Publications

The World Health Organization as an engine of ideational robustness
Jean-Louis Denis
Gaelle Foucault
Pierre Larouche
Catherine Régis
Miriam Cohen
Marie-Andree Girard
2024-03-05
Policy and Society (published)
doi.org
F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching
Shaoning Li
Yusong Wang
Mingyu Li
Bin Shao
Nanning Zheng
Zhang Jian
Jian Tang
2024-03-04
ICLR.cc/2024/Workshop/GEM (poster)
openreview.net
openreview.net
Enhancing and Evaluating Logical Reasoning Abilities of Large Language Models
Shujie Deng
Honghua Dong
Xujie Si
2024-03-04
ICLR.cc/2024/Workshop/SeT_LLM (published)
openreview.net
openreview.net
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Jiarui Lu
Zuobai Zhang
Bozitao Zhong
Chence Shi
Jian Tang
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consum… (see more)ing molecular dynamics (MD) simulations *in silico*. Recently, generative models has been leveraged as a surrogate sampler to obtain conformation ensembles with orders of magnitude faster and without requiring any simulation data (a "zero-shot" inference). However, being agnostic of the underlying energy landscape, the accuracy of such generative model may still be limited. In this work, we explore the few-shot setting of such pre-trained generative sampler which incorporates MD simulations in a tractable manner. Specifically, given a target protein of interest, we first acquire some seeding conformations from the pre-trained sampler followed by a number of physical simulations in parallel starting from these seeding samples. Then we fine-tuned the generative model using the simulation trajectories above to become a target-specific sampler. Experimental results demonstrated the superior performance of such few-shot conformation sampler at a tractable computational cost.
2024-03-04
ICLR.cc/2024/Workshop/GEM (poster)
openreview.net
openreview.net
A Generative Model of Symmetry Transformations
James U. Allingham
Bruno Mlodozeniec
Shreyas Padhy
Javier Antor'an
David Scott Krueger
Richard E. Turner
Eric T. Nalisnick
Jos'e Miguel Hern'andez-Lobato
Correctly capturing the symmetry transformations of data can lead to efficient models with strong generalization capabilities, though method… (see more)s incorporating symmetries often require prior knowledge. While recent advancements have been made in learning those symmetries directly from the dataset, most of this work has focused on the discriminative setting. In this paper, we construct a generative model that explicitly aims to capture symmetries in the data, resulting in a model that learns which symmetries are present in an interpretable way. We provide a simple algorithm for efficiently learning our generative model and demonstrate its ability to capture symmetries under affine and color transformations. Combining our symmetry model with existing generative models results in higher marginal test-log-likelihoods and robustness to data sparsification.
2024-03-04
ArXiv (preprint)
doi.org
arxiv.org
MagicClay: Sculpting Meshes With Generative Neural Fields
Amir Barda
Vladimir Kim
Noam Aigerman
Amit H. Bermano
Thibault Groueix
The recent developments in neural fields have brought phenomenal capabilities to the field of shape generation, but they lack crucial proper… (see more)ties, such as incremental control - a fundamental requirement for artistic work. Triangular meshes, on the other hand, are the representation of choice for most geometry related tasks, offering efficiency and intuitive control, but do not lend themselves to neural optimization. To support downstream tasks, previous art typically proposes a two-step approach, where first a shape is generated using neural fields, and then a mesh is extracted for further processing. Instead, in this paper we introduce a hybrid approach that maintains both a mesh and a Signed Distance Field (SDF) representations consistently. Using this representation, we introduce MagicClay - an artist friendly tool for sculpting regions of a mesh according to textual prompts while keeping other regions untouched. Our framework carefully and efficiently balances consistency between the representations and regularizations in every step of the shape optimization; Relying on the mesh representation, we show how to render the SDF at higher resolutions and faster. In addition, we employ recent work in differentiable mesh reconstruction to adaptively allocate triangles in the mesh where required, as indicated by the SDF. Using an implemented prototype, we demonstrate superior generated geometry compared to the state-of-the-art, and novel consistent control, allowing sequential prompt-based edits to the same mesh for the first time.
2024-03-04
ArXiv (preprint)
doi.org
arxiv.org
Predicting Grokking Long Before it Happens: A look into the loss landscape of models which grok
Tikeng Notsawo Pascal Junior
Pascal Notsawo
Hattie Zhou
Mohammad Pezeshki
Irina Rish
Guillaume Dumas
2024-03-04
ICLR.cc/2024/Workshop/ME-FoMo (poster)
doi.org
openreview.net
Self-evaluation and self-prompting to improve the reliability of LLMs
Alexandre Piché
Aristides Milios
Dzmitry Bahdanau
Chris Pal
In order to safely deploy Large Language Models (LLMs), they must be capable of dynamically adapting their behavior based on their level of … (see more)knowledge and uncertainty associated with specific topics. This adaptive behavior, which we refer to as self-restraint, is non-trivial to teach since it depends on the internal knowledge of an LLM. By default, LLMs are trained to maximize the next token likelihood which does not teach the model to modulate its answer based on its level of uncertainty. In order to learn self-restraint, we devise a simple objective that can encourage the model to produce generation that the model is confident in. To optimize this objective, we introduce ReSearch, an iterative search algorithm based on self-evaluation and self-prompting. Our method results in fewer hallucinations overall, both for known and unknown topics, as the model learns to selectively restrain itself. In addition, our method elegantly incorporates the ability to decline, when the model assesses that it cannot provide a response without a high proportion of hallucination.
2024-03-04
ICLR.cc/2024/Workshop/SeT_LLM (published)
openreview.net
openreview.net
Self-evaluation and self-prompting to improve the reliability of LLMs
Alexandre Piché
Aristides Milios
Dzmitry Bahdanau
Chris Pal
In order to safely deploy Large Language Models (LLMs), they must be capable of dynamically adapting their behavior based on their level of … (see more)knowledge and uncertainty associated with specific topics. This adaptive behavior, which we refer to as self-restraint, is non-trivial to teach since it depends on the internal knowledge of an LLM. By default, LLMs are trained to maximize the next token likelihood which does not teach the model to modulate its answer based on its level of uncertainty. In order to learn self-restraint, we devise a simple objective that can encourage the model to produce generation that the model is confident in. To optimize this objective, we introduce ReSearch, an iterative search algorithm based on self-evaluation and self-prompting. Our method results in fewer hallucinations overall, both for known and unknown topics, as the model learns to selectively restrain itself. In addition, our method elegantly incorporates the ability to decline, when the model assesses that it cannot provide a response without a high proportion of hallucination.
2024-03-04
ICLR.cc/2024/Workshop/SeT_LLM (published)
openreview.net
openreview.net
Structure-Informed Protein Language Model
Zuobai Zhang
Jiarui Lu
Vijil Chenthamarakshan
Aurelie Lozano
Payel Das
Jian Tang
Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. Ho… (see more)wever, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights will be made available upon acceptance.
2024-03-04
ICLR.cc/2024/Workshop/GEM (poster)
openreview.net
openreview.net
Towards DNA-Encoded Library Generation with GFlowNets
Michał Koziarski
Mohammed Abukalam
Vedant Shah
Louis Vaillancourt
Doris Alexandra Schuetz
Moksh J. Jain
Almer M. van der Sloot
Mathieu Bourgey
Anne Marinier
Yoshua Bengio
2024-03-04
ICLR.cc/2024/Workshop/GEM (poster)
doi.org
openreview.net
Communicating Study Design Trade-offs in Software Engineering
Martin P. Robillard
Deeksha M. Arya
Neil Ernst
Jin Guo
Maxime Lamothe
Mathieu Nassif
Nicole Novielli
Alexander Serebrenik
Igor Steinmacher
Klaas-Jan Stol
2024-03-02
ACM Transactions on Software Engineering and Methodology (published)
doi.org