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Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has proved the efficiency of this field. Despite the existing tools for protein retrieval, they prioritize sequence similarity and probably overlook proteins that are dissimilar but share homology or functionality. In order to tackle this problem, we propose a novel protein retrieval framework that mitigates the bias towards sequence similarity. Our framework initiatively harnesses protein language models (PLMs) to embed protein sequences within a high-dimensional feature space, thereby enhancing the representation capacity for subsequent analysis. Subsequently, an accelerated indexed vector database is constructed to facilitate expedited access and retrieval of dense vectors. Extensive experiments demonstrate that our framework can equally retrieve both similar and dissimilar proteins. Moreover, this approach enables the identification of proteins that conventional methods fail to uncover. This framework will effectively assist in protein mining and empower the development of biology., Comment: 16 pages, 12 figures

We contribute an unsupervised method that effectively learns from raw observation and disentangles its latent space into content and style representations. Unlike most disentanglement algorithms that rely on domain-specific labels and knowledge, our method is based on the insight of domain-general statistical differences between content and style -- content varies more among different fragments within a sample but maintains an invariant vocabulary across data samples, whereas style remains relatively invariant within a sample but exhibits more significant variation across different samples. We integrate such inductive bias into an encoder-decoder architecture and name our method after V3 (variance-versus-invariance). Experimental results show that V3 generalizes across two distinct domains in different modalities, music audio and images of written digits, successfully learning pitch-timbre and digit-color disentanglements, respectively. Also, the disentanglement robustness significantly outperforms baseline unsupervised methods and is even comparable to supervised counterparts. Furthermore, symbolic-level interpretability emerges in the learned codebook of content, forging a near one-to-one alignment between machine representation and human knowledge.

Perceptual rivalry, where conflicting sensory information leads to alternating perceptions crucial for associated cognitive function, has attracted researcher's attention for long. Despite progresses being made, recent studies have revealed limitations and inconsistencies in our understanding across various rivalry contexts. We develop a unified physical framework, where perception undergoes a consecutive phase transition process encompassing different multi-state competitions. We reveal the underlying mechanisms of perceptual rivalry by identifying dominant switching paths among perceptual states and quantifying mean perceptual durations, switching frequencies, and proportions of different perceptions. We uncover the underlying nonequilibrium dynamics and thermodynamics by analyzing average nonequilibrium flux and entropy production rate, while associated time series irreversibility reflects the underlying nonequilibrium mechanism of perceptual rivalry and link thermodynamical results with neuro-electrophysiological experiments. Our framework provides a global and physical understanding of brain perception, which may go beyond cognitive science or psychology but embodies the connection with wider fields as decision-making., Comment: 26 pages, 10 figures

The growing market and massive use of Internet of Things nodes is placing unprecedented demands of energy efficient hardware for edge computing and microwave devices. In particular, magnetic tunnel junctions (MTJs), as main building blocks of spintronic microwave technology, can offer a path for the development of compact and high-performance microwave detectors. On the other hand, the fascinating field of skyrmionics is bridging together concepts from topology and spintronics. Here, we show the proof of concept of a topological spin-torque diode realized with an MTJ on top of a skyrmionic material at room temperature and for a wide region of applied fields, including the zero-field case. Our spin torque diode electrical measurements show the electrical excitation of a skyrmion resonant mode with frequencies near 4 GHz and a selectivity one order of magnitude smaller than the uniform modes excited in the same device. Micromagnetic simulations identify these dynamics with the excitation of the breathing mode and point out the role of thickness dependent magnetic parameters (magnetic anisotropy field and Dzyaloshinkii Moriya interaction) in both stabilizing and exciting the magnetic skyrmions. This work marks a milestone for the development of topological spin-torque diodes.

The convergence rate of various first-order optimization algorithms is a pivotal concern within the numerical optimization community, as it directly reflects the efficiency of these algorithms across different optimization problems. Our goal is making a significant step forward in the formal mathematical representation of optimization techniques using the Lean4 theorem prover. We first formalize the gradient for smooth functions and the subgradient for convex functions on a Hilbert space, laying the groundwork for the accurate formalization of algorithmic structures. Then, we extend our contribution by proving several properties of differentiable convex functions that have not yet been formalized in Mathlib. Finally, a comprehensive formalization of these algorithms is presented. These developments are not only noteworthy on their own but also serve as essential precursors to the formalization of a broader spectrum of numerical algorithms and their applications in machine learning as well as many other areas.

We investigate the finite-temperature superfluid behavior of ultracold atomic Fermi gases in quasi-two-dimensional Lieb lattices with a short-range attractive interaction, using a pairing fluctuation theory within the BCS-BEC crossover framework. We find that the presence of a flat band, along with van Hove singularities, leads to exotic quantum phenomena. As the Fermi level enters the flat band, both the gap and the superfluid transition temperature $T_c$ as a function of interaction change from a conventional exponential behavior into an unusual power law, and the evolution of superfluid densities with temperature also follows a power law even at weak interactions. The quantum geometric effects, manifested by an enhanced effective pair hopping integral, may contribute significantly to both $T_c$ and the superfluidities. As the chemical potential crosses the van Hove singularities in the weak interaction regime, the nature of pairing changes between particle-like and hole-like. A pair density wave state emerges at high densities with a relatively strong interaction strength., Comment: 10 pages, 6 figures. arXiv admin note: text overlap with arXiv:2310.12944

Nearly every massive galaxy contains a supermassive black hole (BH) at its center. For decades, both theory and numerical simulations have indicated that BHs play a central role in regulating the growth and quenching of galaxies. Specifically, BH feedback by heating or blowing out the interstellar medium (ISM) serves as the groundwork for current models of massive galaxy formation. However, direct evidence for such an impact on the galaxy-wide ISM from BHs has only been found in some extreme objects. For general galaxy populations, it remains unclear whether and how BHs impact the ISM. Here based on a large sample of nearby galaxies with measurements of masses of both black holes and atomic hydrogen, the major component of cold ISM, we reveal that the atomic hydrogen content ($f_{\rm HI} = M_{\rm HI}/M_{\star}$) is tightly and anti-correlated with black hole mass ($M_{\rm BH}$) with $f_{\rm HI} \propto M^{-\alpha}_{\rm BH}$ ($\alpha \sim 0.5-0.6$). This correlation is valid across five orders of magnitude in $M_{\rm BH}$. Once this correlation is taken into account, $f_{\rm HI}$ loses dependence on other galactic parameters, demonstrating that $M_{\rm BH}$ serves as the primary driver of $f_{\rm HI}$. These findings provide critical evidence for how the accumulated energy from BH accretion impacts galaxy-wide ISM, representing a crucial step forward in our understanding on the role of BHs in regulating the growth and quenching of massive galaxies., Comment: 24 pages, 7 figures. Submitted to Nature

The ground-state superfluid behavior of ultracold atomic Fermi gases with a short-range attractive interaction in a quasi-two-dimensional Lieb lattice is studied using BCS mean-field theory, within the context of BCS-BEC crossover. We find that the flat band leads to nontrivial exotic effects. As the Fermi level enters the flat band, both the pairing gap and the in-plane superfluid density exhibit an unusual power law as a function of interaction, with strongly enhanced quantum geometric effects, in addition to a dramatic increase of compressibility as the interaction approaches the BCS limit. As the Fermi level crosses the van Hove singularities, the character of pairing changes from particle-like to hole-like or vice versa. We present the computed phase diagram, in which a pair density wave state emerges at high densities with relatively strong interaction strength., Comment: 9 pages, 6 figures in color

In this study, we generalize the work of Farhi, Guth and Guven [Nucl. Phys. B 339 (1990) 417] to include a wormhole effect. We study the influence of the wormhole on the tunneling of the false vacuum bubble. The spherically symmetric bubble has two domain walls. The classical dynamics of each domain wall are constrained by two classically forbidden regions. We find that the wormhole has increased the number of instantons and thus can enhance the tunneling rate. We have analytically derived the formula for the bubble tunneling rate, which is consistent with the result obtained by Farhi, Guth and Guven when the wormhole disappears. We show that the tunneling rate increases with the throat radius of the wormhole. Furthermore, we illustrate that the tunneling rate increases with an increases in the mass of the black hole or the surface tension. In the case where a wormhole exists within a bubble and is connected to another universe, we demonstrate that the bubble can enter into another universe through quantum tunneling.

Music motif, as a conceptual building block of composition, is crucial for music structure analysis and automatic composition. While human listeners can identify motifs easily, existing computational models fall short in representing motifs and their developments. The reason is that the nature of motifs is implicit, and the diversity of motif variations extends beyond simple repetitions and modulations. In this study, we aim to learn the implicit relationship between motifs and their variations via representation learning, using the Siamese network architecture and a pretraining and fine-tuning pipeline. A regularization-based method, VICReg, is adopted for pretraining, while contrastive learning is used for fine-tuning. Experimental results on a retrieval-based task show that these two methods complement each other, yielding an improvement of 12.6% in the area under the precision-recall curve. Lastly, we visualize the acquired motif representations, offering an intuitive comprehension of the overall structure of a music piece. As far as we know, this work marks a noteworthy step forward in computational modeling of music motifs. We believe that this work lays the foundations for future applications of motifs in automatic music composition and music information retrieval.

The widespread adoption of speech-based online services raises security and privacy concerns regarding the data that they use and share. If the data were compromised, attackers could exploit user speech to bypass speaker verification systems or even impersonate users. To mitigate this, we propose DeID-VC, a speaker de-identification system that converts a real speaker to pseudo speakers, thus removing or obfuscating the speaker-dependent attributes from a spoken voice. The key components of DeID-VC include a Variational Autoencoder (VAE) based Pseudo Speaker Generator (PSG) and a voice conversion Autoencoder (AE) under zero-shot settings. With the help of PSG, DeID-VC can assign unique pseudo speakers at speaker level or even at utterance level. Also, two novel learning objectives are added to bridge the gap between training and inference of zero-shot voice conversion. We present our experimental results with word error rate (WER) and equal error rate (EER), along with three subjective metrics to evaluate the generated output of DeID-VC. The result shows that our method substantially improved intelligibility (WER 10% lower) and de-identification effectiveness (EER 5% higher) compared to our baseline. Code and listening demo: https://github.com/a43992899/DeID-VC, Comment: Accepted by Interspeech 2022

We employ a typical genetic circuit model to explore how noise can influence the dynamic structure. With the increase of a key interactive parameter, the model will deterministically go through two bifurcations and three dynamic structure regions. We find that a new quasi-periodic component, which is not allowed by deterministic dynamics, will be generated by noise inducing in the first two regions, and this quasi-period will be more and more stable along with the noise increasing. Especially, in the second region, the quasi-period will compete with a stable limit cycle and perform a new transient rhythm. Furthermore, we ascertain the entropy production rate (EPR) and the heat dissipation rate (HDR), and discover a minimal value with elucidating theoretically. In the end, we unveil the mechanism of the quasi-periods forming, and show a practical biological instance. We expect that this work is helpful to solve some biological or ecological problems, such as genetic origin of periodical cicadas and population dynamics with fluctuation.

Despite commercial airlines mandating masks, there have been multiple documented events of COVID-19 superspreading on flights. We used available data from three flights, including cabin layout and seat locations of infected and uninfected passengers, to suggest interventions to mitigate COVID-19 superspreading events during air travel. Specifically, we studied: 1) London to Hanoi with 201 passengers, including 13 secondary infections among passengers; 2) Singapore to Hangzhou with 321 passengers, including 12 to 14 secondary infections; 3) a non-superspreading event on a private jet in Japan with 9 passengers and no secondary infections. We show that inclusion of passenger movement better explains the infection spread patterns than conventional models do. We also found that FFP2/N95 mask usage would have reduced infection by 95-100%, while cloth masks would have reduced it by only 40-80%. This suggests the need for more stringent guidelines to reduce aviation-related superspreading events of COVID-19.