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Diffusion-based image generation models such as DALL-E 3 and Stable Diffusion-XL demonstrate remarkable capabilities in generating images with realistic and unique compositions. Yet, these models are not robust in precisely reasoning about physical and spatial configurations of objects, especially when instructed with unconventional, thereby out-of-distribution descriptions, such as "a chair with five legs". In this paper, we propose a language agent with chain-of-3D-thoughts (L3GO), an inference-time approach that can reason about part-based 3D mesh generation of unconventional objects that current data-driven diffusion models struggle with. More concretely, we use large language models as agents to compose a desired object via trial-and-error within the 3D simulation environment. To facilitate our investigation, we develop a new benchmark, Unconventionally Feasible Objects (UFO), as well as SimpleBlenv, a wrapper environment built on top of Blender where language agents can build and compose atomic building blocks via API calls. Human and automatic GPT-4V evaluations show that our approach surpasses the standard GPT-4 and other language agents (e.g., ReAct and Reflexion) for 3D mesh generation on ShapeNet. Moreover, when tested on our UFO benchmark, our approach outperforms other state-of-the-art text-to-2D image and text-to-3D models based on human evaluation.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C$^2$LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at //github.com/Zhihan1996/DNABERT_S.

Most text-to-3D generators build upon off-the-shelf text-to-image models trained on billions of images. They use variants of Score Distillation Sampling (SDS), which is slow, somewhat unstable, and prone to artifacts. A mitigation is to fine-tune the 2D generator to be multi-view aware, which can help distillation or can be combined with reconstruction networks to output 3D objects directly. In this paper, we further explore the design space of text-to-3D models. We significantly improve multi-view generation by considering video instead of image generators. Combined with a 3D reconstruction algorithm which, by using Gaussian splatting, can optimize a robust image-based loss, we directly produce high-quality 3D outputs from the generated views. Our new method, IM-3D, reduces the number of evaluations of the 2D generator network 10-100x, resulting in a much more efficient pipeline, better quality, fewer geometric inconsistencies, and higher yield of usable 3D assets.

We investigate fine-grained algorithmic aspects of identification problems in graphs and set systems, with a focus on Locating-Dominating Set and Test Cover. We prove, among other things, the following three (tight) conditional lower bounds. \begin{enumerate} \item \textsc{Locating-Dominating Set} does not admit an algorithm running in time $2^{o(k^2)} \cdot poly(n)$, nor a polynomial time kernelization algorithm that reduces the solution size and outputs a kernel with $2^{o(k)}$ vertices, unless the \ETH\ fails. \end{enumerate} To the best of our knowledge, \textsc{Locating-Dominating Set} is the first problem that admits such an algorithmic lower-bound (with a quadratic function in the exponent) when parameterized by the solution size. \begin{enumerate}[resume] \item \textsc{Test Cover} does not admit an algorithm running in time $2^{2^{o(k)}} \cdot poly(|U| + |\calF|)$. \end{enumerate} After \textsc{Edge Clique Cover} and \textsc{BiClique Cover}, this is the only example that we know of that admits a double exponential lower bound when parameterized by the solution size. \begin{enumerate}[resume] \item \textsc{Locating-Dominating Set} (respectively, \textsc{Test Cover}) parameterized by the treewidth of the input graph (respectively, of the natural auxiliary graph) does not admit an algorithm running in time $2^{2^{o(\tw)}} \cdot poly(n)$ (respectively, $2^{2^{o(\tw)}} \cdot poly(|U| + |\calF|))$. \end{enumerate} This result augments the small list of NP-Complete problems that admit double exponential lower bounds when parameterized by treewidth. We also present algorithms whose running times match the above lower bounds. We also investigate the parameterizations by several other structural graph parameters, answering some open problems from the literature.

Large language models~(LLMs) demonstrate significant potential to revolutionize software engineering (SE) by exhibiting outstanding performance in SE tasks such as code and document generation. However, the high reliability and risk control requirements in software engineering raise concerns about the lack of interpretability of LLMs. To address this concern, we conducted a study to evaluate the capabilities of LLMs and their limitations for code analysis in SE. We break down the abilities needed for artificial intelligence~(AI) models to address SE tasks related to code analysis into three categories: 1) syntax understanding, 2) static behavior understanding, and 3) dynamic behavior understanding. Our investigation focused on the ability of LLMs to comprehend code syntax and semantic structures, which include abstract syntax trees (AST), control flow graphs (CFG), and call graphs (CG). We employed four state-of-the-art foundational models, GPT4, GPT3.5, StarCoder and CodeLlama-13b-instruct. We assessed the performance of LLMs on cross-language tasks involving C, Java, Python, and Solidity. Our findings revealed that while LLMs have a talent for understanding code syntax, they struggle with comprehending code semantics, particularly dynamic semantics. We conclude that LLMs possess capabilities similar to an Abstract Syntax Tree (AST) parser, demonstrating initial competencies in static code analysis. Furthermore, our study highlights that LLMs are susceptible to hallucinations when interpreting code semantic structures and fabricating nonexistent facts. These results indicate the need to explore methods to verify the correctness of LLM output to ensure its dependability in SE. More importantly, our study provides an initial answer to why the codes generated by LLM are usually syntax-correct but vulnerable.

Referring expression segmentation (RES), a task that involves localizing specific instance-level objects based on free-form linguistic descriptions, has emerged as a crucial frontier in human-AI interaction. It demands an intricate understanding of both visual and textual contexts and often requires extensive training data. This paper introduces RESMatch, the first semi-supervised learning (SSL) approach for RES, aimed at reducing reliance on exhaustive data annotation. Extensive validation on multiple RES datasets demonstrates that RESMatch significantly outperforms baseline approaches, establishing a new state-of-the-art. Although existing SSL techniques are effective in image segmentation, we find that they fall short in RES. Facing the challenges including the comprehension of free-form linguistic descriptions and the variability in object attributes, RESMatch introduces a trifecta of adaptations: revised strong perturbation, text augmentation, and adjustments for pseudo-label quality and strong-weak supervision. This pioneering work lays the groundwork for future research in semi-supervised learning for referring expression segmentation.

Large language models (LLMs) have made significant advancements in code-related tasks, yet many LLMs treat code as simple sequences, neglecting its structured nature. We introduce AST-T5, a novel pretraining paradigm that leverages the Abstract Syntax Tree (AST) for enhanced code generation, transpilation, and understanding. Using dynamic programming, our AST-Aware Segmentation retains code structure, while our AST-Aware Span Corruption objective equips the model to reconstruct various code structures. Unlike other models, AST-T5 avoids intricate program analyses or architectural changes, so it integrates seamlessly with any encoder-decoder Transformer. Evaluations show that AST-T5 consistently outperforms similar-sized LMs across various code-related tasks. Structure-awareness makes AST-T5 particularly powerful in code-to-code tasks, surpassing CodeT5 by 2 points in exact match score for the Bugs2Fix task and by 3 points in exact match score for Java-C# Transpilation in CodeXGLUE. Our code and model are publicly available at //github.com/gonglinyuan/ast_t5.

The scarcity of class-labeled data is a ubiquitous bottleneck in many machine learning problems. While abundant unlabeled data typically exist and provide a potential solution, it is highly challenging to exploit them. In this paper, we address this problem by leveraging Positive-Unlabeled~(PU) classification and the conditional generation with extra unlabeled data \emph{simultaneously}. In particular, we present a novel training framework to jointly target both PU classification and conditional generation when exposed to extra data, especially out-of-distribution unlabeled data, by exploring the interplay between them: 1) enhancing the performance of PU classifiers with the assistance of a novel Classifier-Noise-Invariant Conditional GAN~(CNI-CGAN) that is robust to noisy labels, 2) leveraging extra data with predicted labels from a PU classifier to help the generation. Theoretically, we prove the optimal condition of CNI-CGAN, and experimentally, we conducted extensive evaluations on diverse datasets, verifying the simultaneous improvements in both classification and generation.

Retrieving object instances among cluttered scenes efficiently requires compact yet comprehensive regional image representations. Intuitively, object semantics can help build the index that focuses on the most relevant regions. However, due to the lack of bounding-box datasets for objects of interest among retrieval benchmarks, most recent work on regional representations has focused on either uniform or class-agnostic region selection. In this paper, we first fill the void by providing a new dataset of landmark bounding boxes, based on the Google Landmarks dataset, that includes $94k$ images with manually curated boxes from $15k$ unique landmarks. Then, we demonstrate how a trained landmark detector, using our new dataset, can be leveraged to index image regions and improve retrieval accuracy while being much more efficient than existing regional methods. In addition, we further introduce a novel regional aggregated selective match kernel (R-ASMK) to effectively combine information from detected regions into an improved holistic image representation. R-ASMK boosts image retrieval accuracy substantially at no additional memory cost, while even outperforming systems that index image regions independently. Our complete image retrieval system improves upon the previous state-of-the-art by significant margins on the Revisited Oxford and Paris datasets. Code and data will be released.

High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.