Fault Localization in Deep Learning-based Software: A System-level Approach
Mohammad Mehdi Morovati
Amin Nikanjam
Foutse Khomh
2024-11-12
ArXiv (prépublication)
doi.org
arxiv.org
Investigating the Effectiveness of Explainability Methods in Parkinson's Detection from Speech
Eleonora Mancini
Francesco Paissan
Paolo Torroni
Mirco Ravanelli
Cem Subakan
Speech impairments in Parkinson's disease (PD) provide significant early indicators for diagnosis. While models for speech-based PD detectio… (voir plus)n have shown strong performance, their interpretability remains underexplored. This study systematically evaluates several explainability methods to identify PD-specific speech features, aiming to support the development of accurate, interpretable models for clinical decision-making in PD diagnosis and monitoring. Our methodology involves (i) obtaining attributions and saliency maps using mainstream interpretability techniques, (ii) quantitatively evaluating the faithfulness of these maps and their combinations obtained via union and intersection through a range of established metrics, and (iii) assessing the information conveyed by the saliency maps for PD detection from an auxiliary classifier. Our results reveal that, while explanations are aligned with the classifier, they often fail to provide valuable information for domain experts.
2024-11-12
ArXiv (prépublication)
doi.org
arxiv.org
Investigating the Effectiveness of Explainability Methods in Parkinson's Detection from Speech
Eleonora Mancini
Francesco Paissan
Paolo Torroni
Mirco Ravanelli
Cem Subakan
Speech impairments in Parkinson's disease (PD) provide significant early indicators for diagnosis. While models for speech-based PD detectio… (voir plus)n have shown strong performance, their interpretability remains underexplored. This study systematically evaluates several explainability methods to identify PD-specific speech features, aiming to support the development of accurate, interpretable models for clinical decision-making in PD diagnosis and monitoring. Our methodology involves (i) obtaining attributions and saliency maps using mainstream interpretability techniques, (ii) quantitatively evaluating the faithfulness of these maps and their combinations obtained via union and intersection through a range of established metrics, and (iii) assessing the information conveyed by the saliency maps for PD detection from an auxiliary classifier. Our results reveal that, while explanations are aligned with the classifier, they often fail to provide valuable information for domain experts.
2024-11-12
ArXiv (prépublication)
doi.org
arxiv.org
Refining SARS-CoV-2 Intra-host Variation by Leveraging Large-scale Sequencing Data
Fatima Mostefai
Jean-Christophe Grenier
Raphael Poujol
Julie Hussin
2024-11-12
NAR Genomics and Bioinformatics (publié)
doi.org
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… (voir plus)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.
2024-11-11
ArXiv (prépublication)
doi.org
arxiv.org
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… (voir plus)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.
2024-11-11
ArXiv (prépublication)
doi.org
arxiv.org
Comparing Bottom-Up and Top-Down Steering Approaches on In-Context Learning Tasks
Madeline Brumley
Joe Kwon
David Scott Krueger
Dmitrii Krasheninnikov
Usman Anwar
A key objective of interpretability research on large language models (LLMs) is to develop methods for robustly steering models toward desir… (voir plus)ed behaviors. To this end, two distinct approaches to interpretability -- ``bottom-up"and ``top-down"-- have been presented, but there has been little quantitative comparison between them. We present a case study comparing the effectiveness of representative vector steering methods from each branch: function vectors (FV; arXiv:2310.15213), as a bottom-up method, and in-context vectors (ICV; arXiv:2311.06668) as a top-down method. While both aim to capture compact representations of broad in-context learning tasks, we find they are effective only on specific types of tasks: ICVs outperform FVs in behavioral shifting, whereas FVs excel in tasks requiring more precision. We discuss the implications for future evaluations of steering methods and for further research into top-down and bottom-up steering given these findings.
2024-11-11
ArXiv (prépublication)
doi.org
arxiv.org
Feature learning as alignment: a structural property of gradient descent in non-linear neural networks
Daniel Beaglehole
Ioannis Mitliagkas
Atish Agarwala
Understanding the mechanisms through which neural networks extract statistics from input-label pairs through feature learning is one of the … (voir plus)most important unsolved problems in supervised learning. Prior works demonstrated that the gram matrices of the weights (the neural feature matrices, NFM) and the average gradient outer products (AGOP) become correlated during training, in a statement known as the neural feature ansatz (NFA). Through the NFA, the authors introduce mapping with the AGOP as a general mechanism for neural feature learning. However, these works do not provide a theoretical explanation for this correlation or its origins. In this work, we further clarify the nature of this correlation, and explain its emergence. We show that this correlation is equivalent to alignment between the left singular structure of the weight matrices and the newly defined pre-activation tangent features at each layer. We further establish that the alignment is driven by the interaction of weight changes induced by SGD with the pre-activation features, and analyze the resulting dynamics analytically at early times in terms of simple statistics of the inputs and labels. We prove the derivative alignment occurs with high probability in specific high dimensional settings. Finally, motivated by the observation that the NFA is driven by this centered correlation, we introduce a simple optimization rule that dramatically increases the NFA correlations at any given layer and improves the quality of features learned.
2024-11-11
TMLR (accepté)
openreview.net
openreview.net
Impact of LLM-based Review Comment Generation in Practice: A Mixed Open-/Closed-source User Study
Doriane Olewicki
Léuson M. P. Da Silva
Suhaib Mujahid
Arezou Amini
Benjamin Mah
Marco Castelluccio
Sarra Habchi
Foutse Khomh
Bram Adams
We conduct a large-scale empirical user study in a live setup to evaluate the acceptance of LLM-generated comments and their impact on the r… (voir plus)eview process. This user study was performed in two organizations, Mozilla (which has its codebase available as open source) and Ubisoft (fully closed-source). Inside their usual review environment, participants were given access to RevMate, an LLM-based assistive tool suggesting generated review comments using an off-the-shelf LLM with Retrieval Augmented Generation to provide extra code and review context, combined with LLM-as-a-Judge, to auto-evaluate the generated comments and discard irrelevant cases. Based on more than 587 patch reviews provided by RevMate, we observed that 8.1% and 7.2%, respectively, of LLM-generated comments were accepted by reviewers in each organization, while 14.6% and 20.5% other comments were still marked as valuable as review or development tips. Refactoring-related comments are more likely to be accepted than Functional comments (18.2% and 18.6% compared to 4.8% and 5.2%). The extra time spent by reviewers to inspect generated comments or edit accepted ones (36/119), yielding an overall median of 43s per patch, is reasonable. The accepted generated comments are as likely to yield future revisions of the revised patch as human-written comments (74% vs 73% at chunk-level).
2024-11-11
ArXiv (prépublication)
doi.org
arxiv.org
Non-Adversarial Inverse Reinforcement Learning via Successor Feature Matching
Arnav Kumar Jain
Harley Wiltzer
Jesse Farebrother
Irina Rish
Glen Berseth
Sanjiban Choudhury
In inverse reinforcement learning (IRL), an agent seeks to replicate expert demonstrations through interactions with the environment. Tradit… (voir plus)ionally, IRL is treated as an adversarial game, where an adversary searches over reward models, and a learner optimizes the reward through repeated RL procedures. This game-solving approach is both computationally expensive and difficult to stabilize. In this work, we propose a novel approach to IRL by direct policy optimization: exploiting a linear factorization of the return as the inner product of successor features and a reward vector, we design an IRL algorithm by policy gradient descent on the gap between the learner and expert features. Our non-adversarial method does not require learning a reward function and can be solved seamlessly with existing actor-critic RL algorithms. Remarkably, our approach works in state-only settings without expert action labels, a setting which behavior cloning (BC) cannot solve. Empirical results demonstrate that our method learns from as few as a single expert demonstration and achieves improved performance on various control tasks.
2024-11-11
ArXiv (prépublication)
doi.org
arxiv.org
Specific inhibition and disinhibition in the higher-order structure of a cortical connectome
Michael W. Reimann
Daniela Egas Santander
András Ecker
Eilif Benjamin Muller
Neuronal network activity is thought to be structured around the activation of assemblies, or low-dimensional manifolds describing states of… (voir plus) activity. Both views describe neurons acting not independently, but in concert, likely facilitated by strong recurrent excitation between them. The role of inhibition in these frameworks – if considered at all – is often reduced to blanket inhibition with no specificity with respect to which excitatory neurons are targeted. We analyzed the structure of excitation and inhibition in the MICrONS 1mm3 dataset, an electron microscopic reconstruction of a piece of cortical tissue. We found that excitation was structured around a feed-forward flow in non-random motifs of seven or more neurons. This revealed a structure of information flow from a small number of sources to a larger number of potential targets that became only visible when larger motifs were considered instead of individual pairs. Inhibitory neurons targeted and were targeted by neurons in specific sequential positions of these motifs. Additionally, disynaptic inhibition was strongest between target motifs excited by the same group of source neurons, implying competition between them. The structure of this inhibition was also highly specific and symmetrical, contradicting the idea of non-specific blanket inhibition. None of these trends are detectable in only pairwise connectivity, demonstrating that inhibition is specifically structured by these large motifs. Further, we found that these motifs represent higher order connectivity patterns which are present, but to a lesser extent in a recently released, detailed computational model, and not at all in a distance-dependent control. These findings have important implications for how synaptic plasticity reorganizes neocortical connectivity to implement learning and for the specific role of inhibition in this process.
2024-11-11
Cerebral Cortex (New York, NY) (publié)
doi.org
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua
Jiarui Lu
Yong Liu
Odin Zhang
Jian Tang
Rex Ying
Wengong Jin
Guy Wolf
Doina Precup
Shuangjia Zheng
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interact… (voir plus)ion prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.
2024-11-10
ArXiv (prépublication)
arxiv.org
arxiv.org