordered Colloidal Nanoparticle Assemblies in Spherical Confinement

Melanin is a ubiquitous natural pigment that exhibits broadband absorption and high refractive index. Despite its widespread use in structural color production, how the absorbing material, melanin, affects the generated color is unknown. Using a combined molecular dynamics and finite‐difference time‐domain computational approach, this paper investigates structural color generation in one‐component melanin nanoparticle‐based supraparticles (called supraballs) as well as binary mixtures of melanin and silica (nonabsorbing) nanoparticle‐based supraballs. Experimentally produced one‐component melanin and one‐component silica supraballs, with thoroughly characterized primary particle characteristics using neutron scattering, produce reflectance profiles similar to the computational analogs, confirming that the computational approach correctly simulates both absorption and multiple scattering from the self‐assembled nanoparticles. These combined approaches demonstrate that melanin's broadband absorption increases the primary reflectance peak wavelength, increases saturation, and decreases lightness factor. In addition, the dispersity of nanoparticle size more strongly influences the optical properties of supraballs than packing fraction, as evidenced by the production of a larger range of colors when size dispersity is varied versus packing fraction. For binary melanin and silica supraballs, the chemistry‐based stratification allows for more diverse color generation and finer saturation tuning than does the degree of mixing/demixing between the two chemistries.
Predictive Maintenance Model for Ballast Tamping

AbstractIn order to optimally schedule railway track maintenance operations, it is essential to accurately estimate future track conditions. This study proposes a railway track geometry degradation model that considers uncertainties in the forecast by defining a track geometry reliability parameter. The degradation model is integrated in a multiobjective optimization approach to assess railway track maintenance strategies considering a cost–reliability trade off. Finally, a numerical application of the model to a real case study is presented. The results show the usefulness of the proposed approach to guarantee a required track geometry performance with effective maintenance investments.
A new perspective on cerebrospinal fluid dynamics after subarachnoid hemorrhage: From normal physiology to pathophysiological changes

Knowledge about the dynamic metabolism and function of cerebrospinal fluid (CSF) physiology has rapidly progressed in recent decades. It has traditionally been suggested that CSF is produced by the choroid plexus and drains to the arachnoid villi. However, recent findings have revealed that the brain parenchyma produces a large portion of CSF and drains through the perivascular glymphatic system and meningeal lymphatic vessels into the blood. The primary function of CSF is not limited to maintaining physiological CNS homeostasis but also participates in clearing waste products resulting from neurodegenerative diseases and acute brain injury. Aneurysmal subarachnoid hemorrhage (SAH), a disastrous subtype of acute brain injury, is associated with high mortality and morbidity. Post-SAH complications contribute to the poor outcomes associated with SAH. Recently, abnormal CSF flow was suggested to play an essential role in the post-SAH pathophysiological changes, such as increased intracerebral pressure, brain edema formation, hydrocephalus, and delayed blood clearance. An in-depth understanding of CSF dynamics in post-SAH events would shed light on potential development of SAH treatment options. This review summarizes and updates the latest physiological characteristics of CSF dynamics and discusses potential pathophysiological changes and therapeutic targets after SAH.
Identity-Preserving Pose-Robust Face Hallucination Through Face Subspace Prior

Over the past few decades, numerous attempts have been made to address the problem of recovering a high-resolution (HR) facial image from its corresponding low-resolution (LR) counterpart, a task commonly referred to as face hallucination. Despite the impressive performance achieved by position-patch and deep learning-based methods, most of these techniques are still unable to recover identity-specific features of faces. The former group of algorithms often produces blurry and oversmoothed outputs particularly in the presence of higher levels of degradation, whereas the latter generates faces which sometimes by no means resemble the individuals in the input images. In this paper, a novel face super-resolution approach will be introduced, in which the hallucinated face is forced to lie in a subspace spanned by the available training faces. Therefore, in contrast to the majority of existing face hallucination techniques and thanks to this face subspace prior, the reconstruction is performed in favor of recovering person-specific facial features, rather than merely increasing image quantitative scores. Furthermore, inspired by recent advances in the area of 3D face reconstruction, an efficient 3D dictionary alignment scheme is also presented, through which the algorithm becomes capable of dealing with low-resolution faces taken in uncontrolled conditions. In extensive experiments carried out on several well-known face datasets, the proposed algorithm shows remarkable performance by generating detailed and close to ground truth results which outperform the state-of-the-art face hallucination algorithms by significant margins both in quantitative and qualitative evaluations.
Vulcan: Solving the Steiner Tree Problem with Graph Neural Networks and Deep Reinforcement Learning

Steiner Tree Problem (STP) in graphs aims to find a tree of minimum weight in the graph that connects a given set of vertices. It is a classic NP-hard combinatorial optimization problem and has many real-world applications (e.g., VLSI chip design, transportation network planning and wireless sensor networks). Many exact and approximate algorithms have been developed for STP, but they suffer from high computational complexity and weak worst-case solution guarantees, respectively. Heuristic algorithms are also developed. However, each of them requires application domain knowledge to design and is only suitable for specific scenarios. Motivated by the recently reported observation that instances of the same NP-hard combinatorial problem may maintain the same or similar combinatorial structure but mainly differ in their data, we investigate the feasibility and benefits of applying machine learning techniques to solving STP. To this end, we design a novel model Vulcan based on novel graph neural networks and deep reinforcement learning. The core of Vulcan is a novel, compact graph embedding that transforms highdimensional graph structure data (i.e., path-changed information) into a low-dimensional vector representation. Given an STP instance, Vulcan uses this embedding to encode its pathrelated information and sends the encoded graph to a deep reinforcement learning component based on a double deep Q network (DDQN) to find solutions. In addition to STP, Vulcan can also find solutions to a wide range of NP-hard problems (e.g., SAT, MVC and X3C) by reducing them to STP. We implement a prototype of Vulcan and demonstrate its efficacy and efficiency with extensive experiments using real-world and synthetic datasets.
Modeling Traffic Crash-Flow Relationships for Intersections: Dispersion Parameter, Functional Form, and Bayes Versus Empirical Bayes Methods

Statistical relationships between traffic crashes and traffic flows at roadway intersections have been extensively modeled and evaluated in recent years. The underlying assumptions adopted in the popular models for intersections are challenged. First, the assumption that the dispersion parameter is a fixed parameter across sites and time periods is challenged. Second, the mathematical limitations of some functional forms used in these models, particularly their properties at the boundaries, are examined. It is also demonstrated that, for a given data set, a large number of plausible functional forms with almost the same overall statistical goodness of fit (GOF) is possible, and an alternative class of logical formulations that may enable a richer interpretation of the data is introduced. A comparison of site estimates from the empirical Bayes and full Bayes methods is also presented. All discussions and comparisons are illustrated with a set of data collected for an urban four-legged signalized intersection in Toronto, Ontario, Canada, from 1990 to 1995. In discussing functional forms, the need for some goodness-of-logic measures, in addition to the GOF measure, is emphasized and demonstrated. Finally, analysts are advised to be mindful of the underlying assumptions adopted in the popular models, especially the assumption that the dispersion parameter is a fixed parameter, and the limitations of the functional forms used. Promising directions in which this study may be extended are also discussed.
Sublinear quantum algorithms for estimating von Neumann entropy

Entropy is a fundamental property of both classical and quantum systems, spanning myriad theoretical and practical applications in physics and computer science. We study the problem of obtaining estimates to within a multiplicative factor $\gamma>1$ of the Shannon entropy of probability distributions and the von Neumann entropy of mixed quantum states. Our main results are: $\quad\bullet$ an $\widetilde{\mathcal{O}}\left( n^{\frac{1+\eta}{2\gamma^2}}\right)$-query quantum algorithm that outputs a $\gamma$-multiplicative approximation of the Shannon entropy $H(\mathbf{p})$ of a classical probability distribution $\mathbf{p} = (p_1,\ldots,p_n)$; $\quad\bullet$ an $\widetilde{\mathcal{O}}\left( n^{\frac12+\frac{1+\eta}{2\gamma^2}}\right)$-query quantum algorithm that outputs a $\gamma$-multiplicative approximation of the von Neumann entropy $S(\rho)$ of a density matrix $\rho\in\mathbb{C}^{n\times n}$. In both cases, the input is assumed to have entropy bounded away from zero by a quantity determined by the parameter $\eta>0$, since, as we prove, no polynomial query algorithm can multiplicatively approximate the entropy of distributions with arbitrarily low entropy. In addition, we provide $\Omega\left(n^{\frac{1}{3\gamma^2}}\right)$ lower bounds on the query complexity of $\gamma$-multiplicative estimation of Shannon and von Neumann entropies. We work with the quantum purified query access model, which can handle both classical probability distributions and mixed quantum states, and is the most general input model considered in the literature.
Online Beam Current Estimation in Particle Beam Microscopy

In conventional particle beam microscopy, knowledge of the beam current is essential for accurate micrograph formation and sample milling. This generally necessitates offline calibration of the instrument. In this work, we establish that beam current can be estimated online, from the same secondary electron count data that is used to form micrographs. Our methods depend on the recently introduced time-resolved measurement concept, which combines multiple short measurements at a single pixel and has previously been shown to partially mitigate the effect of beam current variation on micrograph accuracy. We analyze the problem of jointly estimating beam current and secondary electron yield using the Cramér–Rao bound. Joint estimators operating at a single pixel and estimators that exploit models for inter-pixel correlation and Markov beam current variation are proposed and tested on synthetic microscopy data. Our estimates of secondary electron yield that incorporate explicit beam current estimation beat state-of-the-art methods, resulting in micrograph accuracy nearly indistinguishable from what is obtained with perfect beam current knowledge. Our novel beam current estimation could help improve milling outcomes, prevent sample damage, and enable online instrument diagnostics.
A systematic approach to modeling of power semiconductor devices based on charge control principles

The charge control approach to modeling is extended to power devices by converting device equations to charge modules, which can then be used to assemble device models. This method represents a systematic technique for constructing models for power electronic circuit simulation. The resulting models are represented by relatively simple functions which are valid over a wide range of operation. <<ETX>>
Generation Drawing/Grinding Trajectoy Based on Hierarchical CVAE

In this study, we propose a method to model the local and global features of the drawing/grinding trajectory with hierarchical Variational Autoencoders (VAEs). By combining two separately trained VAE models in a hierarchical structure, it is possible to generate trajectories with high reproducibility for both local and global features. The hierarchical generation network enables the generation of higher-order trajectories with a relatively small amount of training data. The simulation and experimental results demonstrate the generalization performance of the proposed method. In addition, we confirmed that it is possible to generate new trajectories, which have never been learned in the past, by changing the combination of the learned models.
Towards Integrative Multi-Modal Personal Health Navigation Systems: Framework and Application

It is well understood that an individual’s health trajectory is influenced by choices made in each moment, such as from lifestyle or medical decisions. With the advent of modern sensing technologies, individuals have more data and information about themselves than any other time in history. How can we use this data to make the best decisions to keep the health state optimal? We propose a generalized Personal Health Navigation (PHN) framework. PHN takes individuals towards their personal health goals through a system which perpetually digests data streams, estimates current health status, computes the best route through intermediate states utilizing personal models, and guides the best inputs that carry a user towards their goal.In addition to describing the general framework, we test the PHN system in two experiments within the field of cardiology. First, we prospectively test a knowledge-infused cardiovascular PHN system with a pilot clinical trial of 41 users. Second, we build a data-driven personalized model on cardiovascular exercise response variability on a smartwatch data-set of 33,269 real-world users. We conclude with critical challenges in health computing for PHN systems that require deep future investigation.
Plankton image classification using novel parallel-training learning vector quantization network

At the base of the food chain in the ocean, plankton have a large impact on marine ecosystem dynamics. Rapid mapping of plankton abundance together with taxonomic and size composition is very important for ocean environmental research but difficult or impossible to accomplish using traditional techniques. In this paper, the authors develop a new pattern recognition system to classify large numbers of plankton images detected in real time by a towed underwater video system. The difficulty of such classification is compounded because the data sets are not only noisier but the plankton are non-rigid, projection-variant, and often in partial occlusion. The approach described combines traditional invariant moments features and Fourier boundary descriptors with gray-scale morphological granulometries to form a feature vector capturing both shape and texture information of plankton images. With a novel parallel-training learning vector quantization network classifier, the authors achieve 95% classification accuracy on six plankton taxa taken from more than 2,000 images, making possible for the first time a fully automated, at-sea approach to real-time mapping of plankton.