Publications

MATES: A Deep Learning-Based Model for Locus-specific Quantification of Transposable Elements in Single Cell

Ruohan Wang

Yumin Zheng

Zijian Zhang

Kailu Song

Erxi Wu

Xiaopeng Zhu

Tao P. Wu

Jun Ding

Transposable elements (TEs) are crucial for genetic diversity and gene regulation. Current single-cell quantification methods often align mu… (see more)lti-mapping reads to either ‘best-mapped’ or ‘random-mapped’ locations and categorize them at sub-family levels, overlooking the biological necessity for accurate, locus-specific TE quantification. Moreover, these existing methods are primarily designed for and focused on transcriptomics data, which restricts their adaptability to single-cell data of other modalities. To address these challenges, here we introduce MATES, a novel deep-learning approach that accurately allocates multi-mapping reads to specific loci of TEs, utilizing context from adjacent read alignments flanking the TE locus. When applied to diverse single-cell omics datasets, MATES shows improved performance over existing methods, enhancing the accuracy of TE quantification and aiding in the identification of marker TEs for identified cell populations. This development enables exploring single-cell heterogeneity and gene regulation through the lens of TEs, offering a transformative tool for the single-cell genomics community.

2024-10-11

Nature Communications (published)

Physical Simulation for Multi-agent Multi-machine Tending

Abdalwhab Abdalwhab

Giovanni Beltrame

David St-Onge

2024-10-11

ArXiv (preprint)

PoisonBench: Assessing Large Language Model Vulnerability to Data Poisoning

Tingchen Fu

Mrinank Sharma

Philip Torr

Shay B. Cohen

David Scott Krueger

Fazl Barez

Preference learning is a central component for aligning current LLMs, but this process can be vulnerable to data poisoning attacks. To addre… (see more)ss this concern, we introduce PoisonBench, a benchmark for evaluating large language models' susceptibility to data poisoning during preference learning. Data poisoning attacks can manipulate large language model responses to include hidden malicious content or biases, potentially causing the model to generate harmful or unintended outputs while appearing to function normally. We deploy two distinct attack types across eight realistic scenarios, assessing 21 widely-used models. Our findings reveal concerning trends: (1) Scaling up parameter size does not inherently enhance resilience against poisoning attacks; (2) There exists a log-linear relationship between the effects of the attack and the data poison ratio; (3) The effect of data poisoning can generalize to extrapolated triggers that are not included in the poisoned data. These results expose weaknesses in current preference learning techniques, highlighting the urgent need for more robust defenses against malicious models and data manipulation.

2024-10-11

ArXiv (preprint)

Predicting Drug Effects from High-Dimensional, Asymmetric Drug Datasets by Using Graph Neural Networks: A Comprehensive Analysis of Multitarget Drug Effect Prediction

Joey Bose

Guojing Cong

Graph neural networks (GNNs) have emerged as one of the most effective ML techniques for drug effect prediction from drug molecular graphs. … (see more)Despite having immense potential, GNN models lack performance when using datasets that contain high-dimensional, asymmetrically co-occurrent drug effects as targets with complex correlations between them. Training individual learning models for each drug effect and incorporating every prediction result for a wide spectrum of drug effects are impractical. Therefore, an opportunity exists to address this challenge as multitarget prediction problems and predict all drug effects at a time. We developed standard and hybrid GNNs to perform two separate tasks: multiregression for continuous values and multilabel classification for categorical values contained in our datasets. Because multilabel classification makes the target data even more sparse and introduces asymmetric label co-occurrence, learning these models becomes difficult and heavily impacts the GNN's performance. To address these challenges, we propose a new data oversampling technique to improve multilabel classification performances on all the given imbalanced molecular graph datasets. Using the technique, we improve the data imbalance ratio of the drug effects while protecting the datasets' integrity. Finally, we evaluate the multilabel classification performance of the best-performing hybrid GNN model on all the oversampled datasets obtained from the proposed oversampling technique. In all the evaluation metrics (i.e., precision, recall, and F1 score), this model significantly outperforms other ML models, including GNN models when they are trained on the original datasets or oversampled datasets with MLSMOTE, which is a well-known oversampling technique.

2024-10-11

ArXiv (preprint)

SOAK: Same/Other/All K-fold cross-validation for estimating similarity of patterns in data subsets

Toby Dylan Hocking

Gabrielle Thibault

C. Bodine

Paul Nelson Arellano

Alexander F Shenkin

Olivia J. Lindly

In many real-world applications of machine learning, we are interested to know if it is possible to train on the data that we have gathered … (see more)so far, and obtain accurate predictions on a new test data subset that is qualitatively different in some respect (time period, geographic region, etc). Another question is whether data subsets are similar enough so that it is beneficial to combine subsets during model training. We propose SOAK, Same/Other/All K-fold cross-validation, a new method which can be used to answer both questions. SOAK systematically compares models which are trained on different subsets of data, and then used for prediction on a fixed test subset, to estimate the similarity of learnable/predictable patterns in data subsets. We show results of using SOAK on six new real data sets (with geographic/temporal subsets, to check if predictions are accurate on new subsets), 3 image pair data sets (subsets are different image types, to check that we get smaller prediction error on similar images), and 11 benchmark data sets with predefined train/test splits (to check similarity of predefined splits).

2024-10-11

ArXiv (preprint)

"I Am the One and Only, Your Cyber BFF": Understanding the Impact of GenAI Requires Understanding the Impact of Anthropomorphic AI

Myra Cheng

Alicia DeVrio

Lisa Egede

Su Lin Blodgett

Alexandra Olteanu

Many state-of-the-art generative AI (GenAI) systems are increasingly prone to anthropomorphic behaviors, i.e., to generating outputs that ar… (see more)e perceived to be human-like. While this has led to scholars increasingly raising concerns about possible negative impacts such anthropomorphic AI systems can give rise to, anthropomorphism in AI development, deployment, and use remains vastly overlooked, understudied, and underspecified. In this perspective, we argue that we cannot thoroughly map the social impacts of generative AI without mapping the social impacts of anthropomorphic AI, and outline a call to action.

2024-10-11

ArXiv (preprint)

ACCO: Accumulate while you Communicate, Hiding Communications in Distributed LLM Training

Adel Nabli

Louis Fournier

Pierre ERBACHER

Louis Serrano

Eugene Belilovsky

Edouard Oyallon

2024-10-10

NeurIPS.cc/2024/Workshop/OPT (published)

AgentMerge: Enhancing Generalization in Fine-Tuned LLM Agents

Megh Thakkar

Léo Boisvert

Thibault Le Sellier de Chezelles

Alexandre Piché

Maxime Gasse

Alexandre Lacoste

Massimo Caccia

2024-10-10

NeurIPS.cc/2024/Workshop/AFM (poster)

BigDocs: An Open and Permissively-Licensed Dataset for Training Multimodal Models on Document and Code Tasks

Juan A. Rodriguez

Xiangru Jian

Siba Smarak Panigrahi

Tianyu Zhang

Aarash Feizi

Abhay Puri

Akshay Kalkunte Suresh

François Savard

Ahmed Masry

Shravan Nayak

Rabiul Awal

Mahsa Massoud

Amirhossein Abaskohi

Zichao Li

Suyuchen Wang

Pierre-Andre Noel

Mats Leon Richter

Saverio Vadacchino

Shubham Agarwal

Sanket Biswas … (see 23 more)

Sara Shanian

Ying Zhang

Noah Bolger

Kurt MacDonald

Simon Fauvel

Sathwik Tejaswi Madhusudhan

Srinivas Sunkara

Joao Monteiro

Krishnamurthy Dj Dvijotham

Torsten Scholak

Nicolas Chapados

Sepideh Kharaghani

Sean Hughes

M. Özsu

Issam Hadj Laradji

Spandana Gella

Perouz Taslakian

David Vazquez

Sai Rajeswar

Multimodal AI has the potential to significantly enhance document-understanding tasks, such as processing receipts, understanding workflows,… (see more) extracting data from documents, and summarizing reports. Code generation tasks that require long-structured outputs can also be enhanced by multimodality. Despite this, their use in commercial applications is often limited due to limited access to training data and restrictive licensing, which hinders open access. To address these limitations, we introduce BigDocs-7.5M, a high-quality, open-access dataset comprising 7.5 million multimodal documents across 30 tasks. We use an efficient data curation process to ensure our data is high-quality and license-permissive. Our process emphasizes accountability, responsibility, and transparency through filtering rules, traceable metadata, and careful content analysis. Additionally, we introduce BigDocs-Bench, a benchmark suite with 10 novel tasks where we create datasets that reflect real-world use cases involving reasoning over Graphical User Interfaces (GUI) and code generation from images. Our experiments show that training with BigDocs-Bench improves average performance up to 25.8% over closed-source GPT-4o in document reasoning and structured output tasks such as Screenshot2HTML or Image2Latex generation. Finally, human evaluations showed a preference for outputs from models trained on BigDocs over GPT-4o. This suggests that BigDocs can help both academics and the open-source community utilize and improve AI tools to enhance multimodal capabilities and document reasoning. The project is hosted at https://bigdocs.github.io .

2024-10-10

NeurIPS.cc/2024/Workshop/RBFM (poster)

Combining Domain and Alignment Vectors to Achieve Better Knowledge-Safety Trade-offs in LLMs

Megh Thakkar

Yash More

Quentin Fournier

Matthew D Riemer

Pin-Yu Chen

Amal Zouaq

Payel Das

Sarath Chandar

There is a growing interest in training domain-expert LLMs that excel in specific technical fields compared to their general-purpose instruc… (see more)tion-tuned counterparts. However, these expert models often experience a loss in their safety abilities in the process, making them capable of generating harmful content. As a solution, we introduce an efficient and effective merging-based alignment method called \textsc{MergeAlign} that interpolates the domain and alignment vectors, creating safer domain-specific models while preserving their utility. We apply \textsc{MergeAlign} on Llama3 variants that are experts in medicine and finance, obtaining substantial alignment improvements with minimal to no degradation on domain-specific benchmarks. We study the impact of model merging through model similarity metrics and contributions of individual models being merged. We hope our findings open new research avenues and inspire more efficient development of safe expert LLMs.

2024-10-10

NeurIPS.cc/2024/Workshop/AFM (poster)