Miracle-dz/UniFAR-FTUs huggingface dataset:
DiscoGen: Learning to Discover Gene Regulatory Networks

Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs, perturbational data is required. However, most GRN discovery methods only operate on observational data. Recent advances in neural network-based causal discovery methods have significantly improved causal discovery, including handling interventional data, improvements in performance and scalability. However, applying state-of-the-art (SOTA) causal discovery methods in biology poses challenges, such as noisy data and a large number of samples. Thus, adapting the causal discovery methods is necessary to handle these challenges. In this paper, we introduce DiscoGen, a neural network-based GRN discovery method that can denoise gene expression measurements and handle interventional data. We demonstrate that our model outperforms SOTA neural network-based causal discovery methods.
SuperpixelGraph: Semi-automatic generation of building footprint through semantic-sensitive superpixel and neural graph networks

Most urban applications necessitate building footprints in the form of concise vector graphics with sharp boundaries rather than pixel-wise raster images. This need contrasts with the majority of existing methods, which typically generate over-smoothed footprint polygons. Editing these automatically produced polygons can be inefficient, if not more time-consuming than manual digitization. This paper introduces a semi-automatic approach for building footprint extraction through semantically-sensitive superpixels and neural graph networks. Drawing inspiration from object-based classification techniques, we first learn to generate superpixels that are not only boundary-preserving but also semantically-sensitive. The superpixels respond exclusively to building boundaries rather than other natural objects, while simultaneously producing semantic segmentation of the buildings. These intermediate superpixel representations can be naturally considered as nodes within a graph. Consequently, graph neural networks are employed to model the global interactions among all superpixels and enhance the representativeness of node features for building segmentation. Classical approaches are utilized to extract and regularize boundaries for the vectorized building footprints. Utilizing minimal clicks and straightforward strokes, we efficiently accomplish accurate segmentation outcomes, eliminating the necessity for editing polygon vertices. Our proposed approach demonstrates superior precision and efficacy, as validated by experimental assessments on various public benchmark datasets. A significant improvement of 8% in AP50 was observed in vector graphics evaluation, surpassing established techniques. Additionally, we have devised an optimized and sophisticated pipeline for interactive editing, poised to further augment the overall quality of the results.
Mathematical and Linguistic Characterization of Orhan Pamuk's Nobel Works

In this study, Nobel Laureate Orhan Pamuk’s works are chosen as examples of Turkish literature. By counting the number of letters and words in his texts, we find it possible to study his works statistically. It has been known that there is a geometrical order in text structures. Here, the method based on the basic assumption of fractal geometry is introduced for calculating the fractal dimensions of Pamuk’s texts. The results are compared with the applications of Zipf’s law, which is successfully applied for letters and words, where two concepts, namely Zipf’s dimension and Zipf’s order, are introduced. The Zipf dimension of the novel _My Name is Red_ is found to be much different than his other novels. However, it is linguistically observed that there is no fundamental difference between his corpora. The results are interpreted in terms of fractal dimensions and the Turkish language.
ASL Citizen: A Community-Sourced Dataset for Advancing Isolated Sign Language Recognition

Sign languages are used as a primary language by approximately 70 million D/deaf people world-wide. However, most communication technologies operate in spoken and written languages, creating inequities in access. To help tackle this problem, we release ASL Citizen, the first crowdsourced Isolated Sign Language Recognition (ISLR) dataset, collected with consent and containing 83,399 videos for 2,731 distinct signs filmed by 52 signers in a variety of environments. We propose that this dataset be used for sign language dictionary retrieval for American Sign Language (ASL), where a user demonstrates a sign to their webcam to retrieve matching signs from a dictionary. We show that training supervised machine learning classifiers with our dataset advances the state-of-the-art on metrics relevant for dictionary retrieval, achieving 63% accuracy and a recall-at-10 of 91%, evaluated entirely on videos of users who are not present in the training or validation sets. An accessible PDF of this article is available at the following link: https://aashakadesai.github. io/research/ASLCitizen_arxiv_updated. pdf
Boosted Prompt Ensembles for Large Language Models

Methods such as chain-of-thought prompting and self-consistency have pushed the frontier of language model reasoning performance with no additional training. To further improve performance, we propose a prompt ensembling method for large language models, which uses a small dataset to construct a set of few shot prompts that together comprise a ``boosted prompt ensemble''. The few shot examples for each prompt are chosen in a stepwise fashion to be ``hard'' examples on which the previous step's ensemble is uncertain. We show that this outperforms single-prompt output-space ensembles and bagged prompt-space ensembles on the GSM8k and AQuA datasets, among others. We propose both train-time and test-time versions of boosted prompting that use different levels of available annotation and conduct a detailed empirical study of our algorithm.
Localisation of Regularised and Multiview Support Vector Machine Learning

We prove a few representer theorems for a localised version of the regularised and multiview support vector machine learning problem introduced by H.Q. ~Minh, L. ~Bazzani, and V. ~Murino, \textit{Journal of Machine Learning Research}, \textbf{17}(2016) 1--72, that involves operator valued positive semidefinite kernels and their reproducing kernel Hilbert spaces. The results concern general cases when convex or nonconvex loss functions and finite or infinite dimensional input spaces are considered. We show that the general framework allows infinite dimensional input spaces and nonconvex loss functions for some special cases, in particular in case the loss functions are G\^ateaux differentiable. Detailed calculations are provided for the exponential least squares loss functions that leads to partially nonlinear problems.
Critical Gaussian Multiplicative Chaos for singular measures

Given $d\ge 1$, we provide a construction of the random measure - the critical Gaussian Multiplicative Chaos - formally defined $e^{\sqrt{2d}X}\mathrm{d} \mu$ where $X$ is a $\log$-correlated Gaussian field and $\mu$ is a locally finite measure on $\mathbb R^d$. Our construction generalizes the one performed in the case where $\mu$ is the Lebesgue measure. It requires that the measure $\mu$ is sufficiently spread out, namely that for $\mu$ almost every $x$ we have $$ \int_{B(0,1)}\frac{\mu(\mathrm{d} y)}{|x-y|^{d}e^{\rho\left(\log \frac{1}{|x-y|} \right)}}<\infty, $$ for any compact set where $\rho:\mathbb R_+\to \mathbb R_+$ can be chosen to be any lower envelope function for the $3$-Bessel process (this includes $\rho(x)=x^{\alpha}$ with $\alpha\in (0,1/2)$). We prove that three distinct random objects converge to a common limit which defines the critical GMC: the derivative martingale, the critical martingale, and the exponential of the mollified field. We also show that the above criterion for the measure $\mu$ is in a sense optimal.
Multistability and intermediate tipping of the Atlantic Ocean circulation

Tipping points (TP) in climate subsystems are usually thought to occur at a well-defined, critical forcing parameter threshold, via destabilization of the system state by a single, dominant positive feedback. However, coupling to other subsystems, additional feedbacks, and spatial heterogeneity may promote further small-amplitude, abrupt reorganizations of geophysical flows at forcing levels lower than the critical threshold. Using a primitive-equation ocean model, we simulate a collapse of the Atlantic Meridional Overturning Circulation (AMOC) due to increasing glacial melt. Considerably before the collapse, various abrupt, qualitative changes in AMOC variability occur. These intermediate tipping points (ITP) are transitions between multiple stable circulation states. Using 2.75 million years of model simulations, we uncover a very rugged stability landscape featuring parameter regions of up to nine coexisting stable states. The path to an AMOC collapse via a sequence of ITPs depends on the rate of change of the meltwater input. This challenges our ability to predict and define safe limits for TPs.
Mesh2Tex: Generating Mesh Textures from Image Queries

Remarkable advances have been achieved recently in learning neural representations that characterize object geometry, while generating textured objects suitable for downstream applications and 3D rendering remains at an early stage. In particular, reconstructing textured geometry from images of real objects is a significant challenge - reconstructed geometry is often inexact, making realistic texturing a significant challenge. We present Mesh2Tex, which learns a realistic object texture manifold from uncorrelated collections of 3D object geometry and photorealistic RGB images, by leveraging a hybrid mesh-neural-field texture representation. Our texture representation enables compact encoding of high-resolution textures as a neural field in the barycentric coordinate system of the mesh faces. The learned texture manifold enables effective navigation to generate an object texture for a given 3D object geometry that matches to an input RGB image, which maintains robustness even under challenging real-world scenarios where the mesh geometry approximates an inexact match to the underlying geometry in the RGB image. Mesh2Tex can effectively generate realistic object textures for an object mesh to match real images observations towards digitization of real environments, significantly improving over previous state of the art.
Predicting subgroup treatment effects for a new study: Motivations, results and learnings from running a data challenge in a pharmaceutical corporation.

We present the motivation, experience, and learnings from a data challenge conducted at a large pharmaceutical corporation on the topic of subgroup identification. The data challenge aimed at exploring approaches to subgroup identification for future clinical trials. To mimic a realistic setting, participants had access to 4 Phase III clinical trials to derive a subgroup and predict its treatment effect on a future study not accessible to challenge participants. A total of 30 teams registered for the challenge with around 100 participants, primarily from Biostatistics organization. We outline the motivation for running the challenge, the challenge rules, and logistics. Finally, we present the results of the challenge, the participant feedback as well as the learnings. We also present our view on the implications of the results on exploratory analyses related to treatment effect heterogeneity.
Improving Diffusion Models for Scene Text Editing with Dual Encoders

Scene text editing is a challenging task that involves modifying or inserting specified texts in an image while maintaining its natural and realistic appearance. Most previous approaches to this task rely on style-transfer models that crop out text regions and feed them into image transfer models, such as GANs. However, these methods are limited in their ability to change text style and are unable to insert texts into images. Recent advances in diffusion models have shown promise in overcoming these limitations with text-conditional image editing. However, our empirical analysis reveals that state-of-the-art diffusion models struggle with rendering correct text and controlling text style. To address these problems, we propose DIFFSTE to improve pre-trained diffusion models with a dual encoder design, which includes a character encoder for better text legibility and an instruction encoder for better style control. An instruction tuning framework is introduced to train our model to learn the mapping from the text instruction to the corresponding image with either the specified style or the style of the surrounding texts in the background. Such a training method further brings our method the zero-shot generalization ability to the following three scenarios: generating text with unseen font variation, e.g., italic and bold, mixing different fonts to construct a new font, and using more relaxed forms of natural language as the instructions to guide the generation task. We evaluate our approach on five datasets and demonstrate its superior performance in terms of text correctness, image naturalness, and style controllability. Our code is publicly available. https://github.com/UCSB-NLP-Chang/DiffSTE
High-Resolution Spectroscopy of X-ray Binaries

X-ray binaries, as bright local sources with short variability timescales for a wide range of accretion processes, represent ideal targets for high-resolution X-ray spectroscopy. In this chapter, we present a high-resolution X-ray spectral perspective on X-ray binaries, focusing on black holes and neutron stars. The majority of the chapter is devoted to observational and theoretical signatures of mass ejection via accretion disk winds: we discuss their appearance (including an overview of photoionization and thermodynamic processes that determine their visibility in X-ray spectra) and their life cycles (including efforts to constrain their time-dependent mass loss rates), and we provide a broad overview of the primary accretion disk wind driving mechanisms that have been considered in the literature: (1) radiation pressure, where radiation accelerates a wind by scattering off electrons or atoms in the disk or its atmosphere; (2) thermal driving, where Compton heating of the outer accretion disk causes gas thermal velocities to exceed the local escape speed; and (3) magnetohydrodynamic processes, where gas may be ejected from the disk via magnetic pressure gradients or magnetocentrifugal effects. We then turn to spectroscopic constraints on the geometry of accreting systems, from relativistically blurred emission lines to dipping sources, clumpy, structured stellar winds, and baryonic jets. We conclude with discussions of measurements of the interstellar medium and the potential of next-generation high-resolution X-ray spectroscopy for X-ray binaries.
Exploiting Logic Locking for a Neural Trojan Attack on Machine Learning Accelerators

Logic locking has been proposed to safeguard intellectual property (IP) during chip fabrication. Logic locking techniques protect hardware IP by making a subset of combinational modules in a design dependent on a secret key that is withheld from untrusted parties. If an incorrect secret key is used, a set of deterministic errors is produced in locked modules, restricting unauthorized use. A common target for logic locking is neural accelerators, especially as machine-learning-as-a-service becomes more prevalent. In this work, we explore how logic locking can be used to compromise the security of a neural accelerator it protects. Specifically, we show how the deterministic errors caused by incorrect keys can be harnessed to produce neural-trojan-style backdoors. To do so, we first outline a motivational attack scenario where a carefully chosen incorrect key, which we call a trojan key, produces misclassifications for an attacker-specified input class in a locked accelerator. We then develop a theoretically-robust attack methodology to automatically identify trojan keys. To evaluate this attack, we launch it on several locked accelerators. In our largest benchmark accelerator, our attack identified a trojan key that caused a 74% decrease in classification accuracy for attacker-specified trigger inputs, while degrading accuracy by only 1.7% for other inputs on average.
Best Practices for 2-Body Pose Forecasting

The task of collaborative human pose forecasting stands for predicting the future poses of multiple interacting people, given those in previous frames. Predicting two people in interaction, instead of each separately, promises better performance, due to their body-body motion correlations. But the task has remained so far primarily unexplored.In this paper, we review the progress in human pose forecasting and provide an in-depth assessment of the single-person practices that perform best for 2-body collaborative motion forecasting. Our study confirms the positive impact of frequency input representations, space-time separable and fully-learnable interaction adjacencies for the encoding GCN and FC decoding. Other single-person practices do not transfer to 2-body, so the proposed best ones do not include hierarchical body modeling or attention-based interaction encoding.We further contribute a novel initialization procedure for the 2-body spatial interaction parameters of the encoder, which benefits performance and stability. Altogether, our proposed 2-body pose forecasting best practices yield a performance improvement of 21.9% over the state-of-the-art on the most recent ExPI dataset, whereby the novel initialization accounts for 3.5%. See our project page at https://www.pinlab. org/bestpractices2body
NoisyTwins: Class-Consistent and Diverse Image Generation Through StyleGANs

StyleGANs are at the forefront of controllable image generation as they produce a latent space that is semantically disentangled, making it suitable for image editing and manipulation. However, the performance of StyleGANs severely degrades when trained via class-conditioning on large-scale long-tailed datasets. We find that one reason for degradation is the collapse of latents for each class in the $\mathcal{W}$ latent space. With NoisyTwins, we first introduce an effective and inexpensive augmentation strategy for class embeddings, which then decorrelates the latents based on self-supervision in the $\mathcal{W}$ space. This decorrelation mitigates collapse, ensuring that our method preserves intra-class diversity with class-consistency in image generation. We show the effectiveness of our approach on large-scale real-world long-tailed datasets of ImageNet-LT and iNaturalist 2019, where our method outperforms other methods by ∼ 19% on FID, establishing a new state-of-the-art.
Norm of matrix-valued polynomials in random unitaries and permutations

We consider a non-commutative polynomial in several independent $N$-dimensional random unitary matrices, uniformly distributed over the unitary, orthogonal or symmetric groups, and assume that the coefficients are $n$-dimensional matrices. The main purpose of this paper is to study the operator norm of this random non-commutative polynomial. We compare it with its counterpart where the the random unitary matrices are replaced by the unitary generators of the free group von Neumann algebra. Our first result is that these two norms are overwhelmingly close to each other in the large $N$ limit, and this estimate is uniform over all matrix coefficients as long as $n \le\exp (N^\alpha)$ for some explicit $\alpha>0$. Such results had been obtained by very different techniques for various regimes, all falling in the category $n\ll N$. Our result provides a new proof of the Peterson-Thom conjecture. Our second result is a universal quantitative lower bound for the operator norm of polynomials in independent $N$-dimensional random unitary and permutation matrices with coefficients in an arbitrary $C^*$-algebra. A variant of this result for permutation matrices generalizes the Alon-Boppana lower bound in two directions. Firstly, it applies for arbitrary polynomials and not only linear polynomials, and secondly, it applies for coefficients of an arbitrary $C^*$-algebra with non-negative joint moments and not only for non-negative real numbers.
Evaluating Classifier Confidence for Surface EMG Pattern Recognition

Surface electromyogram (EMG) can be employed as an interface signal for various devices and software via pattern recognition. In EMG-based pattern recognition, the classifier should not only be accurate, but also output an appropriate confidence (i.e., probability of correctness) for its prediction. If the confidence accurately reflects the likelihood of true correctness, then it will be useful in various application tasks, such as motion rejection and online adaptation. The aim of this paper is to identify the types of classifiers that provide higher accuracy and better confidence in EMG pattern recognition. We evaluate the performance of various discriminative and generative classifiers on four EMG datasets, both visually and quantitatively. The analysis results show that while a discriminative classifier based on a deep neural network exhibits high accuracy, it outputs a confidence that differs from true probabilities. By contrast, a scale mixture model-based classifier, which is a generative classifier that can account for uncertainty in EMG variance, exhibits superior performance in terms of both accuracy and confidence.
Observation of the Schmid-Bulgadaev dissipative quantum phase transition

Although quantum mechanics applies to many macroscopic superconducting devices, one basic prediction remained controversial for decades. Namely, a Josephson junction connected to a resistor must undergo a dissipation-induced quantum phase transition from superconductor to insulator once the resistor's value exceeds $h/4e^2 \approx 6.5~\textrm{k}\Omega$ ($h$ is Planck's constant, $e$ is the electron charge). Here we finally demonstrate this transition by observing the resistor's internal dynamics. Implementing our resistor as a long transmission line section, we find that a junction scatters electromagnetic excitations in the line as either inductance (superconductor) or capacitance (insulator), depending solely on the line's wave impedance. At the phase boundary, the junction itself acts as ideal resistance: in addition to elastic scattering, incident photons can spontaneously down-convert with a frequency-independent probability, which provides a novel marker of quantum-critical behavior.
A Topology by Geometrization for Sub-Iterated Immediate Snapshot Message Adversaries and Applications to Set-Agreement

The Iterated Immediate Snapshot model (IIS) is a central model in the message adversary setting. We consider general message adversaries whose executions are arbitrary subsets of the executions of the IIS message adversary. We present a new topological approach for such general adversaries, based upon geometric simplicial complexes. We are able to define a topology directly on the considered sets of executions, which gives both simpler and more powerful ways of using topology for distributed computability. As application of this new framework, we present a complete characterization and lower bounds for solving set-agreement for general sub-IIS message adversaries.