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Closed-source agents suffer from several issues such as a lack of affordability, transparency, and reproducibility, particularly on complex interactive tasks. This motivates the development of open-source alternatives. We introduce LUMOS, one of the first frameworks for training open-source LLM-based agents. LUMOS features a learnable, unified, and modular architecture with a planning module that learns high-level subgoal generation, and a grounding module trained to translate these into actions using various tools in the execution module. The design allows for modular upgrades and wider applicability to diverse interactive tasks. To foster generalizable agent learning, we collect large-scale, unified, and high-quality training annotations derived from diverse ground-truth reasoning rationales across various complex interactive tasks. On 9 datasets, LUMOS exhibits several key advantages: (1) LUMOS excels multiple larger open-source agents on the held-out datasets (unused for training) for each task type. LUMOS even surpasses GPT agents on QA and web tasks; (2) LUMOS outperforms open-source agents produced by chain-of-thoughts and unmodularized integrated training; and (3) LUMOS effectively generalizes to unseen tasks, outperforming 33B-scale agents and domain-specific agents.

Early detection and accurate diagnosis can predict the risk of malignant disease transformation, thereby increasing the probability of effective treatment. A mild syndrome with small infected regions is an ominous warning and is foremost in the early diagnosis of diseases. Deep learning algorithms, such as convolutional neural networks (CNNs), have been used to segment natural or medical objects, showing promising results. However, analyzing medical objects of small areas in images remains a challenge due to information losses and compression defects caused by convolution and pooling operations in CNNs. These losses and defects become increasingly significant as the network deepens, particularly for small medical objects. To address these challenges, we propose a novel scale-variant attention-based network (SvANet) for accurate small-scale object segmentation in medical images. The SvANet consists of Monte Carlo attention, scale-variant attention, and vision transformer, which incorporates cross-scale features and alleviates compression artifacts for enhancing the discrimination of small medical objects. Quantitative experimental results demonstrate the superior performance of SvANet, achieving 96.12%, 96.11%, 89.79%, 84.15%, 80.25%, 73.05%, and 72.58% in mean Dice coefficient for segmenting kidney tumors, skin lesions, hepatic tumors, polyps, surgical excision cells, retinal vasculatures, and sperms, which occupy less than 1% of the image areas in KiTS23, ISIC 2018, ATLAS, PolypGen, TissueNet, FIVES, and SpermHealth datasets, respectively.

Binary similarity involves determining whether two binary programs exhibit similar functionality, often originating from the same source code. In this work, we propose VexIR2Vec, an approach for binary similarity using VEX-IR, an architecture-neutral Intermediate Representation (IR). We extract the embeddings from sequences of basic blocks, termed peepholes, derived by random walks on the control-flow graph. The peepholes are normalized using transformations inspired by compiler optimizations. The VEX-IR Normalization Engine mitigates, with these transformations, the architectural and compiler-induced variations in binaries while exposing semantic similarities. We then learn the vocabulary of representations at the entity level of the IR using the knowledge graph embedding techniques in an unsupervised manner. This vocabulary is used to derive function embeddings for similarity assessment using VexNet, a feed-forward Siamese network designed to position similar functions closely and separate dissimilar ones in an n-dimensional space. This approach is amenable for both diffing and searching tasks, ensuring robustness against Out-Of-Vocabulary (OOV) issues. We evaluate VexIR2Vec on a dataset comprising 2.7M functions and 15.5K binaries from 7 projects compiled across 12 compilers targeting x86 and ARM architectures. In diffing experiments, VexIR2Vec outperforms the nearest baselines by $40\%$, $18\%$, $21\%$, and $60\%$ in cross-optimization, cross-compilation, cross-architecture, and obfuscation settings, respectively. In the searching experiment, VexIR2Vec achieves a mean average precision of $0.76$, outperforming the nearest baseline by $46\%$. Our framework is highly scalable and is built as a lightweight, multi-threaded, parallel library using only open-source tools. VexIR2Vec is $3.1$-$3.5 \times$ faster than the closest baselines and orders-of-magnitude faster than other tools.

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score.

Human body parsing remains a challenging problem in natural scenes due to multi-instance and inter-part semantic confusions as well as occlusions. This paper proposes a novel approach to decomposing multiple human bodies into semantic part regions in unconstrained environments. Specifically we propose a convolutional neural network (CNN) architecture which comprises of novel semantic and contour attention mechanisms across feature hierarchy to resolve the semantic ambiguities and boundary localization issues related to semantic body parsing. We further propose to encode estimated pose as higher-level contextual information which is combined with local semantic cues in a novel graphical model in a principled manner. In this proposed model, the lower-level semantic cues can be recursively updated by propagating higher-level contextual information from estimated pose and vice versa across the graph, so as to alleviate erroneous pose information and pixel level predictions. We further propose an optimization technique to efficiently derive the solutions. Our proposed method achieves the state-of-art results on the challenging Pascal Person-Part dataset.

Electroencephalography (EEG), a medical imaging technique that captures scalp electrical activity of brain structures via electrodes, has been widely used in affective computing. The spatial domain of EEG is rich in affective information. However, few of the existing studies have simultaneously analyzed EEG signals from multiple perspectives of geometric and anatomical structures in spatial domain. In this paper, we propose a multi-view Graph Transformer (MVGT) based on spatial relations, which integrates information from the temporal, frequency and spatial domains, including geometric and anatomical structures, so as to enhance the expressive power of the model comprehensively. We incorporate the spatial information of EEG channels into the model as encoding, thereby improving its ability to perceive the spatial structure of the channels. Meanwhile, experimental results based on publicly available datasets demonstrate that our proposed model outperforms state-of-the-art methods in recent years. In addition, the results also show that the MVGT could extract information from multiple domains and capture inter-channel relationships in EEG emotion recognition tasks effectively.

AI for cancer detection encounters the bottleneck of data scarcity, annotation difficulty, and low prevalence of early tumors. Tumor synthesis seeks to create artificial tumors in medical images, which can greatly diversify the data and annotations for AI training. However, current tumor synthesis approaches are not applicable across different organs due to their need for specific expertise and design. This paper establishes a set of generic rules to simulate tumor development. Each cell (pixel) is initially assigned a state between zero and ten to represent the tumor population, and a tumor can be developed based on three rules to describe the process of growth, invasion, and death. We apply these three generic rules to simulate tumor development--from pixel to cancer--using cellular automata. We then integrate the tumor state into the original computed tomography (CT) images to generate synthetic tumors across different organs. This tumor synthesis approach allows for sampling tumors at multiple stages and analyzing tumor-organ interaction. Clinically, a reader study involving three expert radiologists reveals that the synthetic tumors and their developing trajectories are convincingly realistic. Technically, we analyze and simulate tumor development at various stages using 9,262 raw, unlabeled CT images sourced from 68 hospitals worldwide. The performance in segmenting tumors in the liver, pancreas, and kidneys exceeds prevailing literature benchmarks, underlining the immense potential of tumor synthesis, especially for earlier cancer detection. The code and models are available at //github.com/MrGiovanni/Pixel2Cancer

Models need appropriate inductive biases to effectively learn from small amounts of data and generalize systematically outside of the training distribution. While Transformers are highly versatile and powerful, they can still benefit from enhanced structural inductive biases for seq2seq tasks, especially those involving syntactic transformations, such as converting active to passive voice or semantic parsing. In this paper, we propose to strengthen the structural inductive bias of a Transformer by intermediate pre-training to perform synthetically generated syntactic transformations of dependency trees given a description of the transformation. Our experiments confirm that this helps with few-shot learning of syntactic tasks such as chunking, and also improves structural generalization for semantic parsing. Our analysis shows that the intermediate pre-training leads to attention heads that keep track of which syntactic transformation needs to be applied to which token, and that the model can leverage these attention heads on downstream tasks.

Complex biological networks, comprising metabolic reactions, gene interactions, and protein interactions, often exhibit scale-free characteristics with power-law degree distributions. However, empirical studies have revealed discrepancies between observed biological network data and ideal power-law fits, highlighting the need for improved modeling approaches. To address this challenge, we propose a novel family of distributions, building upon the baseline Burr distribution. Specifically, we introduce the compounded Burr (CBurr) distribution, derived from a continuous probability distribution family, enabling flexible and efficient modeling of node degree distributions in biological networks. This study comprehensively investigates the general properties of the CBurr distribution, focusing on parameter estimation using the maximum likelihood method. Subsequently, we apply the CBurr distribution model to large-scale biological network data, aiming to evaluate its efficacy in fitting the entire range of node degree distributions, surpassing conventional power-law distributions and other benchmarks. Through extensive data analysis and graphical illustrations, we demonstrate that the CBurr distribution exhibits superior modeling capabilities compared to traditional power-law distributions. This novel distribution model holds great promise for accurately capturing the complex nature of biological networks and advancing our understanding of their underlying mechanisms.

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.