SciSafeEval: A Comprehensive Benchmark for Safety Alignment of Large Language Models in Scientific Tasks

Large language models (LLMs) have had a transformative impact on a variety of scientific tasks across disciplines such as biology, chemistry, medicine, and physics. However, ensuring the safety alignment of these models in scientific research remains an underexplored area, with existing benchmarks primarily focus on textual content and overlooking key scientific representations such as molecular, protein, and genomic languages. Moreover, the safety mechanisms of LLMs in scientific tasks are insufficiently studied. To address these limitations, we introduce SciSafeEval, a comprehensive benchmark designed to evaluate the safety alignment of LLMs across a range of scientific tasks. SciSafeEval spans multiple scientific languages - including textual, molecular, protein, and genomic - and covers a wide range of scientific domains. We evaluate LLMs in zero-shot, few-shot and chain-of-thought settings, and introduce a 'jailbreak' enhancement feature that challenges LLMs equipped with safety guardrails, rigorously testing their defenses against malicious intention. Our benchmark surpasses existing safety datasets in both scale and scope, providing a robust platform for assessing the safety and performance of LLMs in scientific contexts. This work aims to facilitate the responsible development and deployment of LLMs, promoting alignment with safety and ethical standards in scientific research.

STS MICCAI 2023 Challenge: Grand challenge on 2D and 3D semi-supervised tooth segmentation

Computer-aided design (CAD) tools are increasingly popular in modern dental practice, particularly for treatment planning or comprehensive prognosis evaluation. In particular, the 2D panoramic X-ray image efficiently detects invisible caries, impacted teeth and supernumerary teeth in children, while the 3D dental cone beam computed tomography (CBCT) is widely used in orthodontics and endodontics due to its low radiation dose. However, there is no open-access 2D public dataset for children's teeth and no open 3D dental CBCT dataset, which limits the development of automatic algorithms for segmenting teeth and analyzing diseases. The Semi-supervised Teeth Segmentation (STS) Challenge, a pioneering event in tooth segmentation, was held as a part of the MICCAI 2023 ToothFairy Workshop on the Alibaba Tianchi platform. This challenge aims to investigate effective semi-supervised tooth segmentation algorithms to advance the field of dentistry. In this challenge, we provide two modalities including the 2D panoramic X-ray images and the 3D CBCT tooth volumes. In Task 1, the goal was to segment tooth regions in panoramic X-ray images of both adult and pediatric teeth. Task 2 involved segmenting tooth sections using CBCT volumes. Limited labelled images with mostly unlabelled ones were provided in this challenge prompt using semi-supervised algorithms for training. In the preliminary round, the challenge received registration and result submission by 434 teams, with 64 advancing to the final round. This paper summarizes the diverse methods employed by the top-ranking teams in the STS MICCAI 2023 Challenge.

Qwen2 Technical Report

This report introduces the Qwen2 series, the latest addition to our large language models and large multimodal models. We release a comprehensive suite of foundational and instruction-tuned language models, encompassing a parameter range from 0.5 to 72 billion, featuring dense models and a Mixture-of-Experts model. Qwen2 surpasses most prior open-weight models, including its predecessor Qwen1.5, and exhibits competitive performance relative to proprietary models across diverse benchmarks on language understanding, generation, multilingual proficiency, coding, mathematics, and reasoning. The flagship model, Qwen2-72B, showcases remarkable performance: 84.2 on MMLU, 37.9 on GPQA, 64.6 on HumanEval, 89.5 on GSM8K, and 82.4 on BBH as a base language model. The instruction-tuned variant, Qwen2-72B-Instruct, attains 9.1 on MT-Bench, 48.1 on Arena-Hard, and 35.7 on LiveCodeBench. Moreover, Qwen2 demonstrates robust multilingual capabilities, proficient in approximately 30 languages, spanning English, Chinese, Spanish, French, German, Arabic, Russian, Korean, Japanese, Thai, Vietnamese, and more, underscoring its versatility and global reach. To foster community innovation and accessibility, we have made the Qwen2 model weights openly available on Hugging Face and ModelScope, and the supplementary materials including example code on GitHub. These platforms also include resources for quantization, fine-tuning, and deployment, facilitating a wide range of applications and research endeavors.

MoE-CT: A Novel Approach For Large Language Models Training With Resistance To Catastrophic Forgetting

The advent of large language models (LLMs) has predominantly catered to high-resource languages, leaving a disparity in performance for low-resource languages. Conventional Continual Training (CT) approaches to bridge this gap often undermine a model's original linguistic proficiency when expanding to multilingual contexts. Addressing this issue, we introduce a novel MoE-CT architecture, a paradigm that innovatively separates the base model's learning from the multilingual expansion process. Our design freezes the original LLM parameters, thus safeguarding its performance in high-resource languages, while an appended MoE module, trained on diverse language datasets, augments low-resource language proficiency. Our approach significantly outperforms conventional CT methods, as evidenced by our experiments, which show marked improvements in multilingual benchmarks without sacrificing the model's original language performance. Moreover, our MoE-CT framework demonstrates enhanced resistance to forgetting and superior transfer learning capabilities. By preserving the base model's integrity and focusing on strategic parameter expansion, our methodology advances multilingual language modeling and represents a significant step forward for low-resource language inclusion in LLMs, indicating a fruitful direction for future research in language technologies.

Improving Fairness of Automated Chest X-ray Diagnosis by Contrastive Learning

Purpose: Limited studies exploring concrete methods or approaches to tackle and enhance model fairness in the radiology domain. Our proposed AI model utilizes supervised contrastive learning to minimize bias in CXR diagnosis. Materials and Methods: In this retrospective study, we evaluated our proposed method on two datasets: the Medical Imaging and Data Resource Center (MIDRC) dataset with 77,887 CXR images from 27,796 patients collected as of April 20, 2023 for COVID-19 diagnosis, and the NIH Chest X-ray (NIH-CXR) dataset with 112,120 CXR images from 30,805 patients collected between 1992 and 2015. In the NIH-CXR dataset, thoracic abnormalities include atelectasis, cardiomegaly, effusion, infiltration, mass, nodule, pneumonia, pneumothorax, consolidation, edema, emphysema, fibrosis, pleural thickening, or hernia. Our proposed method utilizes supervised contrastive learning with carefully selected positive and negative samples to generate fair image embeddings, which are fine-tuned for subsequent tasks to reduce bias in chest X-ray (CXR) diagnosis. We evaluated the methods using the marginal AUC difference ($\delta$ mAUC). Results: The proposed model showed a significant decrease in bias across all subgroups when compared to the baseline models, as evidenced by a paired T-test (p<0.0001). The $\delta$ mAUC obtained by our method were 0.0116 (95\% CI, 0.0110-0.0123), 0.2102 (95% CI, 0.2087-0.2118), and 0.1000 (95\% CI, 0.0988-0.1011) for sex, race, and age on MIDRC, and 0.0090 (95\% CI, 0.0082-0.0097) for sex and 0.0512 (95% CI, 0.0512-0.0532) for age on NIH-CXR, respectively. Conclusion: Employing supervised contrastive learning can mitigate bias in CXR diagnosis, addressing concerns of fairness and reliability in deep learning-based diagnostic methods.

PolyLM: An Open Source Polyglot Large Language Model

Large language models (LLMs) demonstrate remarkable ability to comprehend, reason, and generate following nature language instructions. However, the development of LLMs has been primarily focused on high-resource languages, such as English, thereby limiting their applicability and research in other languages. Consequently, we present PolyLM, a multilingual LLM trained on 640 billion (B) tokens, avaliable in two model sizes: 1.7B and 13B. To enhance its multilingual capabilities, we 1) integrate bilingual data into training data; and 2) adopt a curriculum learning strategy that increases the proportion of non-English data from 30% in the first stage to 60% in the final stage during pre-training. Further, we propose a multilingual self-instruct method which automatically generates 132.7K diverse multilingual instructions for model fine-tuning. To assess the model's performance, we collect several existing multilingual tasks, including multilingual understanding, question answering, generation, and translation. Extensive experiments show that PolyLM surpasses other open-source models such as LLaMA and BLOOM on multilingual tasks while maintaining comparable performance in English. Our models, alone with the instruction data and multilingual benchmark, are available at: \url{https://modelscope.cn/models/damo/nlp_polylm_13b_text_generation}.

CancerGPT: Few-shot Drug Pair Synergy Prediction using Large Pre-trained Language Models

Large pre-trained language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology, has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Our proposed few-shot learning approach uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features. Our experiments, which involved seven rare tissues from different cancer types, demonstrated that the LLM-based prediction model achieved significant accuracy with very few or zero samples. Our proposed model, the CancerGPT (with $\sim$ 124M parameters), was even comparable to the larger fine-tuned GPT-3 model (with $\sim$ 175B parameters). Our research is the first to tackle drug pair synergy prediction in rare tissues with limited data. We are also the first to utilize an LLM-based prediction model for biological reaction prediction tasks.

Pre-training Tasks for User Intent Detection and Embedding Retrieval in E-commerce Search

BERT-style models pre-trained on the general corpus (e.g., Wikipedia) and fine-tuned on specific task corpus, have recently emerged as breakthrough techniques in many NLP tasks: question answering, text classification, sequence labeling and so on. However, this technique may not always work, especially for two scenarios: a corpus that contains very different text from the general corpus Wikipedia, or a task that learns embedding spacial distribution for a specific purpose (e.g., approximate nearest neighbor search). In this paper, to tackle the above two scenarios that we have encountered in an industrial e-commerce search system, we propose customized and novel pre-training tasks for two critical modules: user intent detection and semantic embedding retrieval. The customized pre-trained models after fine-tuning, being less than 10% of BERT-base's size in order to be feasible for cost-efficient CPU serving, significantly improve the other baseline models: 1) no pre-training model and 2) fine-tuned model from the official pre-trained BERT using general corpus, on both offline datasets and online system. We have open sourced our datasets for the sake of reproducibility and future works.

SCALP -- Supervised Contrastive Learning for Cardiopulmonary Disease Classification and Localization in Chest X-rays using Patient Metadata

Computer-aided diagnosis plays a salient role in more accessible and accurate cardiopulmonary diseases classification and localization on chest radiography. Millions of people get affected and die due to these diseases without an accurate and timely diagnosis. Recently proposed contrastive learning heavily relies on data augmentation, especially positive data augmentation. However, generating clinically-accurate data augmentations for medical images is extremely difficult because the common data augmentation methods in computer vision, such as sharp, blur, and crop operations, can severely alter the clinical settings of medical images. In this paper, we proposed a novel and simple data augmentation method based on patient metadata and supervised knowledge to create clinically accurate positive and negative augmentations for chest X-rays. We introduce an end-to-end framework, SCALP, which extends the self-supervised contrastive approach to a supervised setting. Specifically, SCALP pulls together chest X-rays from the same patient (positive keys) and pushes apart chest X-rays from different patients (negative keys). In addition, it uses ResNet-50 along with the triplet-attention mechanism to identify cardiopulmonary diseases, and Grad-CAM++ to highlight the abnormal regions. Our extensive experiments demonstrate that SCALP outperforms existing baselines with significant margins in both classification and localization tasks. Specifically, the average classification AUCs improve from 82.8% (SOTA using DenseNet-121) to 83.9% (SCALP using ResNet-50), while the localization results improve on average by 3.7% over different IoU thresholds.

Negative Sample Matters: A Renaissance of Metric Learning for Temporal Grounding

Temporal grounding aims to temporally localize a video moment in the video whose semantics are related to a given natural language query. Existing methods typically apply a detection or regression pipeline on the fused representation with a focus on designing complicated heads and fusion strategies. Instead, from a perspective on temporal grounding as a metric-learning problem, we present a Dual Matching Network (DMN), to directly model the relations between language queries and video moments in a joint embedding space. This new metric-learning framework enables fully exploiting negative samples from two new aspects: constructing negative cross-modal pairs from a dual matching scheme and mining negative pairs across different videos. These new negative samples could enhance the joint representation learning of two modalities via cross-modal pair discrimination to maximize their mutual information. Experiments show that DMN achieves highly competitive performance compared with state-of-the-art methods on four video grounding benchmarks. Based on DMN, we present a winner solution for STVG challenge of the 3rd PIC workshop. This suggests that metric-learning is still a promising method for temporal grounding via capturing the essential cross-modal correlation in a joint embedding space.