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Pre-trained large language models have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular domains. Here, we target bioinformatics due to the amount of specialized domain knowledge, algorithms, and data operations this discipline requires. We present BioCoder, a benchmark developed to evaluate large language models (LLMs) in generating bioinformatics-specific code. BioCoder spans a broad spectrum of the field and covers cross-file dependencies, class declarations, and global variables. It incorporates 1026 Python functions and 1243 Java methods extracted from GitHub, along with 253 examples from the Rosalind Project, all pertaining to bioinformatics. Using topic modeling we show that overall coverage of the included code is representative of the full spectrum of bioinformatics calculations. BioCoder incorporates a fuzz-testing framework for evaluation. We have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, GPT-3.5, and GPT-4. Furthermore, we finetuned StarCoder, demonstrating how our dataset can effectively enhance the performance of LLMs on our benchmark (by >15% in terms of Pass@K in certain prompt configurations and always >3%). The results highlight two key aspects of successful models: (1) Successful models accommodate a long prompt (> ~2600 tokens) with full context, for functional dependencies. (2) They contain specific domain knowledge of bioinformatics, beyond just general coding knowledge. This is evident from the performance gain of GPT-3.5/4 compared to the smaller models on the benchmark (50% vs up to ~25%). Our dataset, benchmark, Docker images, and scripts required for testing are all available at //github.com/gersteinlab/biocoder.

Various heuristic objectives for modeling hand-object interaction have been proposed in past work. However, due to the lack of a cohesive framework, these objectives often possess a narrow scope of applicability and are limited by their efficiency or accuracy. In this paper, we propose HandyPriors, a unified and general pipeline for pose estimation in human-object interaction scenes by leveraging recent advances in differentiable physics and rendering. Our approach employs rendering priors to align with input images and segmentation masks along with physics priors to mitigate penetration and relative-sliding across frames. Furthermore, we present two alternatives for hand and object pose estimation. The optimization-based pose estimation achieves higher accuracy, while the filtering-based tracking, which utilizes the differentiable priors as dynamics and observation models, executes faster. We demonstrate that HandyPriors attains comparable or superior results in the pose estimation task, and that the differentiable physics module can predict contact information for pose refinement. We also show that our approach generalizes to perception tasks, including robotic hand manipulation and human-object pose estimation in the wild.

Generalizable manipulation of articulated objects remains a challenging problem in many real-world scenarios, given the diverse object structures, functionalities, and goals. In these tasks, both semantic interpretations and physical plausibilities are crucial for a policy to succeed. To address this problem, we propose SAGE, a novel framework that bridges the understanding of semantic and actionable parts of articulated objects to achieve generalizable manipulation under language instructions. Given a manipulation goal specified by natural language, an instruction interpreter with Large Language Models (LLMs) first translates them into programmatic actions on the object's semantic parts. This process also involves a scene context parser for understanding the visual inputs, which is designed to generate scene descriptions with both rich information and accurate interaction-related facts by joining the forces of generalist Visual-Language Models (VLMs) and domain-specialist part perception models. To further convert the action programs into executable policies, a part grounding module then maps the object semantic parts suggested by the instruction interpreter into so-called Generalizable Actionable Parts (GAParts). Finally, an interactive feedback module is incorporated to respond to failures, which greatly increases the robustness of the overall framework. Experiments both in simulation environments and on real robots show that our framework can handle a large variety of articulated objects with diverse language-instructed goals. We also provide a new benchmark for language-guided articulated-object manipulation in realistic scenarios.

Testing complex simulation models can be expensive and time consuming. Current state-of-the-art methods that explore this problem are fully-supervised; i.e. they require that all examples are labeled. On the other hand, the GenClu system (introduced in this paper) takes a semi-supervised approach; i.e. (a) only a small subset of information is actually labeled (via simulation) and (b) those labels are then spread across the rest of the data. When applied to five open-source simulation models of cyber-physical systems, GenClu's test generation can be multiple orders of magnitude faster than the prior state of the art. Further, when assessed via mutation testing, tests generated by GenClu were as good or better than anything else tested here. Hence, we recommend semi-supervised methods over prior methods (evolutionary search and fully-supervised learning).

Unsupervised object-centric learning aims to decompose scenes into interpretable object entities, termed slots. Slot-based auto-encoders stand out as a prominent method for this task. Within them, crucial aspects include guiding the encoder to generate object-specific slots and ensuring the decoder utilizes them during reconstruction. This work introduces two novel techniques, (i) an attention-based self-training approach, which distills superior slot-based attention masks from the decoder to the encoder, enhancing object segmentation, and (ii) an innovative patch-order permutation strategy for autoregressive transformers that strengthens the role of slot vectors in reconstruction. The effectiveness of these strategies is showcased experimentally. The combined approach significantly surpasses prior slot-based autoencoder methods in unsupervised object segmentation, especially with complex real-world images. We provide the implementation code at //github.com/gkakogeorgiou/spot .

Magnetic resonance imaging (MRI) is commonly used for brain tumor segmentation, which is critical for patient evaluation and treatment planning. To reduce the labor and expertise required for labeling, weakly-supervised semantic segmentation (WSSS) methods with class activation mapping (CAM) have been proposed. However, existing CAM methods suffer from low resolution due to strided convolution and pooling layers, resulting in inaccurate predictions. In this study, we propose a novel CAM method, Attentive Multiple-Exit CAM (AME-CAM), that extracts activation maps from multiple resolutions to hierarchically aggregate and improve prediction accuracy. We evaluate our method on the BraTS 2021 dataset and show that it outperforms state-of-the-art methods.

The advent of large language models, enabling flexibility through instruction-driven approaches, has revolutionized many traditional generative tasks, but large models for 3D data, particularly in comprehensively handling 3D shapes with other modalities, are still under-explored. By achieving instruction-based shape generations, versatile multimodal generative shape models can significantly benefit various fields like 3D virtual construction and network-aided design. In this work, we present ShapeGPT, a shape-included multi-modal framework to leverage strong pre-trained language models to address multiple shape-relevant tasks. Specifically, ShapeGPT employs a word-sentence-paragraph framework to discretize continuous shapes into shape words, further assembles these words for shape sentences, as well as integrates shape with instructional text for multi-modal paragraphs. To learn this shape-language model, we use a three-stage training scheme, including shape representation, multimodal alignment, and instruction-based generation, to align shape-language codebooks and learn the intricate correlations among these modalities. Extensive experiments demonstrate that ShapeGPT achieves comparable performance across shape-relevant tasks, including text-to-shape, shape-to-text, shape completion, and shape editing.

Multi-object tracking in traffic videos is a crucial research area, offering immense potential for enhancing traffic monitoring accuracy and promoting road safety measures through the utilisation of advanced machine learning algorithms. However, existing datasets for multi-object tracking in traffic videos often feature limited instances or focus on single classes, which cannot well simulate the challenges encountered in complex traffic scenarios. To address this gap, we introduce TrafficMOT, an extensive dataset designed to encompass diverse traffic situations with complex scenarios. To validate the complexity and challenges presented by TrafficMOT, we conducted comprehensive empirical studies using three different settings: fully-supervised, semi-supervised, and a recent powerful zero-shot foundation model Tracking Anything Model (TAM). The experimental results highlight the inherent complexity of this dataset, emphasising its value in driving advancements in the field of traffic monitoring and multi-object tracking.

Video panoptic segmentation requires consistently segmenting (for both `thing' and `stuff' classes) and tracking objects in a video over time. In this work, we present MaXTron, a general framework that exploits Mask XFormer with Trajectory Attention to tackle the task. MaXTron enriches an off-the-shelf mask transformer by leveraging trajectory attention. The deployed mask transformer takes as input a short clip consisting of only a few frames and predicts the clip-level segmentation. To enhance the temporal consistency, MaXTron employs within-clip and cross-clip tracking modules, efficiently utilizing trajectory attention. Originally designed for video classification, trajectory attention learns to model the temporal correspondences between neighboring frames and aggregates information along the estimated motion paths. However, it is nontrivial to directly extend trajectory attention to the per-pixel dense prediction tasks due to its quadratic dependency on input size. To alleviate the issue, we propose to adapt the trajectory attention for both the dense pixel features and object queries, aiming to improve the short-term and long-term tracking results, respectively. Particularly, in our within-clip tracking module, we propose axial-trajectory attention that effectively computes the trajectory attention for tracking dense pixels sequentially along the height- and width-axes. The axial decomposition significantly reduces the computational complexity for dense pixel features. In our cross-clip tracking module, since the object queries in mask transformer are learned to encode the object information, we are able to capture the long-term temporal connections by applying trajectory attention to object queries, which learns to track each object across different clips. Without bells and whistles, MaXTron demonstrates state-of-the-art performances on video segmentation benchmarks.

Deep learning methods are achieving ever-increasing performance on many artificial intelligence tasks. A major limitation of deep models is that they are not amenable to interpretability. This limitation can be circumvented by developing post hoc techniques to explain the predictions, giving rise to the area of explainability. Recently, explainability of deep models on images and texts has achieved significant progress. In the area of graph data, graph neural networks (GNNs) and their explainability are experiencing rapid developments. However, there is neither a unified treatment of GNN explainability methods, nor a standard benchmark and testbed for evaluations. In this survey, we provide a unified and taxonomic view of current GNN explainability methods. Our unified and taxonomic treatments of this subject shed lights on the commonalities and differences of existing methods and set the stage for further methodological developments. To facilitate evaluations, we generate a set of benchmark graph datasets specifically for GNN explainability. We summarize current datasets and metrics for evaluating GNN explainability. Altogether, this work provides a unified methodological treatment of GNN explainability and a standardized testbed for evaluations.