Miracle-dz/UniFAR-FTUs huggingface dataset:
Late 20th century land change in the Central California Valley ecoregion

This research challenges two general assumptions of land-cover change in California's Central Valley ecoregion. They are (1) the primary land-cover change occurring in urbanization of agricultural lands, and (2) that the ecoregion experienced a rapid decline in farmland between 1973 and 2000. Our findings indicate that while urbanization is significant, it is secondary to conversions occurring between agriculture and rangelands (grasslands/shrublands). Furthermore, we estimate that farmland increased in area over the study period, expanding from 71.6% of the ecoregion in 1973 to 72.4% in 2000, a net increase of 357 New agricultural lands were often found at the ecoregion periphery in the form of nut orchards and grapes, indicating a general shift away from traditional low-risk and low-value field crops to high-risk and high-value specialty crops. Rangeland is estimated to have declined by nearly 20%, from 19.2% of the ecoregion in 1973 to 15.4% in 2000, while developed lands increased from 6.5% to 9.0% over the same time period. Changes between agriculture and rangeland accounted for over 70% of all estimated change, while changes directly associated with urbanization accounted for approximately 14% of all identified land-cover change. Across all land-cover classes, we estimated that 12.4% of the ecoregion changed from one land-cover type to another during the 27 -year study and that the period of highest change was between 1973 and 1980. Many drivers may explain these results, including the influence of regional climate variability and drought. This research suggests that drought, if severe enough over an extended number of years, has the potential to significantly influence rates and types of regional land-cover change. Understanding these coupled human-environment relationships has implications for monitoring biogeochemical systems, natural resources, and ecosystem services at local to regional scales.
Locality-Sensitive Hashing-Based Efficient Point Transformer with Applications in High-Energy Physics

This study introduces a novel transformer model optimized for large-scale point cloud processing in scientific domains such as high-energy physics (HEP) and astrophysics. Addressing the limitations of graph neural networks and standard transformers, our model integrates local inductive bias and achieves near-linear complexity with hardware-friendly regular operations. One contribution of this work is the quantitative analysis of the error-complexity tradeoff of various sparsification techniques for building efficient transformers. Our findings highlight the superiority of using locality-sensitive hashing (LSH), especially OR \&AND-construction LSH, in kernel approximation for large-scale point cloud data with local inductive bias. Based on this finding, we propose LSH-based Efficient Point Transformer (\textbf{HEPT}), which combines E$^2$LSH with OR \&AND constructions and is built upon regular computations. HEPT demonstrates remarkable performance in two critical yet time-consuming HEP tasks, significantly outperforming existing GNNs and transformers in accuracy and computational speed, marking a significant advancement in geometric deep learning and large-scale scientific data processing. Our code is available at \url{https://github.com/Graph-COM/HEPT}.
Investigating the Impact of Model Instability on Explanations and Uncertainty

Explainable AI methods facilitate the understanding of model behaviour, yet, small, imperceptible perturbations to inputs can vastly distort explanations. As these explanations are typically evaluated holistically, before model deployment, it is difficult to assess when a particular explanation is trustworthy. Some studies have tried to create confidence estimators for explanations, but none have investigated an existing link between uncertainty and explanation quality. We artificially simulate epistemic uncertainty in text input by introducing noise at inference time. In this large-scale empirical study, we insert different levels of noise perturbations and measure the effect on the output of pre-trained language models and different uncertainty metrics. Realistic perturbations have minimal effect on performance and explanations, yet masking has a drastic effect. We find that high uncertainty doesn't necessarily imply low explanation plausibility; the correlation between the two metrics can be moderately positive when noise is exposed during the training process. This suggests that noise-augmented models may be better at identifying salient tokens when uncertain. Furthermore, when predictive and epistemic uncertainty measures are over-confident, the robustness of a saliency map to perturbation can indicate model stability issues. Integrated Gradients shows the overall greatest robustness to perturbation, while still showing model-specific patterns in performance; however, this phenomenon is limited to smaller Transformer-based language models.
Induced Model Matching: How Restricted Models Can Help Larger Ones

We consider scenarios where a very accurate predictive model using restricted features is available at the time of training of a larger, full-featured, model. This restricted model may be thought of as"side-information", derived either from an auxiliary exhaustive dataset or on the same dataset, by forcing the restriction. How can the restricted model be useful to the full model? We propose an approach for transferring the knowledge of the restricted model to the full model, by aligning the full model's context-restricted performance with that of the restricted model's. We call this methodology Induced Model Matching (IMM) and first illustrate its general applicability by using logistic regression as a toy example. We then explore IMM's use in language modeling, the application that initially inspired it, and where it offers an explicit foundation in contrast to the implicit use of restricted models in techniques such as noising. We demonstrate the methodology on both LSTM and transformer full models, using $N$-grams as restricted models. To further illustrate the potential of the principle whenever it is much cheaper to collect restricted rather than full information, we conclude with a simple RL example where POMDP policies can improve learned MDP policies via IMM.
Contractivity of neural ODEs: an eigenvalue optimization problem

We propose a novel methodology to solve a key eigenvalue optimization problem which arises in the contractivity analysis of neural ODEs. When looking at contractivity properties of a one layer weight-tied neural ODE $\dot{u}(t)=\sigma(Au(t)+b)$ (with $u,b \in {\mathbb R}^n$, $A$ is a given $n \times n$ matrix, $\sigma : {\mathbb R} \to {\mathbb R}^+$ denotes an activation function and for a vector $z \in {\mathbb R}^n$, $\sigma(z) \in {\mathbb R}^n$ has to be interpreted entry-wise), we are led to study the logarithmic norm of a set of products of type $D A$, where $D$ is a diagonal matrix such that ${\mathrm{diag}}(D) \in \sigma'({\mathbb R}^n)$. Specifically, given a real number $c$ (usually $c=0$), the problem consists in finding the largest positive interval $\chi\subseteq \mathbb [0,\infty)$ such that the logarithmic norm $\mu(DA) \le c$ for all diagonal matrices $D$ with $D_{ii}\in \chi$. We propose a two-level nested methodology: an inner level where, for a given $\chi$, we compute an optimizer $D^\star(\chi)$ by a gradient system approach, and an outer level where we tune $\chi$ so that the value $c$ is reached by $\mu(D^\star(\chi)A)$. We extend the proposed two-level approach to the general multilayer, and possibly time-dependent, case $\dot{u}(t) = \sigma( A_k(t) \ldots \sigma ( A_{1}(t) u(t) + b_{1}(t) ) \ldots + b_{k}(t) )$ and we propose several numerical examples to illustrate its behaviour, including its stabilizing performance on a one-layer neural ODE applied to the classification of the MNIST handwritten digits dataset.
UniCell: Universal Cell Nucleus Classification via Prompt Learning

The recognition of multi-class cell nuclei can significantly facilitate the process of histopathological diagnosis. Numerous pathological datasets are currently available, but their annotations are inconsistent. Most existing methods require individual training on each dataset to deduce the relevant labels and lack the use of common knowledge across datasets, consequently restricting the quality of recognition. In this paper, we propose a universal cell nucleus classification framework (UniCell), which employs a novel prompt learning mechanism to uniformly predict the corresponding categories of pathological images from different dataset domains. In particular, our framework adopts an end-to-end architecture for nuclei detection and classification, and utilizes flexible prediction heads for adapting various datasets. Moreover, we develop a Dynamic Prompt Module (DPM) that exploits the properties of multiple datasets to enhance features. The DPM first integrates the embeddings of datasets and semantic categories, and then employs the integrated prompts to refine image representations, efficiently harvesting the shared knowledge among the related cell types and data sources. Experimental results demonstrate that the proposed method effectively achieves the state-of-the-art results on four nucleus detection and classification benchmarks. Code and models are available at https://github.com/lhaof/UniCell
Handling Ambiguity in Emotion: From Out-of-Domain Detection to Distribution Estimation

The subjective perception of emotion leads to inconsistent labels from human annotators. Typically, utterances lacking majority-agreed labels are excluded when training an emotion classifier, which cause problems when encountering ambiguous emotional expressions during testing. This paper investigates three methods to handle ambiguous emotion. First, we show that incorporating utterances without majority-agreed labels as an additional class in the classifier reduces the classification performance of the other emotion classes. Then, we propose detecting utterances with ambiguous emotions as out-of-domain samples by quantifying the uncertainty in emotion classification using evidential deep learning. This approach retains the classification accuracy while effectively detects ambiguous emotion expressions. Furthermore, to obtain fine-grained distinctions among ambiguous emotions, we propose representing emotion as a distribution instead of a single class label. The task is thus re-framed from classification to distribution estimation where every individual annotation is taken into account, not just the majority opinion. The evidential uncertainty measure is extended to quantify the uncertainty in emotion distribution estimation. Experimental results on the IEMOCAP and CREMA-D datasets demonstrate the superior capability of the proposed method in terms of majority class prediction, emotion distribution estimation, and uncertainty estimation.
An Autonomous Large Language Model Agent for Chemical Literature Data Mining

Chemical synthesis, which is crucial for advancing material synthesis and drug discovery, impacts various sectors including environmental science and healthcare. The rise of technology in chemistry has generated extensive chemical data, challenging researchers to discern patterns and refine synthesis processes. Artificial intelligence (AI) helps by analyzing data to optimize synthesis and increase yields. However, AI faces challenges in processing literature data due to the unstructured format and diverse writing style of chemical literature. To overcome these difficulties, we introduce an end-to-end AI agent framework capable of high-fidelity extraction from extensive chemical literature. This AI agent employs large language models (LLMs) for prompt generation and iterative optimization. It functions as a chemistry assistant, automating data collection and analysis, thereby saving manpower and enhancing performance. Our framework's efficacy is evaluated using accuracy, recall, and F1 score of reaction condition data, and we compared our method with human experts in terms of content correctness and time efficiency. The proposed approach marks a significant advancement in automating chemical literature extraction and demonstrates the potential for AI to revolutionize data management and utilization in chemistry.
Choosing a Suitable Requirement Prioritization Method: A Survey

Software requirements prioritization plays a crucial role in software development. It can be viewed as the process of ordering requirements by determining which requirements must be done first and which can be done later. Powerful requirements prioritization techniques are of paramount importance to finish the implementation on time and within budget. Many factors affect requirement prioritization such as stakeholder expectations, complexity, dependency, scalability, risk, and cost. Therefore, finding the proper order of requirements is a challenging process. Hence, different types of requirements prioritization techniques have been developed to support this task. In this survey, we propose a novel classification that can classify the prioritization techniques under two major classes: relative and exact prioritization techniques class, where each class is divided into two subclasses. We depend in our classification on the way the value of ranking is given to the requirement, either explicitly as a specific value in the case of the exact prioritization techniques class, or implicitly in the case of the Relative prioritization technique class. An overview of fifteen different requirements prioritization techniques are presented and organized according to the proposed classification criteria's. Moreover, we make a comparison between methods that are related to the same subclass to analyze their strengths and weaknesses. Based on the comparison results, the properties for each proposed subclass of techniques are identified. Depending on these properties, we present some recommendations to help project managers in the process of selecting the most suitable technique to prioritize requirements based on their project characteristics (number of requirements, time, cost, and accuracy).
ConVQG: Contrastive Visual Question Generation with Multimodal Guidance

Asking questions about visual environments is a crucial way for intelligent agents to understand rich multi-faceted scenes, raising the importance of Visual Question Generation (VQG) systems. Apart from being grounded to the image, existing VQG systems can use textual constraints, such as expected answers or knowledge triplets, to generate focused questions. These constraints allow VQG systems to specify the question content or leverage external commonsense knowledge that can not be obtained from the image content only. However, generating focused questions using textual constraints while enforcing a high relevance to the image content remains a challenge, as VQG systems often ignore one or both forms of grounding. In this work, we propose Contrastive Visual Question Generation (ConVQG), a method using a dual contrastive objective to discriminate questions generated using both modalities from those based on a single one. Experiments on both knowledge-aware and standard VQG benchmarks demonstrate that ConVQG outperforms the state-of-the-art methods and generates image-grounded, text-guided, and knowledge-rich questions. Our human evaluation results also show preference for ConVQG questions compared to non-contrastive baselines.
Stack Representation of Finitely Presented Heyting Pretoposes I

This is the first of a series of papers on stack representation of finitely presented Heyting pretoposes. In this paper, we provide the first step by constructing a (2, 1)-site, which can be thought of as the site of finite Kripke frames, such that the (2,1)-category of finitely presented Heyting pretoposes contravariantly embeds into the (2,1)- topos of stacks on this (2, 1)-site. This provides an entry point to use categorical and higher sheaf-theoretic tools to study the properties of certain classes of intuitionistic first-order theories.
Equivariant Pretrained Transformer for Unified Geometric Learning on Multi-Domain 3D Molecules

Pretraining on a large number of unlabeled 3D molecules has showcased superiority in various scientific applications. However, prior efforts typically focus on pretraining models on a specific domain, either proteins or small molecules, missing the opportunity to leverage the cross-domain knowledge. To mitigate this gap, we introduce Equivariant Pretrained Transformer (EPT), a novel pretraining framework designed to harmonize the geometric learning of small molecules and proteins. To be specific, EPT unifies the geometric modeling of multi-domain molecules via the block-enhanced representation that can attend a broader context of each atom. Upon transformer framework, EPT is further enhanced with E(3) equivariance to facilitate the accurate representation of 3D structures. Another key innovation of EPT is its block-level pretraining task, which allows for joint pretraining on datasets comprising both small molecules and proteins. Experimental evaluations on a diverse group of benchmarks, including ligand binding affinity prediction, molecular property prediction, and protein property prediction, show that EPT significantly outperforms previous SOTA methods for affinity prediction, and achieves the best or comparable performance with existing domain-specific pretraining models for other tasks.
A fully-integrated lattice Boltzmann method for fluid-structure interaction

We present a fully-integrated lattice Boltzmann (LB) method for fluid--structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples finite-strain solids to the LB fluid on the same fixed computational grid with the reference map technique (RMT). An integral part of the LBRMT is a new LB boundary condition for moving deformable interfaces across different densities. With this fully Eulerian solid--fluid coupling, the LBRMT is well-suited for parallelization and simulating multi-body contact without remeshing or extra meshes. We validate its accuracy via a benchmark of a deformable solid in a lid-driven cavity, then showcase its versatility through examples of soft solids rotating and settling. With simulations of complex suspensions mixing, we highlight potentials of the LBRMT for studying collective behavior in soft matter and biofluid dynamics.
ModelGPT: Unleashing LLM's Capabilities for Tailored Model Generation

The rapid advancement of Large Language Models (LLMs) has revolutionized various sectors by automating routine tasks, marking a step toward the realization of Artificial General Intelligence (AGI). However, they still struggle to accommodate the diverse and specific needs of users and simplify the utilization of AI models for the average user. In response, we propose ModelGPT, a novel framework designed to determine and generate AI models specifically tailored to the data or task descriptions provided by the user, leveraging the capabilities of LLMs. Given user requirements, ModelGPT is able to provide tailored models at most 270x faster than the previous paradigms (e.g. all-parameter or LoRA finetuning). Comprehensive experiments on NLP, CV, and Tabular datasets attest to the effectiveness of our framework in making AI models more accessible and user-friendly. Our code is available at https://github.com/IshiKura-a/ModelGPT.
Ultrafast dynamics of a fermion chain in a terahertz field-driven optical cavity

We study the effect of a terahertz field-driven single cavity mode for ultrafast control of a fermion chain with dissipation-induced nonlinearity and quadratic coupling to an infrared-active phonon mode. Without photon loss from the cavity, we uncover a first-order phase transition in the nonequilibrium steady state only for the lower phonon-polariton, accompanied by polaritons whose frequency response is asymmetric with respect to the photon frequency due to the direct laser-induced dressing effect on the photon. A weak laser field fails to induce the phase transition but renders the polaritons symmetrical. Finally, we show that sufficiently strong photon loss from the cavity eliminates the polaritons and the associated phase transition. The experimental feasibility of these phenomena is also proposed.
Denoising OCT Images Using Steered Mixture of Experts with Multi-Model Inference

In Optical Coherence Tomography (OCT), speckle noise significantly hampers image quality, affecting diagnostic accuracy. Current methods, including traditional filtering and deep learning techniques, have limitations in noise reduction and detail preservation. Addressing these challenges, this study introduces a novel denoising algorithm, Block-Matching Steered-Mixture of Experts with Multi-Model Inference and Autoencoder (BM-SMoE-AE). This method combines block-matched implementation of the SMoE algorithm with an enhanced autoencoder architecture, offering efficient speckle noise reduction while retaining critical image details. Our method stands out by providing improved edge definition and reduced processing time. Comparative analysis with existing denoising techniques demonstrates the superior performance of BM-SMoE-AE in maintaining image integrity and enhancing OCT image usability for medical diagnostics.
Understanding and Mitigating the Threat of Vec2Text to Dense Retrieval Systems

The introduction of Vec2Text, a technique for inverting text embeddings, has raised serious privacy concerns within dense retrieval systems utilizing text embeddings, including those provided by OpenAI and Cohere. This threat comes from the ability for a malicious attacker with access to text embeddings to reconstruct the original text. In this paper, we investigate various aspects of embedding models that could influence the recoverability of text using Vec2Text. Our exploration involves factors such as distance metrics, pooling functions, bottleneck pre-training, training with noise addition, embedding quantization, and embedding dimensions -- aspects not previously addressed in the original Vec2Text paper. Through a thorough analysis of these factors, our aim is to gain a deeper understanding of the critical elements impacting the trade-offs between text recoverability and retrieval effectiveness in dense retrieval systems. This analysis provides valuable insights for practitioners involved in designing privacy-aware dense retrieval systems. Additionally, we propose a straightforward fix for embedding transformation that ensures equal ranking effectiveness while mitigating the risk of text recoverability. Furthermore, we extend the application of Vec2Text to the separate task of corpus poisoning, where, theoretically, Vec2Text presents a more potent threat compared to previous attack methods. Notably, Vec2Text does not require access to the dense retriever's model parameters and can efficiently generate numerous adversarial passages. In summary, this study highlights the potential threat posed by Vec2Text to existing dense retrieval systems, while also presenting effective methods to patch and strengthen such systems against such risks.