Integrating food webs in species distribution models can improve ecological niche estimation and predictions
Giovanni Poggiato
Jérémy Andréoletti
Wilfried Thuiller
Integrating food webs in species distribution models can improve ecological niche estimation and predictions
Giovanni Poggiato
Jérémy Andréoletti
Wilfried Thuiller
Biotic interactions play a fundamental role in shaping multitrophic species communities, yet incorporating these interactions into species d… (voir plus)istribution models (SDMs) remains challenging. With the growing availability of species interaction networks, it is now feasible to integrate these interactions into SDMs for more comprehensive predictions. Here, we propose a novel framework that combines trophic interaction networks with Bayesian structural equation models, enabling each species to be modeled based on its interactions with predators or prey alongside environmental factors. This framework addresses issues of multicollinearity and error propagation, making it possible to predict species distributions in unobserved locations or under future environmental conditions, even when prey or predator distributions are unknown. We tested and validated our framework on realistic simulated communities spanning different theoretical models and ecological setups. scenarios. Our approach significantly improved the estimation of both potential and realized niches compared to single SDMs, with mean performance gains of 8% and 6%, respectively. These improvements were especially notable for species strongly regulated by biotic factors, thereby enhancing model predictive accuracy. Our framework supports integration with various SDM extensions, such as occupancy and integrated models, offering flexibility and adaptability for future developments. While not a universal solution that consistently outperforms single SDMs, our approach provides a valuable new tool for modeling multitrophic community distributions when biotic interactions are known or assumed.
Symmetry-Aware Generative Modeling through Learned Canonicalization
Kusha Sareen
Daniel Levy
Arnab Kumar Mondal
Sékou-Oumar Kaba
Tara Akhound-Sadegh
Generative modeling of symmetric densities has a range of applications in AI for science, from drug discovery to physics simulations. The ex… (voir plus)isting generative modeling paradigm for invariant densities combines an invariant prior with an equivariant generative process. However, we observe that this technique is not necessary and has several drawbacks resulting from the limitations of equivariant networks. Instead, we propose to model a learned slice of the density so that only one representative element per orbit is learned. To accomplish this, we learn a group-equivariant canonicalization network that maps training samples to a canonical pose and train a non-equivariant generative model over these canonicalized samples. We implement this idea in the context of diffusion models. Our preliminary experimental results on molecular modeling are promising, demonstrating improved sample quality and faster inference time.
The oneirogen hypothesis: modeling the hallucinatory effects of classical psychedelics in terms of replay-dependent plasticity mechanisms
Colin Bredenberg
Fabrice Normandin
Classical psychedelics induce complex visual hallucinations in humans, generating percepts that are co-herent at a low level, but which have… (voir plus) surreal, dream-like qualities at a high level. While there are many hypotheses as to how classical psychedelics could induce these effects, there are no concrete mechanistic models that capture the variety of observed effects in humans, while remaining consistent with the known pharmacological effects of classical psychedelics on neural circuits. In this work, we propose the “oneirogen hypothesis”, which posits that the perceptual effects of classical psychedelics are a result of their pharmacological actions inducing neural activity states that truly are more similar to dream-like states. We simulate classical psychedelics’ effects via manipulating neural network models trained on perceptual tasks with the Wake-Sleep algorithm. This established machine learning algorithm leverages two activity phases, a perceptual phase (wake) where sensory inputs are encoded, and a generative phase (dream) where the network internally generates activity consistent with stimulus-evoked responses. We simulate the action of psychedelics by partially shifting the model to the ‘Sleep’ state, which entails a greater influence of top-down connections, in line with the impact of psychedelics on apical dendrites. The effects resulting from this manipulation capture a number of experimentally observed phenomena including the emergence of hallucinations, increases in stimulus-conditioned variability, and large increases in synaptic plasticity. We further provide a number of testable predictions which could be used to validate or invalidate our oneirogen hypothesis.
AFRIDOC-MT: Document-level MT Corpus for African Languages
Jesujoba Oluwadara Alabi
Israel Abebe Azime
Miaoran Zhang
Cristina España-Bonet
Rachel Bawden
Dawei Zhu
Clement Odoje
Idris Akinade
Iffat Maab
Davis David
Shamsuddeen Hassan Muhammad
Neo Putini
David O. Ademuyiwa
Andrew Caines
Dietrich Klakow
This paper introduces AFRIDOC-MT, a document-level multi-parallel translation dataset covering English and five African languages: Amharic, … (voir plus)Hausa, Swahili, Yor\`ub\'a, and Zulu. The dataset comprises 334 health and 271 information technology news documents, all human-translated from English to these languages. We conduct document-level translation benchmark experiments by evaluating neural machine translation (NMT) models and large language models (LLMs) for translations between English and these languages, at both the sentence and pseudo-document levels. These outputs are realigned to form complete documents for evaluation. Our results indicate that NLLB-200 achieved the best average performance among the standard NMT models, while GPT-4o outperformed general-purpose LLMs. Fine-tuning selected models led to substantial performance gains, but models trained on sentences struggled to generalize effectively to longer documents. Furthermore, our analysis reveals that some LLMs exhibit issues such as under-generation, repetition of words or phrases, and off-target translations, especially for African languages.
AFRIDOC-MT: Document-level MT Corpus for African Languages
Jesujoba Oluwadara Alabi
Israel Abebe Azime
Miaoran Zhang
Cristina España-Bonet
Rachel Bawden
Dawei Zhu
Clement Odoje
Idris Akinade
Iffat Maab
Davis David
Shamsuddeen Hassan Muhammad
Neo Putini
David O. Ademuyiwa
Andrew Caines
Dietrich Klakow
This paper introduces AFRIDOC-MT, a document-level multi-parallel translation dataset covering English and five African languages: Amharic, … (voir plus)Hausa, Swahili, Yor\`ub\'a, and Zulu. The dataset comprises 334 health and 271 information technology news documents, all human-translated from English to these languages. We conduct document-level translation benchmark experiments by evaluating neural machine translation (NMT) models and large language models (LLMs) for translations between English and these languages, at both the sentence and pseudo-document levels. These outputs are realigned to form complete documents for evaluation. Our results indicate that NLLB-200 achieved the best average performance among the standard NMT models, while GPT-4o outperformed general-purpose LLMs. Fine-tuning selected models led to substantial performance gains, but models trained on sentences struggled to generalize effectively to longer documents. Furthermore, our analysis reveals that some LLMs exhibit issues such as under-generation, repetition of words or phrases, and off-target translations, especially for African languages.
AFRIDOC-MT: Document-level MT Corpus for African Languages
Jesujoba Oluwadara Alabi
Israel Abebe Azime
Miaoran Zhang
Cristina España-Bonet
Rachel Bawden
D. Zhu
Clement Odoje
Idris Akinade
Iffat Maab
Davis David
Shamsuddeen Hassan Muhammad
Neo Putini
David O. Ademuyiwa
Andrew Caines
Dietrich Klakow
This paper introduces AFRIDOC-MT, a document-level multi-parallel translation dataset covering English and five African languages: Amharic, … (voir plus)Hausa, Swahili, Yor\`ub\'a, and Zulu. The dataset comprises 334 health and 271 information technology news documents, all human-translated from English to these languages. We conduct document-level translation benchmark experiments by evaluating neural machine translation (NMT) models and large language models (LLMs) for translations between English and these languages, at both the sentence and pseudo-document levels. These outputs are realigned to form complete documents for evaluation. Our results indicate that NLLB-200 achieved the best average performance among the standard NMT models, while GPT-4o outperformed general-purpose LLMs. Fine-tuning selected models led to substantial performance gains, but models trained on sentences struggled to generalize effectively to longer documents. Furthermore, our analysis reveals that some LLMs exhibit issues such as under-generation, repetition of words or phrases, and off-target translations, especially for African languages.
EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data
Rohan Banerjee
Merve Kaptan
Alexandra Tinnermann
Ali Khatibi
Alice Dabbagh
Christian W. Kündig
Csw Law
Dario Pfyffer
David J. Lythgoe
Dimitra Tsivaka
Dimitri Van De Ville
Falk Eippert
Fauziyya Muhammad
Gary H. Glover
Gergely David
Grace Haynes
Jan Haaker
Jonathan C. W. Brooks
Jürgen Finsterbusch
Katherine T. Martucci … (voir 20 de plus)
Kimberly J. Hemmerling
Mahdi Mobarak-Abadi
Mark A. Hoggarth
Matthew A. Howard
Molly G. Bright
Nawal Kinany
O. Kowalczyk
Patrick Freund
Robert L. Barry
Sean Mackey
Shahabeddin Vahdat
Simon Schading
Stephen B McMahon
Todd Parish
Véronique Marchand-Pauvert
Yufen Chen
Zachary A. Smith
KA Weber
Benjamin De Leener
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (voir plus)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data
Rohan Banerjee
Merve Kaptan
Alexandra Tinnermann
Ali Khatibi
Alice Dabbagh
Christian W. Kündig
Csw Law
Dario Pfyffer
David J. Lythgoe
Dimitra Tsivaka
Dimitri Van De Ville
Falk Eippert
Fauziyya Muhammad
Gary H. Glover
Gergely David
Grace Haynes
Jan Haaker
Jonathan C. W. Brooks
Jürgen Finsterbusch
Katherine T. Martucci … (voir 20 de plus)
Kimberly J. Hemmerling
Mahdi Mobarak-Abadi
Mark A. Hoggarth
Matthew A. Howard
Molly G. Bright
Nawal Kinany
O. Kowalczyk
Patrick Freund
Robert L. Barry
Sean Mackey
Shahabeddin Vahdat
Simon Schading
Stephen B McMahon
Todd Parish
Véronique Marchand-Pauvert
Yufen Chen
Zachary A. Smith
KA Weber
Benjamin De Leener
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (voir plus)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data
Rohan Banerjee
Merve Kaptan
Alexandra Tinnermann
Ali Khatibi
Alice Dabbagh
Christian Büchel
Christine S.W. Law
Christian W. Kündig
Csw Law
Dario Pfyffer
David J. Lythgoe
Dimitra Tsivaka
Dimitri Van De Ville
Falk Eippert
Fauziyya Muhammad
Gary H. Glover
Gergely David
Grace Haynes
Jan Haaker
Jonathan C. W. Brooks … (voir 23 de plus)
Jürgen Finsterbusch
Katherine T. Martucci
Kimberly J. Hemmerling
Mahdi Mobarak-Abadi
Mark A. Hoggarth
Matthew A. Howard
Molly G. Bright
Nawal Kinany
Olivia S. Kowalczyk
Patrick Freund
Robert L. Barry
Sean Mackey
Shahabeddin Vahdat
Simon Schading
Stephen B. McMahon
Todd Parish
Véronique Marchand-Pauvert
Yufen Chen
Kenneth A. Weber
Zachary A. Smith
KA Weber
Benjamin De Leener
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (voir plus)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
Open Problems in Machine Unlearning for AI Safety
Fazl Barez
Tingchen Fu
Ameya Prabhu
Stephen Casper
Amartya Sanyal
Adel Bibi
Aidan O'Gara
Robert Kirk
Benjamin Bucknall
Timothy Fist
Luke Ong
Philip Torr
Kwok-Yan Lam
Robert Trager
Sören Mindermann
Jose Hernandez-Orallo
Mor Geva
Yarin Gal
As AI systems become more capable, widely deployed, and increasingly autonomous in critical areas such as cybersecurity, biological research… (voir plus), and healthcare, ensuring their safety and alignment with human values is paramount. Machine unlearning -- the ability to selectively forget or suppress specific types of knowledge -- has shown promise for privacy and data removal tasks, which has been the primary focus of existing research. More recently, its potential application to AI safety has gained attention. In this paper, we identify key limitations that prevent unlearning from serving as a comprehensive solution for AI safety, particularly in managing dual-use knowledge in sensitive domains like cybersecurity and chemical, biological, radiological, and nuclear (CBRN) safety. In these contexts, information can be both beneficial and harmful, and models may combine seemingly harmless information for harmful purposes -- unlearning this information could strongly affect beneficial uses. We provide an overview of inherent constraints and open problems, including the broader side effects of unlearning dangerous knowledge, as well as previously unexplored tensions between unlearning and existing safety mechanisms. Finally, we investigate challenges related to evaluation, robustness, and the preservation of safety features during unlearning. By mapping these limitations and open challenges, we aim to guide future research toward realistic applications of unlearning within a broader AI safety framework, acknowledging its limitations and highlighting areas where alternative approaches may be required.
Open Problems in Machine Unlearning for AI Safety
Fazl Barez
Tingchen Fu
Ameya Prabhu
Stephen Casper
Amartya Sanyal
Adel Bibi
Aidan O'Gara
Robert Kirk
Benjamin Bucknall
Tim Fist
Luke Ong
Philip H. S. Torr
Kwok-Yan Lam
Robert F. Trager
Sören Mindermann
Jose Hernandez-Orallo
Mor Geva
Yarin Gal
As AI systems become more capable, widely deployed, and increasingly autonomous in critical areas such as cybersecurity, biological research… (voir plus), and healthcare, ensuring their safety and alignment with human values is paramount. Machine unlearning -- the ability to selectively forget or suppress specific types of knowledge -- has shown promise for privacy and data removal tasks, which has been the primary focus of existing research. More recently, its potential application to AI safety has gained attention. In this paper, we identify key limitations that prevent unlearning from serving as a comprehensive solution for AI safety, particularly in managing dual-use knowledge in sensitive domains like cybersecurity and chemical, biological, radiological, and nuclear (CBRN) safety. In these contexts, information can be both beneficial and harmful, and models may combine seemingly harmless information for harmful purposes -- unlearning this information could strongly affect beneficial uses. We provide an overview of inherent constraints and open problems, including the broader side effects of unlearning dangerous knowledge, as well as previously unexplored tensions between unlearning and existing safety mechanisms. Finally, we investigate challenges related to evaluation, robustness, and the preservation of safety features during unlearning. By mapping these limitations and open challenges, we aim to guide future research toward realistic applications of unlearning within a broader AI safety framework, acknowledging its limitations and highlighting areas where alternative approaches may be required.