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Mar 18

TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools

Precision therapeutics require multimodal adaptive models that generate personalized treatment recommendations. We introduce TxAgent, an AI agent that leverages multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools to analyze drug interactions, contraindications, and patient-specific treatment strategies. TxAgent evaluates how drugs interact at molecular, pharmacokinetic, and clinical levels, identifies contraindications based on patient comorbidities and concurrent medications, and tailors treatment strategies to individual patient characteristics. It retrieves and synthesizes evidence from multiple biomedical sources, assesses interactions between drugs and patient conditions, and refines treatment recommendations through iterative reasoning. It selects tools based on task objectives and executes structured function calls to solve therapeutic tasks that require clinical reasoning and cross-source validation. The ToolUniverse consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets. TxAgent outperforms leading LLMs, tool-use models, and reasoning agents across five new benchmarks: DrugPC, BrandPC, GenericPC, TreatmentPC, and DescriptionPC, covering 3,168 drug reasoning tasks and 456 personalized treatment scenarios. It achieves 92.1% accuracy in open-ended drug reasoning tasks, surpassing GPT-4o and outperforming DeepSeek-R1 (671B) in structured multi-step reasoning. TxAgent generalizes across drug name variants and descriptions. By integrating multi-step inference, real-time knowledge grounding, and tool-assisted decision-making, TxAgent ensures that treatment recommendations align with established clinical guidelines and real-world evidence, reducing the risk of adverse events and improving therapeutic decision-making.

IOMatch: Simplifying Open-Set Semi-Supervised Learning with Joint Inliers and Outliers Utilization

Semi-supervised learning (SSL) aims to leverage massive unlabeled data when labels are expensive to obtain. Unfortunately, in many real-world applications, the collected unlabeled data will inevitably contain unseen-class outliers not belonging to any of the labeled classes. To deal with the challenging open-set SSL task, the mainstream methods tend to first detect outliers and then filter them out. However, we observe a surprising fact that such approach could result in more severe performance degradation when labels are extremely scarce, as the unreliable outlier detector may wrongly exclude a considerable portion of valuable inliers. To tackle with this issue, we introduce a novel open-set SSL framework, IOMatch, which can jointly utilize inliers and outliers, even when it is difficult to distinguish exactly between them. Specifically, we propose to employ a multi-binary classifier in combination with the standard closed-set classifier for producing unified open-set classification targets, which regard all outliers as a single new class. By adopting these targets as open-set pseudo-labels, we optimize an open-set classifier with all unlabeled samples including both inliers and outliers. Extensive experiments have shown that IOMatch significantly outperforms the baseline methods across different benchmark datasets and different settings despite its remarkable simplicity. Our code and models are available at https://github.com/nukezil/IOMatch.

Open-Source Large Language Models as Multilingual Crowdworkers: Synthesizing Open-Domain Dialogues in Several Languages With No Examples in Targets and No Machine Translation

The prevailing paradigm in the domain of Open-Domain Dialogue agents predominantly focuses on the English language, encompassing both models and datasets. Furthermore, the financial and temporal investments required for crowdsourcing such datasets for finetuning are substantial, particularly when multiple languages are involved. Fortunately, advancements in Large Language Models (LLMs) have unveiled a plethora of possibilities across diverse tasks. Specifically, instruction-tuning has enabled LLMs to execute tasks based on natural language instructions, occasionally surpassing the performance of human crowdworkers. Additionally, these models possess the capability to function in various languages within a single thread. Consequently, to generate new samples in different languages, we propose leveraging these capabilities to replicate the data collection process. We introduce a pipeline for generating Open-Domain Dialogue data in multiple Target Languages using LLMs, with demonstrations provided in a unique Source Language. By eschewing explicit Machine Translation in this approach, we enhance the adherence to language-specific nuances. We apply this methodology to the PersonaChat dataset. To enhance the openness of generated dialogues and mimic real life scenarii, we added the notion of speech events corresponding to the type of conversation the speakers are involved in and also that of common ground which represents the premises of a conversation.

UFO: A Unified Approach to Fine-grained Visual Perception via Open-ended Language Interface

Generalist models have achieved remarkable success in both language and vision-language tasks, showcasing the potential of unified modeling. However, effectively integrating fine-grained perception tasks like detection and segmentation into these models remains a significant challenge. This is primarily because these tasks often rely heavily on task-specific designs and architectures that can complicate the modeling process. To address this challenge, we present \ours, a framework that Unifies Fine-grained visual perception tasks through an Open-ended language interface. By transforming all perception targets into the language space, \ours unifies object-level detection, pixel-level segmentation, and image-level vision-language tasks into a single model. Additionally, we introduce a novel embedding retrieval approach that relies solely on the language interface to support segmentation tasks. Our framework bridges the gap between fine-grained perception and vision-language tasks, significantly simplifying architectural design and training strategies while achieving comparable or superior performance to methods with intricate task-specific designs. After multi-task training on five standard visual perception datasets, \ours outperforms the previous state-of-the-art generalist models by 12.3 mAP on COCO instance segmentation and 3.3 mIoU on ADE20K semantic segmentation. Furthermore, our method seamlessly integrates with existing MLLMs, effectively combining fine-grained perception capabilities with their advanced language abilities, thereby enabling more challenging tasks such as reasoning segmentation. Code and models will be publicly available.

BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

Prototypical Kernel Learning and Open-set Foreground Perception for Generalized Few-shot Semantic Segmentation

Generalized Few-shot Semantic Segmentation (GFSS) extends Few-shot Semantic Segmentation (FSS) to simultaneously segment unseen classes and seen classes during evaluation. Previous works leverage additional branch or prototypical aggregation to eliminate the constrained setting of FSS. However, representation division and embedding prejudice, which heavily results in poor performance of GFSS, have not been synthetical considered. We address the aforementioned problems by jointing the prototypical kernel learning and open-set foreground perception. Specifically, a group of learnable kernels is proposed to perform segmentation with each kernel in charge of a stuff class. Then, we explore to merge the prototypical learning to the update of base-class kernels, which is consistent with the prototype knowledge aggregation of few-shot novel classes. In addition, a foreground contextual perception module cooperating with conditional bias based inference is adopted to perform class-agnostic as well as open-set foreground detection, thus to mitigate the embedding prejudice and prevent novel targets from being misclassified as background. Moreover, we also adjust our method to the Class Incremental Few-shot Semantic Segmentation (CIFSS) which takes the knowledge of novel classes in a incremental stream. Extensive experiments on PASCAL-5i and COCO-20i datasets demonstrate that our method performs better than previous state-of-the-art.

MarvelOVD: Marrying Object Recognition and Vision-Language Models for Robust Open-Vocabulary Object Detection

Learning from pseudo-labels that generated with VLMs~(Vision Language Models) has been shown as a promising solution to assist open vocabulary detection (OVD) in recent studies. However, due to the domain gap between VLM and vision-detection tasks, pseudo-labels produced by the VLMs are prone to be noisy, while the training design of the detector further amplifies the bias. In this work, we investigate the root cause of VLMs' biased prediction under the OVD context. Our observations lead to a simple yet effective paradigm, coded MarvelOVD, that generates significantly better training targets and optimizes the learning procedure in an online manner by marrying the capability of the detector with the vision-language model. Our key insight is that the detector itself can act as a strong auxiliary guidance to accommodate VLM's inability of understanding both the ``background'' and the context of a proposal within the image. Based on it, we greatly purify the noisy pseudo-labels via Online Mining and propose Adaptive Reweighting to effectively suppress the biased training boxes that are not well aligned with the target object. In addition, we also identify a neglected ``base-novel-conflict'' problem and introduce stratified label assignments to prevent it. Extensive experiments on COCO and LVIS datasets demonstrate that our method outperforms the other state-of-the-arts by significant margins. Codes are available at https://github.com/wkfdb/MarvelOVD

Text Generation: A Systematic Literature Review of Tasks, Evaluation, and Challenges

Text generation has become more accessible than ever, and the increasing interest in these systems, especially those using large language models, has spurred an increasing number of related publications. We provide a systematic literature review comprising 244 selected papers between 2017 and 2024. This review categorizes works in text generation into five main tasks: open-ended text generation, summarization, translation, paraphrasing, and question answering. For each task, we review their relevant characteristics, sub-tasks, and specific challenges (e.g., missing datasets for multi-document summarization, coherence in story generation, and complex reasoning for question answering). Additionally, we assess current approaches for evaluating text generation systems and ascertain problems with current metrics. Our investigation shows nine prominent challenges common to all tasks and sub-tasks in recent text generation publications: bias, reasoning, hallucinations, misuse, privacy, interpretability, transparency, datasets, and computing. We provide a detailed analysis of these challenges, their potential solutions, and which gaps still require further engagement from the community. This systematic literature review targets two main audiences: early career researchers in natural language processing looking for an overview of the field and promising research directions, as well as experienced researchers seeking a detailed view of tasks, evaluation methodologies, open challenges, and recent mitigation strategies.

Quantune: Post-training Quantization of Convolutional Neural Networks using Extreme Gradient Boosting for Fast Deployment

To adopt convolutional neural networks (CNN) for a range of resource-constrained targets, it is necessary to compress the CNN models by performing quantization, whereby precision representation is converted to a lower bit representation. To overcome problems such as sensitivity of the training dataset, high computational requirements, and large time consumption, post-training quantization methods that do not require retraining have been proposed. In addition, to compensate for the accuracy drop without retraining, previous studies on post-training quantization have proposed several complementary methods: calibration, schemes, clipping, granularity, and mixed-precision. To generate a quantized model with minimal error, it is necessary to study all possible combinations of the methods because each of them is complementary and the CNN models have different characteristics. However, an exhaustive or a heuristic search is either too time-consuming or suboptimal. To overcome this challenge, we propose an auto-tuner known as Quantune, which builds a gradient tree boosting model to accelerate the search for the configurations of quantization and reduce the quantization error. We evaluate and compare Quantune with the random, grid, and genetic algorithms. The experimental results show that Quantune reduces the search time for quantization by approximately 36.5x with an accuracy loss of 0.07 ~ 0.65% across six CNN models, including the fragile ones (MobileNet, SqueezeNet, and ShuffleNet). To support multiple targets and adopt continuously evolving quantization works, Quantune is implemented on a full-fledged compiler for deep learning as an open-sourced project.

Combinational Backdoor Attack against Customized Text-to-Image Models

Recently, Text-to-Image (T2I) synthesis technology has made tremendous strides. Numerous representative T2I models have emerged and achieved promising application outcomes, such as DALL-E, Stable Diffusion, Imagen, etc. In practice, it has become increasingly popular for model developers to selectively adopt various pre-trained text encoders and conditional diffusion models from third-party platforms, integrating them to build customized (personalized) T2I models. However, such an adoption approach is vulnerable to backdoor attacks. In this work, we propose a Combinational Backdoor Attack against Customized T2I models (CBACT2I) targeting this application scenario. Different from previous backdoor attacks against T2I models, CBACT2I embeds the backdoor into the text encoder and the conditional diffusion model separately. The customized T2I model exhibits backdoor behaviors only when the backdoor text encoder is used in combination with the backdoor conditional diffusion model. These properties make CBACT2I more stealthy and flexible than prior backdoor attacks against T2I models. Extensive experiments demonstrate the effectiveness of CBACT2I with different backdoor triggers and different backdoor targets on the open-sourced Stable Diffusion model. This work reveals the backdoor vulnerabilities of customized T2I models and urges countermeasures to mitigate backdoor threats in this scenario.

Scaling of Search and Learning: A Roadmap to Reproduce o1 from Reinforcement Learning Perspective

OpenAI o1 represents a significant milestone in Artificial Inteiligence, which achieves expert-level performances on many challanging tasks that require strong reasoning ability.OpenAI has claimed that the main techinique behinds o1 is the reinforcement learining. Recent works use alternative approaches like knowledge distillation to imitate o1's reasoning style, but their effectiveness is limited by the capability ceiling of the teacher model. Therefore, this paper analyzes the roadmap to achieving o1 from the perspective of reinforcement learning, focusing on four key components: policy initialization, reward design, search, and learning. Policy initialization enables models to develop human-like reasoning behaviors, equipping them with the ability to effectively explore solution spaces for complex problems. Reward design provides dense and effective signals via reward shaping or reward modeling, which is the guidance for both search and learning. Search plays a crucial role in generating high-quality solutions during both training and testing phases, which can produce better solutions with more computation. Learning utilizes the data generated by search for improving policy, which can achieve the better performance with more parameters and more searched data. Existing open-source projects that attempt to reproduce o1 can be seem as a part or a variant of our roadmap. Collectively, these components underscore how learning and search drive o1's advancement, making meaningful contributions to the development of LLM.

Toxicity of the Commons: Curating Open-Source Pre-Training Data

Open-source large language models are becoming increasingly available and popular among researchers and practitioners. While significant progress has been made on open-weight models, open training data is a practice yet to be adopted by the leading open-weight models creators. At the same time, there researchers are working to make language models safer. We propose a data curation pipeline to reduce harmful outputs by models trained on public domain data. There are unique challenges to working with public domain data, as these sources differ from web text in both form and content. Many sources are historical documents and are the result of Optical Character Recognition (OCR). Consequently, current state-of-the-art approaches to toxicity filtering are often infeasible or inappropriate for open data models. In this paper, we introduce a new fully open-source pipeline for open-data toxicity filtering. Our contributions are threefold. We create a custom training dataset, ToxicCommons, which is composed of texts which have been classified across five different dimensions (racial/origin-based, gender/sex-based, religious, ability-based discrimination, and violence). We use this dataset to train a custom classifier, Celadon, that can be used to detect toxic content in open data more efficiently at a larger scale. Finally, we describe the balanced approach to content filtration that optimizes safety filtering with respect to the filtered data available for training.