-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathindex.xml
2596 lines (2435 loc) · 249 KB
/
index.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>MSAIL</title>
<link>https://MSAIL.github.io/</link>
<atom:link href="https://MSAIL.github.io/index.xml" rel="self" type="application/rss+xml" />
<description>MSAIL</description>
<generator>Source Themes Academic (https://sourcethemes.com/academic/)</generator><language>en-us</language><lastBuildDate>Thu, 28 Mar 2024 18:00:00 -0400</lastBuildDate>
<image>
<url>https://MSAIL.github.io/media/logo.png</url>
<title>MSAIL</title>
<link>https://MSAIL.github.io/</link>
</image>
<item>
<title>MSAIL TECH TALK w/ Wesley Tian</title>
<link>https://MSAIL.github.io/talk/wesleytian_240324/</link>
<pubDate>Thu, 28 Mar 2024 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/wesleytian_240324/</guid>
<description><p>University of Michigan alumni and former MSAIL member Wesley Tian, the Co-founder and CEO of Aragon.ai, will talk about his journey, share what he learned from starting his AI company, and offer career advice.</p>
<p>RSVP for this event
<a href="hhttps://forms.gle/724P8z5wdHryhCf5A">here</a>!</p>
</description>
</item>
<item>
<title>MSAIL TECH TALK w/ Kiran Prasad</title>
<link>https://MSAIL.github.io/talk/prasad_210324/</link>
<pubDate>Thu, 21 Mar 2024 19:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/prasad_210324/</guid>
<description><p>University of Michigan and Carnegie Mellon alumni Kiran Prasad will share his professional journey, thoughts about Grad School, and give a talk about machine learning concepts that he uses in industry. Kiran is a Senior ML Engineer at Gather, where he works on end-to-end AI system design. He previously was an Applied Scientist on the Microsoft Turing team (Microsoft&rsquo;s NLP v-team that created CoPilot and spearheaded collaboration with OpenAI).</p>
<p>RSVP for this event
<a href="https://docs.google.com/forms/d/e/1FAIpQLSdXVZybnuUJ2zZRsa2jNBnoK4MXrEcgPn41f2HTH5G8vI5Kuw/viewform" target="_blank" rel="noopener">here</a>!</p>
</description>
</item>
<item>
<title>An Overview of Binarized Neural Networks</title>
<link>https://MSAIL.github.io/talk/bnn_041222/</link>
<pubDate>Tue, 12 Apr 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/bnn_041222/</guid>
<description><p>Binarized neural networks (BNNs) are an extreme version of quantized neural networks where all weights and activations are quantized to +/- 1. A key motivation for such a network is to enable one to run powerful neural networks on small battery-powered devices. This talk introduced BNNs, explained how one can train such a network and reviewed some recent work in the area.</p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<ol>
<li>
<a href="https://arxiv.org/abs/1602.02830" target="_blank" rel="noopener">Binarized Neural Networks: Training Deep Neural Networks with Weights and Activations Constrained to +1 or -1, by Courbariaux et al.</a></li>
<li>
<a href="https://www.mdpi.com/2079-9292/8/6/661" target="_blank" rel="noopener">A review of Binarized Neural Networks, by Simons et al.</a></li>
<li>
<a href="https://openreview.net/pdf?id=rJfUCoR5KX" target="_blank" rel="noopener">An Empirical Study of Binarized Neural Networks&rsquo; Optimization, by Alizadeh et al.</a></li>
</ol>
</description>
</item>
<item>
<title>Machine Learning for Intraoperative Diagnosis of Brain Tumors Imaged using Stimulated Raman Histology</title>
<link>https://MSAIL.github.io/talk/brain_tumor_040522/</link>
<pubDate>Tue, 05 Apr 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/brain_tumor_040522/</guid>
<description><h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://www.nature.com/articles/s41591-019-0715-9" target="_blank" rel="noopener">Paper 1: Near real-time intraoperative brain tumor diagnosis using stimulated Raman histology and deep neural networks</a><br>
<a href="https://journals.lww.com/neurosurgery/Abstract/9900/Rapid_Automated_Analysis_of_Skull_Base_Tumor.184.aspx" target="_blank" rel="noopener">Paper 2: Rapid Automated Analysis of Skull Base Tumor Specimens Using Intraoperative Optical Imaging and Artificial Intelligence</a></p>
</description>
</item>
<item>
<title>The Devil is in the Details: Spatial and Temporal Super-Resolution of Global Climate Models using Adversarial Deep Learning</title>
<link>https://MSAIL.github.io/talk/climate_adversarial_032922/</link>
<pubDate>Tue, 29 Mar 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/climate_adversarial_032922/</guid>
<description><p>Physics-based global climate simulations are computationally expensive and limited to low spatial and temporal resolutions, making it difficult to predict and track highly localized extreme weather phenomena. To overcome these limitations, we present a novel application of super-resolution using deep convolutional generative adversarial networks (GANs) to increase the resolution of global climate models in both space and time. In this project, we demonstrate the potential to reduce climate simulation computation and storage requirements by two orders of magnitude, as well as democratize relevant and actionable climate information for disaster responses. This work won the Best Paper Award in the 2020 ProjectX international ML research competition hosted by the University of Toronto.</p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://drive.google.com/file/d/1cbwTb7DNe0vRZiN9hg53W5MZdRbXJqsg/view" target="_blank" rel="noopener">Paper, by Chen et al.</a></p>
</description>
</item>
<item>
<title>Generating Molecular Conformations via Normalizing Flows and Neural ODEs</title>
<link>https://MSAIL.github.io/post/molecular_iclr_2022/</link>
<pubDate>Fri, 25 Mar 2022 00:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/post/molecular_iclr_2022/</guid>
<description><p>This post was an accepted submission from MSAIL to the
<a href="https://iclr-blog-track.github.io/" target="_blank" rel="noopener">ICLR 2022 Blog Track</a>. You can find the original post
<a href="https://iclr-blog-track.github.io/2022/03/25/conformation-generation/" target="_blank" rel="noopener">here</a>.</p>
<p>In this post, we provide an in-depth overview of methods outlined in the paper &ldquo;Learning Neural Generative Dynamics for Molecular Conformation Generation,&rdquo; discuss the impact of the work in the context of other conformation generation approaches, and additionally discuss future potential applications to improve the diversity and stability of generated conformations.</p>
<ol>
<li>
<a href="#introduction">Introduction</a></li>
<li>
<a href="#generative-overview">An Overview of the Deep Generative Approach</a></li>
<li>
<a href="#distances">Modeling distributions of distances</a></li>
<li>
<a href="#conformations">Modeling distributions of conformations</a></li>
<li>
<a href="#sampling">Sampling</a></li>
<li>
<a href="#future-work">Future Work</a></li>
<li>
<a href="#references">References</a></li>
</ol>
<h2 id="introduction">Introduction</h2>
<p>In drug discovery, generating molecular conformations is useful across a variety of applications. For example, docking of various molecular 3D conformations to a specific protein allows drug hunters to decide whether a small molecule binds to a specific pocket in a multitude of conformations or a select few.</p>
<p align="center">
<img src="vina.jpg" style="width: 300px">
<b>Figure 1:</b> Autodock Vina is a computer program that takes a given 3D conformation of a molecule and protein and predicts the binding free energy. An algorithm like the one discussed in this blog could generate a wide variety of conformations for Autodock Vina to test. (<a href="https://vina.scripps.edu/">Source</a>)
</p>
<p>It may be helpful to define what we mean when we talk about conformations, whether we are talking about a small organic molecule or a macromolecule like a protein. We start off with a graph, with atoms as nodes connected by bonds as edges that represent intramolecular interactions. In essence, we are starting with a specified connectivity defining how atoms are connected to each other. This two-dimensional representation, however, doesn&rsquo;t capture the three-dimensional coordinates of the atoms and how they are spatially arranged.</p>
<p>Therefore, in theory, one molecular graph could capture an astronomical number of conformations capturing all possible permutations and combinations of spatial arrangements of atoms. However, not all of these possible spatial arrangements are relevant as some may be so unstable that they may not occur. The spatial proximity of bulky organic groups – more formally known as “steric clashing” – reduces the number of degrees of freedom when it comes down to which bonds can rotate and how much they can rotate. Therefore, we are only interested in conformations that fall in stable low energy minima.</p>
<p>
<a href="https://en.wikipedia.org/wiki/Levinthal%27s_paradox#:~:text=Levinthal%27s%20paradox%20is%20a%20thought,astronomical%20number%20of%20possible%20conformations." target="_blank" rel="noopener">Levinthal’s Paradox</a> is a principle stating that if a protein were to sample all of its possible molecular conformations before arriving in its native state, it would take longer than the age of the universe. Though it may seem excessive to directly extend this analogy to small molecules, which are orders of magnitude less complex than proteins, it becomes intuitive that computationally simulating all of the possible conformations for a large molecule with a large number of rotatable bonds is highly infeasible. For every single bond and the associated substituents, if there are three stable conformations, then there is a maximum bound of $3^n$ stable conformations for a molecule with $n$ bonds. For example, a molecule with ten rotatable bonds could have a maximum of 59,049 conformations.
Now, we’ve arrived at the question that drives this blog post and the work that we’re about to discuss: <strong>Given a molecular graph and its associated connectivity constraints, can we generate a set of low energy stable molecular conformations (a multimodal distribution) that capture the relative spatial positions of atoms in three-dimensional space?</strong>
There are two subtle components to the question above that address some deficiencies in prior attempts to solve this problem:</p>
<ul>
<li>
<p>A multimodal distribution – there are multiple low energy minima when it comes to the joint distribution of distances between atoms that defines a conformation. In approaches where distances between pairs of atoms or 3D coordinates are randomly sampled to construct a conformation, dependencies and correlations between atomic spatial positions are not captured and the corresponding joint distribution is inaccurate.</p>
</li>
<li>
<p>Relative spatial positions – some approaches use
<a href="https://distill.pub/2021/gnn-intro/" target="_blank" rel="noopener">graph neural networks</a> directly on molecular graphs to compute representations for the individual nodes (atoms). These nodes can be further fed into other feedforward networks to predict the 3D coordinates of the atoms in a specified conformation. However, directly predicting the 3D coordinates does not capture the idea that a conformation is defined by the relative spatial arrangement and distances between atoms in 3D space. Put another way, if a rotation or translation transformation was applied to the 3D coordinates, the model should not classify that as an entirely different conformation (rotation/translation invariance is not captured). Distances, rather than 3D coordinates could also be predicted; however (mirroring the bullet point above), since distances are predicted independently of each other, there could only be one predicted conformational mode.</p>
</li>
</ul>
<h2 id="an-overview-of-the-deep-generative-approach">An Overview of the Deep Generative Approach</h2>
<p>In “Learning Neural Generative Dynamics for Molecular Conformation Generation,” Xu et. al approach the above deficiencies, generating low energy conformations while modeling dependencies between atoms.</p>
<p>Let’s keep in mind – the final goal is to optimize a set of parameters $\theta$ to predict the likelihood of a conformation $R$ given a graph $G$. (i.e. to find $ p_\theta(R|G) $).</p>
<p>To model this distribution, it is necessary to model intermediate distributions and marginalize over one of the variables:</p>
<ul>
<li>
<p>We also need to find $p_\theta(d|G)$ (the distribution of distances $d_{uv}$ between pairs of atoms $u$ and $v$ in the graph).</p>
</li>
<li>
<p>Finally, we need to find $p_\theta(\boldsymbol{R}|d,G)$ – the probability of a conformation (specified by a set of 3D coordinates given a set of intramolecular distances and an underlying graph).</p>
</li>
</ul>
<p>With these two distributions, we can find our intended distribution by integrating over the possible distances.</p>
<p>$$\int{p(\boldsymbol{R}|d,G)*p(d|G)dd}$$</p>
<p>Let’s walk through the approaches to modeling each of these individual distributions.</p>
<h2 id="modeling-distributions-of-distances">Modeling Distributions of Distances</h2>
<p>In this approach, the distribution of distances given a graph is modeled using a continuous normalizing flow. To understand this approach, we need to define its sub-techniques and understand how they interact with each other.</p>
<ul>
<li>
<p>Normalizing flows: We initially sample $z_0$ from a starting distribution $p(z_0)$ and a series of invertible transformations transform the initial density function. Here’s a strong
<a href="https://lilianweng.github.io/lil-log/2018/10/13/flow-based-deep-generative-models.html" target="_blank" rel="noopener">primer</a> on flows.</p>
<ul>
<li>In this work, $z(t)$ represents our distances between pairs of atoms $d(t)$. The initial distances are pulled from a normal distribution with mean zero and variance one (for all distances). Correspondingly, the initial probability density function $p(z_0)$ is represented by the initial distribution of distances $N(0, \mathbf{I})$.</li>
</ul>
</li>
<li>
<p>
<a href="https://arxiv.org/pdf/1806.07366.pdf" target="_blank" rel="noopener">Neural ODE systems</a>: In a neural ODE, we specify an initial value problem that uses a neural network to specify the “dynamics” of the system (or the derivative of the “state” with respect to time). More concretely, we have that $y(0) = y_0$ and that $\frac{dy}{dt} = f(y(t), t, \theta)$. Using an ODE solver such as <code>odeint</code>, we can calculate the value of $y$ at any time $t$ as in any initial value problem. <br> In fact, y can be thought of as a
<a href="http://implicit-layers-tutorial.org/neural_odes/" target="_blank" rel="noopener">residual network</a> where we take the limit with respect to the number of layers.</p>
<ul>
<li>Correspondingly, in this work, the purpose of instantiating an ODE is to be able to predict $d(t)$ – the distances between each pair of atoms at any time point. $\frac{d\mathbf{d}}{dt}$ can be predicted at any time point given $d(t)$, the time point, $t$, the molecular graph, and the parameters of the assigned neural network (in our case an MPNN).</li>
</ul>
</li>
</ul>
<p>$$\boldsymbol{d} = F_\theta(\boldsymbol{d}(t_0), \mathcal{G}) = \boldsymbol{d}(t_0) + \int_{t_0}^{t_1} f_\theta(\boldsymbol{d}(t), t; \mathcal{G})dt$$</p>
<p>To combine the two methods above: We take $z_0$ and define it as the initial value. $\frac{dz}{dt}$ is calculated using a neural network that takes in $z(t)$, $t$, and $\theta$. With $z_0$ and a function $f$ to calculate $\frac{dz}{dt}$ at any time point, $z(t)$ can be calculated as per the traditional initial value problem formulation. The ODESolver also predicts the $\textrm{log}(p(z(t))$ at any time point, thereby encoding the density function for $z(t)$ in addition to just the values of $z(t)$ alone (Figure 2).</p>
<p align="center">
<img src="ode.png">
<b> Figure 2: </b> The neural ODE system computes $\boldsymbol{d}(t)$ and $\textrm{log}(p(\boldsymbol{d}(t))$ at various time points in order to try and approximate the actual functions for $\boldsymbol{d}(t)$ and $\textrm{log}(p(\boldsymbol{d}(t))$.
</p>
<p>In this case, our $z(t)$ is $\boldsymbol{d}(t)$, a function that outputs a vector with pairwise intramolecular distances. The “continuous-time dynamics&quot; is a function that takes in neural network parameters, the time, and the current state to output the derivative of the distances with respect to time. The neural network is a graph
<a href="https://paperswithcode.com/method/mpnn" target="_blank" rel="noopener">message passing neural network</a> (MPNN) that calculates node and edge representations and aggregates the node and edge representations for each bond to calculate $\frac{dd_{uv}}{dt}$ – the change of the distance between two atoms with respect to time (Figure 3).</p>
<p align="center">
<img src="mpnn.png">
<b> Figure 3: </b> First, the individual nodes and edges are embedded using feedforward networks and sent through message passing layers. For every single bond, the final embeddings for the edge and atoms on each (atoms $u$ and $v$) end are concatenated and sent into a final feedforward network to result in a prediction for $\frac{dd_{uv}}{dt}$.
</p>
<p>At a higher level, by combining normalizing flows (Figure 4a) with an ODE system, the authors intended to effectively create a normalizing flow with an infinite number of transformations (in the limit) that can therefore model very long-range dependencies between atoms in all the transformations that occur from time $t_0$ to $t_1$ (Figure 4b).</p>
<p align="center">
<img src="nflow.png">
<b> Figure 4a (Left): </b> Traditional normalizing flow. <b> Figure 4b (Right): </b> Continuous normalizing flow with $z(t)$ as $d(t)$.
</p>
<h2 id="modeling-distributions-of-conformations">Modeling Distributions of Conformations</h2>
<p>After the distances are sampled and predicted based on the graph, the conformations can be sampled so as to minimize the difference between the a priori distances generated by the continuous graph normalizing flow (CGNF) and the pairwise distances in the sampled conformation.</p>
<p>$$p(\boldsymbol{R}|d, \mathcal{G}) = \frac{1}{Z}\textrm{exp}{-\sum_{e_{uv}\in{\mathcal{E}}} a_{uv}(\lVert r_u - r_v \rVert_2 - d_{uv})^2}$$</p>
<p>The euclidean norm of the difference between the position vectors represents the distance between two atoms in a sampled conformation ($\lVert r_u - r_v \rVert_2$). The distance associated with the edge between atoms u and v from the distribution modeled using the CGNF is ($d_{uv}$). The lower the difference between these two values, the higher the numerator. The higher the numerator, the higher the probability of the conformation given the proposed distances and molecular graph.</p>
<p>In the way that
<a href="http://yann.lecun.com/exdb/publis/pdf/lecun-06.pdf" target="_blank" rel="noopener">LeCun et. al</a> initially describe energy-based models, they describe the energy-based function $E(X, Y)$ to calculate the “goodness” or the “badness” of the possible configurations of $X$ and $Y$ or the “degree of compatibility” between the values of $X$ and $Y$. The same idea can be applied when considering the meaning of the energy function taking in a molecular conformation and a graph as input.</p>
<p>The loss function with which the energy-based model (EBM) is optimized provides additional insight into how it helps guide the generation of conformations.</p>
<p align="center">
<img src="nce_loss.png">
</p>
<p>Here, $p_{data}$ and $p_{\theta}$ are two different distributions that generate distances between pairs of atoms. $p_{data}$ pulls from vectors of true distances between atoms in actual conformations, while $p_{\theta}$ pulls from vectors of generated distances from the continuous flow. Therefore, the conformations represented in the second term on the right-hand side of this equation are noisier than the conformations represented in the first term. By being trained against this objective function, the model learns to distinguish real conformations based on true distances from unreal noisy conformations.</p>
<h2 id="sampling">Sampling</h2>
<p>Conformations are sampled by pulling an initial vector of distances from a normal distribution, passing it through the continuous graph normalizing flow, and finding an initial conformation $R_0$ that minimizes the energy. Then, conformations are sampled using two steps of stochastic gradient
<a href="https://henripal.github.io/blog/langevin" target="_blank" rel="noopener">Langevin Dynamics</a>. As in traditional stochastic gradient descent, we subtract the gradient of a secondary energy function that uses both the initial EBM parameters and CGNF parameters from the coordinates from the prior iteration. The “Langevin” part of this stochastic gradient descent implies there is a noise term ($w$) added, the variance of which is equal to the square root of the step size ($\epsilon$). This noise term, and Langevin dynamics more generally, are inspired by modeling
<a href="https://en.wikipedia.org/wiki/Brownian_motion" target="_blank" rel="noopener">Brownian motion</a> in particles and have been repurposed for sampling in molecular dynamics.</p>
<p>The secondary function takes into account both the initial energy function and the $\textrm{log}(p(\boldsymbol{R}|\mathcal{G}))$. Minimizing $E_{\theta, \phi}(R|\mathcal{G})$ involves $E_{\phi}(R|\mathcal{G})$ and simultaneously minimizing $p(\boldsymbol{R}|\mathcal{G})$.</p>
<p>$$R_k = R_{k-1} - \frac{\epsilon}{2}\nabla_RE_{\theta, \phi}(R|\mathcal{G}) + \sqrt{\epsilon}\omega, \omega \sim \mathcal{N}(0, \mathcal{I})$$</p>
<h2 id="future-work">Future Work</h2>
<p>One could explore different variations on the approach used to compute the continuous-time dynamic – for example,
<a href="https://arxiv.org/abs/2010.09885" target="_blank" rel="noopener">large-scale pretrained transformers applied on SMILES strings</a> – to compare how different architectures that are also able to capture long-range dependencies between atoms perform in generating distance distributions and subsequently conformations. Similar to the way that message passing allows for encoding of long-range dependencies, attention also allows for the same. In fact, attention applied to protein sequences has been shown to recover high-level elements of a three-dimensional structural organization; attention weights are a well-calibrated estimator of the probability that two amino acids are in contact in three-dimensional space (Vig et. al).</p>
<p>One caveat to note concerning the idea above is many models pretrained on protein sequences include evolutionary information regarding the sequences through featurizations such as multiple sequence alignments
(
<a href="https://www.ebi.ac.uk/Tools/msa/#:~:text=Multiple%20Sequence%20Alignment%20%28MSA%29%20is,relationships%20between%20the%20sequences%20studied.&amp;text=Suitable%20for%20medium%2Dlarge%20alignments." target="_blank" rel="noopener">MSA</a>) and position-specific scoring matrices (
<a href="https://en.wikipedia.org/wiki/Position_weight_matrix" target="_blank" rel="noopener">PSSM</a>) (Rao et. al). There are currently no featurizations for small molecules that encode their “structural evolution.”</p>
<p>One could also verify the ability of the different molecular conformation generation methods to generate more stable conformations. Towards the end of the paper, the authors proposed that the EBM shifts generation towards more stable conformations. Developing a metric or computational experiment – for example, calculating the free energy of generated molecules – would verify if this is the case. Or we could potentially even ask the question – is there an architectural or algorithmic knob that we could turn to control the tradeoff the algorithm makes between choosing conformational stability over diversity? To evaluate the model’s ability to especially generate low energy stable conformations, one could re-calculate all metrics solely across reference conformations for molecules bound to a protein in the protein data bank (PDB) (Figure 5) or
<a href="https://www.ccdc.cam.ac.uk/solutions/csd-core/components/csd/" target="_blank" rel="noopener">Cambridge Structural Database</a> (CSD) in a solid-state crystal structure.</p>
<p align="center">
<img src="mol.png" style="width: 300px">
<b> Figure 5: </b> Example of conformational variability for a single PDB ligand between different protein structures (Source: Hawkins et. al).
</p>
<p>Finally, Hawkins et. al make the distinction between systematic methods and stochastic methods for molecular conformation generation. Systematic methods involve a deterministic brute force search through all possible pairwise distances and torsion angles while stochastic methods involve random sampling and are not deterministic. Rather, in stochastic methods, the final generated conformation is in part determined by some initially sampled random variable). Under these definitions, the current method proposed in this work is stochastic, as the generated conformations are a function of the initial $d(t_0)$’s sampled from a normal distribution.</p>
<p>For stochastic approaches to finding multiple local minima, it is necessary to have multiple “starts” in order to cover all local minima. To evaluate the efficiency of the approach, one could measure the number of starts it takes to get a certain threshold of coverage over significant low-energy conformations.</p>
<p>All in all, the approach that Xu et. al employ to generate 3D conformers from a 2D molecular graph is part of a recent frontier in research that involves fewer brute-force physical simulations and more convenient ML-guided predictions that can help accelerate drug discovery.</p>
<h2 id="references">References</h2>
<ol>
<li>
<p>Chen, R. T. Q., Rubanova, Y., Bettencourt, J., &amp; Duvenaud, D. (2019). Neural Ordinary Differential Equations. arXiv [cs.LG]. Opgehaal van
<a href="http://arxiv.org/abs/1806.07366" target="_blank" rel="noopener">http://arxiv.org/abs/1806.07366</a></p>
</li>
<li>
<p>Hawkins, P. C. D. (2017). Conformation Generation: The State of the Art. Journal of Chemical Information and Modeling, 57(8), 1747–1756. doi:10.1021/acs.jcim.7b00221</p>
</li>
<li>
<p>Madani, A., Krause, B., Greene, E. R., Subramanian, S., Mohr, B. P., Holton, J. M., … Naik, N. (2021). Deep neural language modeling enables functional protein generation across families. bioRxiv. doi:10.1101/2021.07.18.452833</p>
</li>
<li>
<p>Rao, R., Bhattacharya, N., Thomas, N., Duan, Y., Chen, X., Canny, J., … Song, Y. S. (2019). Evaluating Protein Transfer Learning with TAPE. arXiv [cs.LG]. Opgehaal van
<a href="http://arxiv.org/abs/1906.08230" target="_blank" rel="noopener">http://arxiv.org/abs/1906.08230</a></p>
</li>
<li>
<p>Vig, J., Madani, A., Varshney, L. R., Xiong, C., Socher, R., &amp; Rajani, N. F. (2020). BERTology Meets Biology: Interpreting Attention in Protein Language Models. bioRxiv. doi:10.1101/2020.06.26.174417</p>
</li>
<li>
<p>Weng, L. (2018). Flow-based Deep Generative Models. lilianweng. github. io/lil-log. Opgehaal van
<a href="http://lilianweng.github.io/lil-log/2018/10/13/flow-based-deep-generative-models.html" target="_blank" rel="noopener">http://lilianweng.github.io/lil-log/2018/10/13/flow-based-deep-generative-models.html</a></p>
</li>
<li>
<p>Xu, M., Luo, S., Bengio, Y., Peng, J., &amp; Tang, J. (2021). Learning Neural Generative Dynamics for Molecular Conformation Generation. arXiv [cs.LG]. Opgehaal van
<a href="http://arxiv.org/abs/2102.10240" target="_blank" rel="noopener">http://arxiv.org/abs/2102.10240</a></p>
</li>
<li>
<p>Yann LeCun, Sumit Chopra, Raia Hadsell, M Ranzato, and F Huang. A tutorial on energy-based learning. Predicting structured data, 1(0), 2006.</p>
</li>
</ol>
</description>
</item>
<item>
<title>Fairness in Machine Learning</title>
<link>https://MSAIL.github.io/talk/fairness_032222/</link>
<pubDate>Tue, 22 Mar 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/fairness_032222/</guid>
<description><p>The purpose of this presentation was to introduce everyone to fairness aspects of machine learning and discuss Serafina&rsquo;s (
<a href="https://cse.engin.umich.edu/stories/undergraduate-researcher-takes-first-place-at-acm-competition" target="_blank" rel="noopener">award-winning!</a>) research in the area.</p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://link.springer.com/chapter/10.1007/978-3-030-93736-2_43" target="_blank" rel="noopener">Robustness of Fairness: An Experimental Analysis, by Kamp et al.</a><br>
<a href="https://docs.google.com/presentation/d/1fVakENisRjTh55vB6K25I0JqMMo3Dh77GLBbFJSc-CA/edit#slide=id.g11d502cf596_0_17" target="_blank" rel="noopener">Slides with additional links and resources</a></p>
</description>
</item>
<item>
<title>An Overview of Attention and Transformer Mechanisms for NLP</title>
<link>https://MSAIL.github.io/talk/attention_031522/</link>
<pubDate>Tue, 15 Mar 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/attention_031522/</guid>
<description><p>Nisreen explained the technical aspects of attention and self attention mechanisms, as well as explored how attention is used in the transformer architecture in order to aid in machine translation tasks.</p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://arxiv.org/abs/1409.0473" target="_blank" rel="noopener">Neural Machine Translation by Jointly Learning to Align and Translate, Bahdanau et al.</a><br>
<a href="https://arxiv.org/abs/1706.03762" target="_blank" rel="noopener">Attention is all you Need, Vaswani et al.</a></p>
</description>
</item>
<item>
<title>Open Problems in Cooperative AI</title>
<link>https://MSAIL.github.io/talk/cooperative_022222/</link>
<pubDate>Tue, 22 Feb 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/cooperative_022222/</guid>
<description><p>A recent area of study in AI has been focused on the problem of cooperation amongst machine learning agents. These cooperation problems are widespread, from routine challenges such as driving on highways and working collaboratively, all the way up to global challenges like commerce, peace, and pandemic preparedness. If AI is to play a larger role in society, it is important that AI agents will be able to cooperate effectively with other agents (other AI, humans, etc).</p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://arxiv.org/pdf/2012.08630.pdf" target="_blank" rel="noopener">Open Problems in Cooperative AI, Dafoe et al.</a><br>
<a href="https://www.nature.com/articles/d41586-021-01170-0" target="_blank" rel="noopener">Cooperative AI: machines must learn to find common ground</a></p>
</description>
</item>
<item>
<title>Scaling Neural Tangent Kernels via Sketching and Random Features</title>
<link>https://MSAIL.github.io/talk/ntk_020122/</link>
<pubDate>Tue, 01 Feb 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/ntk_020122/</guid>
<description><p>Kevin presented
<a href="https://arxiv.org/pdf/2106.07880.pdf" target="_blank" rel="noopener">Scaling Neural Tangent Kernels via Sketching and Random Features</a>, which uses sketching and random feature generation to speed up neural tangent kernels (NTKs). This presentation was really all about introducing the NTK, a mechanism for analyzing the behavior of very wide / infinitely wide neural networks. NTKs made a huge splash in machine learning theory in 2018 for offering a novel approach to analyzing the behavior of neural networks, and there&rsquo;s plenty of ground left to cover with them in research.</p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://towardsdatascience.com/the-kernel-trick-c98cdbcaeb3f" target="_blank" rel="noopener">Kernel trick</a><br>
<a href="https://www.youtube.com/watch?v=DObobAnELkU&amp;feature=youtu.be&amp;ab_channel=SoheilFeizi" target="_blank" rel="noopener">Professor Feizi&rsquo;s lecture</a><br>
<a href="https://rajatvd.github.io/NTK/" target="_blank" rel="noopener">Rajat&rsquo;s blog post</a><br>
<a href="https://arxiv.org/abs/1806.07572" target="_blank" rel="noopener">Paper #1, introduces NTKs</a><br>
<a href="https://arxiv.org/abs/1904.11955" target="_blank" rel="noopener">Paper #2, polynomial bounds NTK complexity and introduces CNTK</a><br>
<a href="https://arxiv.org/abs/1911.00809" target="_blank" rel="noopener">Paper #3, enhanced CNTK</a></p>
</description>
</item>
<item>
<title>Concrete Problems in AI Safety</title>
<link>https://MSAIL.github.io/talk/aisafety_012522/</link>
<pubDate>Tue, 25 Jan 2022 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/aisafety_012522/</guid>
<description><p>Ashwin gave an introduction to the field of AI safety, which studies how to ensure that AI, especially artificial general intelligence and super intelligence, will be safe and trustworthy.</p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://arxiv.org/pdf/1606.06565.pdf" target="_blank" rel="noopener">Concrete Problems in AI Safety, by Amodei et al.</a></p>
</description>
</item>
<item>
<title>Human-in-the-Loop Natural Language Processing</title>
<link>https://MSAIL.github.io/talk/jkk_120621/</link>
<pubDate>Mon, 06 Dec 2021 20:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/jkk_120621/</guid>
<description><p><strong>Speaker(s)</strong>: Dr. Jonathan Kummerfeld<br>
<strong>Topic</strong>: Human-in-the-Loop Natural Language Processing</p>
<p>Dr. Kummerfeld works on NLP, with many projects crossing into HCI, either in the process of creating datasets or developing systems. In this talk, he gave a brief introduction to NLP and Crowdsourcing + Human Computation, and then dove into two research projects. First, he discussed work on task-oriented dialogue (e.g. Siri), where his team developed new ways to collect more diverse data, which in turn leads to more robust models. Second, he discussed work on understanding a set of conversations occurring in a shared channel (e.g. in Slack).</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://jkk.name/" target="_blank" rel="noopener">Dr. Kummerfeld&rsquo;s Website</a></p>
</description>
</item>
<item>
<title>Michigan AI Alumni Panel</title>
<link>https://MSAIL.github.io/talk/alumni_panel111521/</link>
<pubDate>Mon, 15 Nov 2021 20:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/alumni_panel111521/</guid>
<description><p><strong>Speaker(s)</strong>: Anthony Zheng, Kiran Prasad, Andong Li Zhao, Christian Kavouras<br>
<strong>Topic</strong>: Michigan AI Alumni Panel</p>
<p>We hosted a virtual speaker panel with a few UMich alumni who are currently doing very exciting work with AI in industry and academia.</p>
<ul>
<li>Anthony Zheng is an Apple research engineer working on search algorithms for Apple Media Products</li>
<li>Kiran Prasad is an Applied Scientist at Microsoft working on NLP models for Microsoft products and was at CMU for his MS in AI and Innovation</li>
<li>Andong Li Zhao is a CS PhD student at Northwestern working on making information more democratically accessible</li>
<li>Christian Kavouras is a former Applied Scientist intern at Amazon working on ML/NLP applications and graduated from UWashington for his MS in Computational Linguistics</li>
</ul>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://docs.google.com/presentation/d/10JTvSD_VORdCg-E9IYoPhS1mZczLmKywwfkfXWlhOek/edit?usp=sharing" target="_blank" rel="noopener">Andong&rsquo;s Slides</a><br>
<a href="https://docs.google.com/presentation/d/1rKEofg8u7B7gRVuciozTMA2Ob6ykUszGJV6DhDuEmDI/edit?usp=sharing" target="_blank" rel="noopener">Anthony&rsquo;s Slides</a><br>
<a href="https://drive.google.com/file/d/1QpWAzvGtJbur6sh08Yyru6h6KD2bgVVR/view?usp=sharing" target="_blank" rel="noopener">Christian&rsquo;s Slides</a><br>
<a href="https://drive.google.com/file/d/1kmj0a64CNVaoNex9-sCpBqAn-PVUGbEB/view?usp=sharing" target="_blank" rel="noopener">Kiran&rsquo;s Slides</a><br>
Check Slack or
<a href="https://MSAIL.github.io/contact/">contact us</a> if you&rsquo;re interested in getting their contact info!</p>
</description>
</item>
<item>
<title>Understanding MLOps for Computer Vision Pipelines</title>
<link>https://MSAIL.github.io/talk/datature_110821/</link>
<pubDate>Mon, 08 Nov 2021 19:30:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/datature_110821/</guid>
<description><p><strong>Speaker(s)</strong>: Datature Team<br>
<strong>Topic</strong>: Understanding MLOps for Computer Vision Pipelines</p>
<p>We hosted an industry talk with Datature, a no-code platform that allows teams and enterprises to build computer vision models. In this session, they covered key MLOps practices and the shift from &lsquo;model-centric AI&rsquo; development to a &lsquo;data-centric&rsquo; approach in the context of computer vision. There was also a &lsquo;hands-on&rsquo; aspect where students were able to build a facemask detection / chess piece detection model in under 30 minutes using Datature&rsquo;s no-code platform.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>We have a link with a tutorial for using Datature&rsquo;s MLOps platform, but it is UMich only. If you are a UMich student interested in seeing it, please reach out to the
<a href="https://MSAIL.github.io/contact/">MSAIL admin team</a> and we will happily pass it along.</p>
<p>
<a href="https://ml-ops.org/" target="_blank" rel="noopener">MLOps Website</a><br>
<a href="https://blogs.nvidia.com/blog/2020/09/03/what-is-mlops/" target="_blank" rel="noopener">NVIDIA MLOps Blog Post</a></p>
</description>
</item>
<item>
<title>Contrastive Learning with Hard Negative Samples</title>
<link>https://MSAIL.github.io/talk/contrastive_hns_110121/</link>
<pubDate>Mon, 01 Nov 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/contrastive_hns_110121/</guid>
<description><p><strong>Speaker(s)</strong>: Kevin Wang<br>
<strong>Topic</strong>: Contrastive Learning with Hard Negative Samples</p>
<p>Kevin talked about the paper
<a href="https://arxiv.org/abs/2010.04592v2" target="_blank" rel="noopener">Contrastive Learning with Hard Negative Samples</a>, by Joshua Robinson, Ching-Yao Chuang, Suvrit Sra, Stefanie Jegelka. In the past two years, contrastive learning has emerged as a powerful unsupervised computer vision technique for learning effective representations of data for downstream tasks. This theory-focused paper proposes a technique for sampling &ldquo;hard&rdquo; negative examples in contrastive learning. The authors note improved performance on downstream tasks compared to SimCLR and faster training.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://lilianweng.github.io/lil-log/2021/05/31/contrastive-representation-learning.html" target="_blank" rel="noopener">Lilian Weng&rsquo;s blog post on contrastive representation learning</a><br>
<a href="https://towardsdatascience.com/understanding-contrastive-learning-d5b19fd96607" target="_blank" rel="noopener">Ekin Tiu&rsquo;s post on contrastive learning</a><br>
<a href="https://ai.googleblog.com/2020/04/advancing-self-supervised-and-semi.html" target="_blank" rel="noopener">Google SimCLR</a></p>
</description>
</item>
<item>
<title>Latent Semantic Analysis</title>
<link>https://MSAIL.github.io/talk/lsa_102521/</link>
<pubDate>Mon, 25 Oct 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/lsa_102521/</guid>
<description><p><strong>Speaker(s)</strong>: Nisreen Bahrainwala<br>
<strong>Topic</strong>: Latent Semantic Analysis: An Overview</p>
<p>Latent Semantic Analysis is one of the many methods used to help computers &ldquo;understand&rdquo; meaning behind words and phrases, aiding with tasks such as search response relevance. This discussion will introduce the concept of LSA, some of the methods used during its development, and then explore how this technology has shaped modern NLP methods.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p><strong>Paper(s)</strong>:<br>
<a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.333.7403&amp;rep=rep1&amp;type=pdf" target="_blank" rel="noopener">A Solution to Plato&rsquo;s Problem: The Latent Semantic Analysis Theory of Acquisition, Induction, and Representation of Knowledge</a><br>
<a href="http://lsa.colorado.edu/papers/dp1.LSAintro.pdf" target="_blank" rel="noopener">An Introduction to Latent Semantic Analysis</a></p>
</description>
</item>
<item>
<title>Speech Emotion Recognition with ML</title>
<link>https://MSAIL.github.io/talk/speech_emotion_recog_100421/</link>
<pubDate>Mon, 04 Oct 2021 19:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/speech_emotion_recog_100421/</guid>
<description><p><strong>Speaker(s)</strong>: Lance Ying<br>
<strong>Topic</strong>: Speech Emotion Recognition with Machine Learning</p>
<p>This talk begins with a brief introduction of speech emotion recognition (SER) with machine learning and its applications. A few challenges in SER tasks and existing solutions are discussed. The second half of the talk focused on a recent paper and methods (Nonparametric Hierarchical Neural Network) to account for variations in emotional expression due to demographic and contextual factors for SER tasks.</p>
<p>
<a href="https://drive.google.com/file/d/11JTc3HdFXn3P4QY8tO8egKGy0-rVLegY/view?usp=sharing" target="_blank" rel="noopener">You can find a link to the recording here. (UM only)</a></p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://arxiv.org/abs/2109.04316" target="_blank" rel="noopener">Accounting for Variations in Speech Emotion Recognition with Nonparametric Hierarchical Neural Network</a><br>
<a href="https://cse.engin.umich.edu/wp-content/uploads/2019/11/EECS_498_598_Affective_Computing.pdf" target="_blank" rel="noopener">EECS 498 - ML and Affective Computing</a></p>
</description>
</item>
<item>
<title>Learning Effective Representations for Small Molecules</title>
<link>https://MSAIL.github.io/talk/chemdesc_092721/</link>
<pubDate>Mon, 27 Sep 2021 19:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/chemdesc_092721/</guid>
<description><p><strong>Speaker(s)</strong>: Mukundh Murthy<br>
<strong>Topic</strong>: Bioactivity Descriptors for Uncharacterized Chemical Compounds</p>
<p>Quantitative structure-activity modeling (QSAR) in computational chemistry is a task that involves predicting the binding affinity of a small molecule to a protein target given solely its molecular structure. Now, however, we are also interested in predicting more downstream properties including toxicity, side effects, and effects on gene expression – properties that concern both the biological and chemical properties of a molecule. This talk discussed the paper &ldquo;Bioactivity Descriptors for uncharacterized chemical compounds,&rdquo; which revolves around learning a generalizable and multi-modal representation for small molecules that can be applied across a large array of drug-discovery related tasks through integration of 25 small molecule datasets and a triplet network training task.</p>
<p>
<a href="https://drive.google.com/file/d/1sHALTeoucfLeO1aZGyhrLL6SYBXRgovI/view?usp=sharing" target="_blank" rel="noopener">You can find a recording of this talk here (UM only).</a></p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://www.biorxiv.org/content/10.1101/2020.07.21.214197v1.full" target="_blank" rel="noopener">Bioactivity Descriptors for Uncharacterized Chemical Compounds</a><br>
<a href="https://www.notion.so/Computational-Biochemistry-e57c4194c4234a898ecf2db36bb74015" target="_blank" rel="noopener">Computational Biochemistry Primer by Mukundh Murthy and Michael Trinh</a><br>
<a href="https://pubs.acs.org/doi/pdf/10.1021/acs.accounts.0c00699" target="_blank" rel="noopener">ML for Molecular Property Prediction</a><br>
<a href="https://arxiv.org/pdf/1703.00564.pdf" target="_blank" rel="noopener">MoleculeNet</a></p>
</description>
</item>
<item>
<title>AlphaFold 2 and the Protein Folding Problem</title>
<link>https://MSAIL.github.io/talk/alphafold_2_092021/</link>
<pubDate>Mon, 20 Sep 2021 19:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/alphafold_2_092021/</guid>
<description><p><strong>Speaker(s)</strong>: Ashwin Sreevatsa<br>
<strong>Topic</strong>: AlphaFold 2</p>
<p>The protein folding problem is one of the central challenges of biology over the past 50 years. The challenge is to identify the 3D structure of a protein given its amino acid sequence. Recently, DeepMind released a deep learning model called AlphaFold 2 that outperformed the state-of-the-art computational methods and predicted the 3D structures of proteins so accurately that many in the field now consider protein folding to be &lsquo;solved&rsquo;. This talk discussed a brief history of the protein folding problem, the architecture behind AlphaFold 2, and the next steps for protein folding and computational biology as a whole.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://www.nature.com/articles/s41586-021-03819-2.pdf" target="_blank" rel="noopener">AlphaFold 2 Paper in Nature</a><br>
<a href="https://github.com/deepmind/alphafold/" target="_blank" rel="noopener">AlphaFold 2 Source Code on Github</a><br>
<a href="https://deepmind.com/blog/article/AlphaFold-Using-AI-for-scientific-discovery" target="_blank" rel="noopener">DeepMind blog post on the initial AlphaFold</a><br>
<a href="https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology" target="_blank" rel="noopener">DeepMind blog post on AlphaFold 2</a><br>
<a href="https://www.youtube.com/watch?v=nGVFbPKrRWQ" target="_blank" rel="noopener">Video: AlphaFold and the Grand Challenge to solve protein folding by Arxiv Insights</a><br>
<a href="https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb#scrollTo=woIxeCPygt7K" target="_blank" rel="noopener">AlphaFold 2 Example on Google Colab</a></p>
</description>
</item>
<item>
<title>Data privacy and AI</title>
<link>https://MSAIL.github.io/post/federated_learning/</link>
<pubDate>Wed, 19 May 2021 00:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/post/federated_learning/</guid>
<description><p>We interact with machine learning algorithms every day&ndash;from scrolling through social media, to navigating around town, to selecting word recommendations when we text. But what do we know about these machine learning methods? They’re data hungry. More specifically, they’re hungry for OUR data. Many of our interactions with technology must be tracked and stored to develop and improve these algorithms, and this need comes with an inherent privacy risk. By giving up complete access to our sensitive data, we allow ourselves to be vulnerable to both the companies that collect our information and third parties who could be interested in exploiting us. Luckily, there is a set of machine learning and statistical techniques that allow model developers to learn from our data while protecting our privacy first. In this post, we’ll specifically discuss how large companies like Google, Apple, and Microsoft use <strong>federated learning</strong> and <strong>differential privacy</strong> to develop the state of art AI algorithms and relevant insights that we benefit from every day.</p>
<h2 id="federated-learning">Federated Learning</h2>
<p>The first concept we’ll discuss is called federated learning, and it&rsquo;s vital for making sure your data stays local to your device.</p>
<p>Now let&rsquo;s say we wanted to train a
<a href="https://towardsdatascience.com/building-a-next-word-predictor-in-tensorflow-e7e681d4f03f#:~:text=Next%20Word%20Prediction%20or%20what,or%20emails%20without%20realizing%20it." target="_blank" rel="noopener">next word prediction</a> model to give word recommendations to users as they type. This task involves predicting the next word in a sentence given the previous words, and these predictions can be seen above the keyboard as you type.</p>
<p><img src="fig1.png" alt="Next Word Prediction"></p>
<p align="center" style="font-size:15px;">
Next word predictions are shown above your keyboard as your type. Machine learning models are trained to predict the next word you will type given the previous words in the <a href="https://medium.com/@pankaj.karki.786/predicting-the-next-word-f10936cc5d4e">sentence</a>.
</p>
<p>If we had access to all of our users&rsquo; mobile devices, we would need to access samples of text messages and collect them in a central server for us to train our model. But wait&ndash;text messages contain extremely sensitive data, and this would be an extremely invasive data collection process. Instead of bringing all of the data to a central server with the model, we can use federated learning to learn a global model without a user’s data leaving their device.</p>
<p>In a typical federated learning setting, one central server communicates with several clients (in this case, mobile phones) and trains a global model in several rounds. Each round consists of the following steps:</p>
<ol>
<li>
<p>Select a sample of available phones for training and send the current global model to each phone</p>
</li>
<li>
<p>In parallel, train the global model on each phone on their local text messages for one (or a few) epoch(s). Now each phone contains model updates to the global model that were calculated using their own small datasets</p>
</li>
<li>
<p>The model updates from each phone are sent back to the central server and averaged to calculate the gradient update for the global model in this training round.</p>
</li>
</ol>
<p><img src="fig2.png" alt="Central Server Communication"></p>
<p align="center" style="font-size:15px;">
An illustration of how a central server communicates with client servers in federated learning. Produced by <a href="https://blog.ml.cmu.edu/2019/11/12/federated-learning-challenges-methods-and-future-directions/">ML@CMU</a>.
</p>
<p>For next word prediction, some of the text data from the messages you send everyday are accessed for federated learning. Your phone might be selected for federated learning when it is being charged (to ensure your phone’s performance doesn’t drop) and you have strong wifi bandwidth. Next word prediction is a semi-supervised task (meaning we can automatically construct labels from the raw text data), so there is no additional need for labelling your local data. In a
<a href="https://arxiv.org/pdf/1902.01046.pdf" target="_blank" rel="noopener">2018 paper</a>, Google showcased a 1.4 million parameter LSTM model that was trained for 5 days (3000 total rounds!) on over a million users that matched the performance of a centralized server trained model.</p>
<p>Now, let’s examine how Apple uses a similar technique to personalize their news recommendation algorithm. As discussed in a
<a href="https://arxiv.org/pdf/2102.08503.pdf" target="_blank" rel="noopener">recent paper</a>, they use federated learning to not only learn a global model, but to personalize their models to individual users in a privacy-preserving manner. Apple news is an app that curates personalized news article feeds for users to select and read articles from. These recommendations are based on your interactions with specific articles (e.g what articles you click on, how long you read them, etc.). Article-label pairs can be easily constructed and stored on your device (positive label if read, negative if not read). After learning a global recommendation model, the model can be tested on each client device and remotely fine tuned based on the prediction loss on each user’s specific dataset. The model first takes advantage of the huge knowledge base of users to create a powerful global model, and then can further personalize to each user without ever collecting any data.</p>
<p><img src="fig3.png" alt="News Broadcast"></p>
<p align="center" style="font-size:15px;">
An example of how news is broadcasted on the <a href="https://www.macstories.net/news/apple-releases-ios-136-with-apple-news-audio-features-and-expanded-local-news-coverage-plus-digital-car-key-support/">Apple News</a> interface.
</p>
<p>Now federated learning itself has some privacy limitations&ndash;although Google or Apple might not have access to your specific data, they could theoretically learn about your data from the model updates sent back to the server. For better privacy guarantees, Google implements a method called
<a href="https://eprint.iacr.org/2017/281.pdf" target="_blank" rel="noopener">Secure Aggregation</a>. This method encrypts each individual client model update and sends them to a trusted, third party server for encrypted aggregation&ndash;the central server can now only decrypt the aggregated data and has no access to individual model updates.</p>
<p><img src="fig4.png" alt="Model Training"></p>
<p align="center" style="font-size:15px;">
The left picture represents data being sent to a central server to model training. The middle showcases how models are sent to local devices to be trained, and aggregate together on the central server. The right demonstrates how FL can be better secured by sending encrypted updates to a third party server for aggregation, and the decrypted result is made available to the central server. Figure used from <a href="https://eprint.iacr.org/2017/281.pdf">this paper.</a>
</p>
<h2 id="differential-privacy">Differential Privacy</h2>
<p>The next technique that companies use to protect privacy aims to prevent your individual information from leaking through statistical queries, model predictions, and other analyses. This technique is called <strong>differential privacy</strong>.</p>
<p>The simplest definition of differential privacy from its
<a href="https://www.cis.upenn.edu/~aaroth/Papers/privacybook.pdf" target="_blank" rel="noopener">original authors</a> is: “the data holder makes a promise to the data subject that they will not be affected adversely or otherwise by allowing their data to be used in the study/analysis, no matter what other sources are available”. So if you participate in a dataset, differential privacy gives you some mathematical certainty that any statistical query or model trained on it will not reveal your personal data. From a researcher’s perspective, we want to learn about a dataset without learning about individuals that participate in that dataset. Let’s look at a quick example often used in surveys that collect sensitive information.</p>
<p>Since the 1960s, sociologists have used a technique called <em>
<a href="https://en.wikipedia.org/wiki/Randomized_response" target="_blank" rel="noopener">randomized response</a></em> in order to get statistics of a population regarding a sensitive topic while protecting each individual&rsquo;s privacy. If a researcher wanted to know what percentage of a population has jaywalked, for example, they could give each participant in the study the following procedure:</p>
<ol>
<li>
<p>Flip a coin without me seeing it. If it lands on Heads, answer truthfully about whether you’ve jaywalked previously.</p>
</li>
<li>
<p>If it lands on Tails, answer your question according to the next coin flip. “Yes” if Heads, and “No” if tails.</p>
</li>
</ol>
<p>Now, every participant can have <em>plausible deniability</em> if it is discovered they answered yes or no to the question. Furthermore, researchers can still get a rough idea of the true global statistic to the question they asked: if the final amount of “Yes” answers occurs 70% of the time, we know half answered with the probability of the coin flip (50%), and the other half must have answered with the probability of 90%. So in this population, the true statistic must be around 90%. This still may not be exactly accurate due to randomness of the coin flip&ndash;there is some tradeoff between privacy and accuracy when applying random noise to each data point.</p>
<p>This procedure above is an example of <strong>local differential privacy</strong>, where the goal is to add random noise to each <em>individual</em> data point before it is entered into a database. The great thing here is that each individual participant does not need to trust the central data curator&ndash;an ideal setting for the relationship between millions of users and big tech companies.</p>
<p>Now, let’s take a look at how Apple uses this technique when collecting statistics on user activity. Apple must collect user data to determine what emojis are most popular among users or what specific online domains drain the most energy on Safari. The first step is encoding their data of interest (in this example, let’s say an emoji you used recently) into a fixed size matrix representation using a <em>hash function</em>. Then, each bit of this matrix representation is changed to an incorrect value with some tunable probability value (anywhere from 1-25%).</p>
<p><img src="fig5.png" alt="Apple emojis"></p>
<p align="center" style="font-size:15px;">
An example graph of top emojis of US speakers from Apple’s differential privacy <a href="https://www.apple.com/privacy/docs/Differential_Privacy_Overview.pdf">overview</a>. Read more about how Apple obtains this visualization <a href="https://machinelearning.apple.com/research/learning-with-privacy-at-scale">here</a>.</i>
</p>
<p>After this noise is added to each individual’s records, IP and other personal identifiers are stripped before the data is sent to the server. The final statistics are then aggregated on Apple’s servers for their internal use&ndash;for example, Apple can identify the most popular emojis being used and design better ways of accessing/recommending them. If a user’s specific activity data was leaked from Apple’s central server, each user could have some level of plausible deniability that it wasn’t their correct data.</p>
<p>Local DP is used by Google in order to track changes to user&rsquo;s Chrome settings and combat malicious software that changes these settings without user permission. Google also employs DP in user facing analysis features like Google Search Trends and Google Maps&rsquo;
<a href="https://policies.google.com/technologies/anonymization?hl=en-US" target="_blank" rel="noopener">&ldquo;busyness&rdquo; feature</a>, which tells you how busy a place may be at any given time. Whether your data is being used by these companies to improve products or collected and aggregated for users to see, differential privacy is a useful technique that prevents malicious actors from personally identifying your data from a dataset.</p>
<h2 id="other-interesting-notes">Other interesting notes</h2>
<p>Large tech companies have also built open-source tools that support federated learning and differential privacy, which opens the door for researchers and developers to easily adopt these techniques in their applications. Google has built
<a href="https://static.googleusercontent.com/media/research.google.com/en//pubs/archive/42852.pdf" target="_blank" rel="noopener">RAPPOR</a> for differential privacy and
<a href="https://www.tensorflow.org/federated" target="_blank" rel="noopener">TensorFlow Federated</a> for federated learning. Microsoft is using their differential privacy library
<a href="https://github.com/opendp/smartnoise-core" target="_blank" rel="noopener">SmartNoise</a> with nonprofits and health care companies to provide privacy protections to the most sensitive personal data domains.</p>
<h2 id="concluding-remarks">Concluding remarks</h2>
<p>In this post, we learned about the fundamental concepts of federated learning and differential privacy and how Google and Apple access our data while protecting our individual privacy and ownership of that data. The examples discussed are just early use cases of these tools, and future applications are likely to arise. The discussion of data privacy is a very complex one, and these techniques by themselves won’t be the end all solution. At the end of the day, companies control these algorithms and protocols, and can manipulate them however they choose to. But in the world of big data, privacy preserving machine learning techniques can be the technical gateway to allowing users to regain control of their most personal and sensitive data, while maintaining the utility we gain from powerful machine learning models.</p>
<p>What other data hungry applications or research projects do you think could take advantage of these useful techniques?</p>
<h2 id="references">References</h2>
<p>
<a href="https://arxiv.org/pdf/1602.05629.pdf" target="_blank" rel="noopener">Communication-efficient learning of deep networks from decentralized data</a></p>
<p>
<a href="https://arxiv.org/pdf/1902.01046.pdf" target="_blank" rel="noopener">Towards federated learning at scale: system design</a></p>
<p>
<a href="https://www.cis.upenn.edu/~aaroth/Papers/privacybook.pdf" target="_blank" rel="noopener">The algorithmic foundations of differential privacy</a></p>
<p>
<a href="https://en.wikipedia.org/wiki/Randomized_response" target="_blank" rel="noopener">Randomized response</a></p>
<p>
<a href="https://www.apple.com/privacy/docs/Differential_Privacy_Overview.pdf" target="_blank" rel="noopener">Apple&rsquo;s differential privacy overview</a></p>
<p>
<a href="https://policies.google.com/technologies/anonymization?hl=en-US" target="_blank" rel="noopener">How Google anonymizes data</a></p>
<p>
<a href="https://classroom.udacity.com/courses/ud185" target="_blank" rel="noopener">Udacity&rsquo;s Secure and Private AI course</a></p>
</description>
</item>
<item>
<title>How We Built This: TDM Studio and Sentiment Analysis</title>
<link>https://MSAIL.github.io/talk/proquest_041321/</link>
<pubDate>Tue, 13 Apr 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/proquest_041321/</guid>
<description><p><strong>Speaker(s)</strong>: Dan Hepp and John Dillon<br>
<strong>Topic</strong>: How We Built This: TDM Studio and Sentiment Analysis</p>
<p>Dan Hepp is a Data Scientist Lead at ProQuest. Dan has thirty years of experience in research and production settings developing complex systems. He has a demonstrated track record of finding creative solutions to difficult technical problems and making them effective in real-world situations. Dan has expertise in machine learning, data
mining, information extraction, pattern recognition, information retrieval, natural language processing, computer vision, artificial intelligence, and optical character recognition.</p>
<p>John Dillon, Ph.D., is the Text and Data Mining Product Manager at ProQuest. His work focuses on pairing computational text analysis methods with traditional Humanities and Cultural Studies disciplines. He has published papers on Machine Learning and Sentiment Analysis and has worked previously as a postdoctoral researcher with the University of Notre Dame, USAID, and IBM Research.</p>
<p>This presentation consisted of two parts: The first part provided a history and overview of what it took to build TDM Studio from a product development standpoint. TDM Studio is a text and data mining solution offered by ProQuest. In the first part of the presentation, they gave us some practical insights into what to do and what not to do when trying to create a startup-esque product within a mid-sized company. The second portion of the presentation dug a little deeper into one aspect of TDM Studio, sentiment analysis. They discussed their work with the 2020 MDP Sentiment Analysis team and the results of their approach to the problem.</p>
<p>
<a href="https://drive.google.com/file/d/1VwbknZPyXw20qxhKnMmnaw6gxaIYNjK7/view?usp=sharing" target="_blank" rel="noopener">You can view a recording of his talk here.</a></p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://tdmstudio.proquest.com/home" target="_blank" rel="noopener">TDM Studio</a><br>
<a href="https://mdp.engin.umich.edu/sponsor_teams/proquest-ocr/" target="_blank" rel="noopener">MDP Team Description</a></p>
</description>
</item>
<item>
<title>Do convolutional neural networks mimic the human visual system?</title>
<link>https://MSAIL.github.io/post/cnn_human_visual/</link>
<pubDate>Sun, 11 Apr 2021 00:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/post/cnn_human_visual/</guid>
<description><p>Richard Feynman once said “What I cannot create I do not understand.” Therefore, to truly understand the human visual system, we must learn to create it. One of the most effective forms of such creation is the Convolutional Neural Network (CNN) system to mimic the human visual system. Computer Vision models that use the CNN system have achieved near human-level performances on tasks such as image classification and object detection. There is no question the CNNs have shown us mind-blowing performance, but the question is: do they actually resemble the biological visual system? Are we really creating it? As a quest to answer this question, in this article we will explore the similarities and differences between the CNNs and the biological visual system.</p>
<p>To start off, let’s explore the roots of the CNN - how does a CNN function and what are its capabilities? In simple terms, the CNN is able to learn features from images, for example - it is able to deduce if an image has a dog; it is able to deduce if the image is a desert, it can tell if an image is a painting. Let’s take a look at some example features that CNNs can learn to extract from an image. In the image underneath, we can see that for a baseball, the CNN meshes the unique features of a baseball such as rounded shape, stripes, into a filter image. This filter image is then used to cross check against input images to determine whether each input image contains a baseball. The same is done for dogs, clouds and buildings, etc, with their own respective filter images. This way, we can use CNNs for tasks such as classification (labeling an image to a group/class), object detection (detecting the presence of certain objects in an image), and image generation (imitating certain styles and patterns to generate unique images), among many other tasks.</p>
<p><img src="fig1.png" alt="Filters for detecting image features"></p>
<p align="center" style="font-size:15px;">
Use of filters for detecting image features [1]
</p>
<p>So now that we have an idea of how CNNs function, we can move on to discussing how its design compares to the biological visual system. The CNN is composed of image processing layers that deduce and pass down information from one layer to the next. At each layer, information of different abstractions is deduced. Generally, in the earlier layers, simpler and more basic ideas will be deduced while later layers will use the gathered information from the previous layers to deduce more complex ideas. The following figure lays down an example CNN - in the figure, a boat image is passed from the left end layer to the next until it reaches the right-most layer, where it classifies the class of the image; in this case, it should be “Boat”.</p>
<p><img src="fig2.png" alt="Layer structure"></p>
<p align="center" style="font-size:15px;">
Layer Structure of a CNN [6]
</p>
<p>Due to the way the layers learn more complex features the deeper into the network, we can call this a hierarchical learning structure. To see clearly what we mean by the complexity of features, we can observe the following figure. The first group shows the detection of edges - which are simpler features compared to the textures in the second group. The CNN layers detect such “textures” through the combination of “edges” detected in the previous layer. Likewise, the following layers learn patterns through combining textures, and so on and so forth, until the last layers learn the presence of certain objects. In this way, the complexity of features increases as we go deeper down the network, demonstrating a hierarchical learning mechanism.</p>
<p><img src="fig3.png" alt="Complexity of learned features"></p>
<p align="center" style="font-size:15px;">
Different complexity of learned features [1]
</p>
<p>This hierarchical layer structure is actually also utilized in the visual cortex ventral pathway, which is a layerlike pathway consisting of the sequence LGN-V1-V2-V4-IT where each of them represents a certain information processing layer (Figure 4). As we proceed through the visual pathway, the features learned become more complex, just as in the CNN. The receptive visual field size increases as well, as larger receptive field suggests a more holistic and general feature in the image. In a way, this makes sense - to recognize a baseball, the network has to learn stripes and some circular shapes. Likewise, for a dog, the features might be the dog snouts, black and white eyes, furry texture, etc. Such features cannot be instantly detected in just a single step, but rather gathered throughout different layers’ learning, which forms the basis of hierarchical learning.</p>
<p><img src="fig4.png" alt="Visual Cortex Ventral Pathway"></p>
<p align="center" style="font-size:15px;">
Human Visual Cortex Ventral Pathway [3]
</p>
<p>In addition to the concept of hierarchical information processing in CNNs, another fundamental concept called pooling is utilized. Pooling is basically the idea of generalizing or approximating a set of values in an area into a smaller set of values. This concept is explained in the following figure. The input image is a grid of 16 values and pooling is applied on the image to result in a grid of 4 values; each of the 4 values are the maximum values taken from their respective areas represented by the color. By taking the maximum, we reduce the size of the information we are looking at and select the most important values that need to be paid attention to.</p>
<p><img src="fig5.png" alt="Pooling Mechanism"></p>
<p align="center" style="font-size:15px;">
Pooling Mechanism [8]
</p>
<p>To understand at the higher level, the pooling is used to aggregate information gathered into summarized information. This idea of aggregation allows for the hierarchical information processing - the basic features learned are aggregated and then the details are gotten rid of to learn high level features. Pooling reduces the dimension of the representation and “creates an invariance to small shifts and distortions”. Basically this means that switching an image around by slight pixel changes will not affect the information being deduced from the image. Through pooling, we eliminate repeated learning of similar features that are right next to each other in the image feature representation. Interestingly, this idea behind the pooling layer is found in the relation between simple and complex cells in the biological neural system, where simple cells simply evoke a response on each of their particular spatial locations, while complex cells seem to be pooling over responses from the simple cells and thus showing more spatial invariance in their responses.</p>
<p>No matter how neat CNN is in capturing visual information like the biological system, there are some outright flaws in it. One is the possibility of adversarial attacks, which involve hacking the CNN by slightly changing the pixel values of images in a way that is undetectable to a human eye but enough to fool the CNN to make faulty conclusions. An example is shown below, where the panda image is altered to be recognized as a gibbon by a CNN although there seems to be no difference to the human eye (Figure 6). This example shows how the CNN is perceiving ideas through meticulous attention to every single pixel in an image, which might not be the case with human visuals; for humans, perception likely happens through directly seeing the patterns and lines rather than individual pixels.</p>
<p><img src="fig6.png" alt="Adversarial Attack on CNN"></p>
<p align="center" style="font-size:15px;">
Adversarial Attack on CNN (<a href="https://openai.com/blog/adversarial-example-research/">OpenAI</a>)
</p>
<p>On the other hand, this makes us wonder, “Can the human visual system be hacked as well? Are there ways to fool our eyes although maybe to another species there isn’t noticeable change?” It turns out that there are ways to fool our visual perception as well through small image change. Researchers have found a way to generate images that are designed to tip the perception towards a different idea although there isn’t much change in the image composition. Look at the example below - the left image looks like a cat, but when altered slightly to form the right image, it starts to look more like a dog. Such a hack is akin to the idea of subliminal stimuli - visual or auditory stimuli that the conscious mind cannot detect but that the brain subconsciously processes - maybe adversarial attacks are subliminal messages for the CNN.</p>
<p><img src="fig7.png" alt="Adversarial Attack on Human Visual System"></p>
<p align="center" style="font-size:15px;">
Adversarial Attack on Human Visual System [9]
</p>
<p>While it’s quite interesting to ponder such ideas and even question our sensual perception, the conclusion is that there are evidently parallels between the way CNN works and the way the human visual system works. However, there are also some fundamental differences between them - although these differences could possibly be reduced through more complex layers and architectural changes in the CNN design.</p>
<h2 id="references">References</h2>
<p>[1]
<a href="https://distill.pub/2017/feature-visualization/" target="_blank" rel="noopener">Feature Visualization - What are CNNs learning?</a></p>
<p>[2]
<a href="https://distill.pub/2018/building-blocks/" target="_blank" rel="noopener">Interpretation with building blocks</a></p>
<p>[3]
<a href="https://neurdiness.wordpress.com/2018/05/17/deep-convolutional-neural-networks-as-models-of-the-visual-system-qa/" target="_blank" rel="noopener">Neural networks as models of the visual system</a></p>
<p>[4]
<a href="https://www.cs.toronto.edu/~hinton/absps/NatureDeepReview.pdf" target="_blank" rel="noopener">LeCun - Nature Deep Learning Review</a></p>
<p>[5]
<a href="https://machinelearningmastery.com/convolutional-layers-for-deep-learning-neural-networks/" target="_blank" rel="noopener">How Conv layers work</a></p>
<p>[6]
<a href="https://www.vision-systems.com/boards-software/article/14037858/fundamentals-of-deep-neural-networks" target="_blank" rel="noopener">Fundamentals of Deep Neural Networks</a></p>
<p>[7]
<a href="http://fourier.eng.hmc.edu/e180/lectures/v1/node7.html" target="_blank" rel="noopener">Simple and Complex cells in the Human visual system</a></p>
<p>[8]
<a href="https://towardsdatascience.com/understanding-convolutions-and-pooling-in-neural-networks-a-simple-explanation-885a2d78f211" target="_blank" rel="noopener">Understanding Convolutions and Pooling in Neural Networks</a></p>
<p>[9]
<a href="https://spectrum.ieee.org/the-human-os/artificial-intelligence/machine-learning/hacking-the-brain-with-adversarial-images" target="_blank" rel="noopener">Hacking the Brain with Adversarial Images</a></p>
</description>
</item>
<item>
<title>Intelligent Politics: How AI Can Improve Our Political Institutions and Systems</title>
<link>https://MSAIL.github.io/talk/politics_ai_systems_040521/</link>
<pubDate>Tue, 06 Apr 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/politics_ai_systems_040521/</guid>
<description><p><strong>Speaker(s)</strong>:
<a href="https://andongluis.github.io/" target="_blank" rel="noopener">Andong Luis Li Zhao</a><br>
<strong>Topic</strong>: Intelligent Politics: How AI Can Improve Our Political Institutions and Systems</p>
<p>Andong Luis Li Zhao is a Computer Science PhD student at Northwestern University, working in the C3 Lab under Prof. Kristian Hammond. His main research focus is modernizing our political systems through AI. He is currently working on making political information more transparent by building systems that can understand vaguely-articulated questions, obtain the correct data analysis, and identify the most appropriate representation of that analysis.</p>
<p>While his specific focus is currently on providing the public with access to information about our political system, this work is part of a broader goal of improving how society functions through socially-conscious AI grounded in real systems. Too often technologists abdicate their social responsibility by focusing on technical development. Instead, by developing human-centered AI technology that helps inform people and uncover novel insights, we can focus on the betterment of social, political, and economic systems and their impact.</p>
<p>
<a href="https://drive.google.com/file/d/1AvjuKSlNVVurQWtyFg6qUh1F8ZB6X9ft/view?usp=sharing" target="_blank" rel="noopener">You can view a recording of his talk here.</a></p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p>
<a href="https://scales-okn.org/" target="_blank" rel="noopener">SCALES: Transforming the Accessibility and Transparency of Federal Courts</a><br>
<a href="https://sites.northwestern.edu/c3lab/" target="_blank" rel="noopener">C3 Lab</a></p>
</description>
</item>
<item>
<title>Harmful Bias in Natural Language Generation</title>
<link>https://MSAIL.github.io/talk/harmful_bias_nlg/</link>
<pubDate>Tue, 30 Mar 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/harmful_bias_nlg/</guid>
<description><p><strong>Speaker(s)</strong>: Yashmeet Gambhir<br>
<strong>Topic</strong>: Harmful Bias in Natural Language Generation</p>
<p>Large language models have taken over the NLP scene and have led to a surge of state-of-art development in natural language generation tasks (machine translation, story generation, chatbots, etc.). However, these models have been shown to reflect many harmful societal biases that exist in text around the internet. This talk will go over two major papers studying harmful bias in large LMs: the first identifies and quantifies this bias, the second will attempt to mitigate bias.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p><strong>Papers:</strong><br>
<a href="https://arxiv.org/abs/1909.01326" target="_blank" rel="noopener">The Woman worked as a Babysitter: On Biases in Language Generation</a>
<a href="https://www.aclweb.org/anthology/2020.findings-emnlp.291.pdf" target="_blank" rel="noopener">Towards Controllable Biases in Language Generation</a></p>
</description>
</item>
<item>
<title>What could AI do for developing countries?</title>
<link>https://MSAIL.github.io/post/developing_countries/</link>
<pubDate>Sun, 14 Mar 2021 00:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/post/developing_countries/</guid>
<description><p>10% of the world’s population lives in extreme poverty. This means that around 700 million people are living on less than $1.90 a day (1). And while $1.90 is the standard set by the World Bank defining the international poverty line (2), by no means does it imply that a person earning more than this amount has anywhere near suitable standards of living. Poorer populations in countries such as South Sudan, Bolivia, and India (2) still struggle to access basic features that are usually taken for granted in more developed countries, such as clean water, sanitation, education, and healthcare. 2.1 billion people in the world do not have access to safe drinking water (3). Around 1.8 billion people do not have access to adequate sanitation (4). And a report from the World Health Organization and the World Bank found that 400 million do not have access to essential health services (5).</p>
<p>Much work is already being undertaken in attempts to address these key issues, but more is still needed. Artificial intelligence (AI) is one such area where there is potential in alleviating some of the problems accompanying poverty. AI encompasses areas such as natural language processing and robotics, and has seen success in recent years with technology like autonomous vehicles, disease diagnosis, and recommendation algorithms. It is a powerful tool that also has the potential to be applied in ways beneficial to those dealing with the circumstances and living standards that typically go with poverty, especially in the realms of sanitation and education.</p>
<h2 id="sanitation">Sanitation</h2>
<p>Issues of sanitation for impoverished regions encompass topics such as lack of clean water, proper toilet systems, and waste management.</p>
<p>One initiative attempting to address the problem of unsafe drinking water comes from an organization called Clean Water AI. Developers created a device that uses a “deep learning neural network to detect dangerous bacteria and harmful particles in water” (6). This technology employs computer vision to continuously monitor water quality and observe at a microscopic level. Widespread adoption of such an application could be beneficial for avoiding illnesses that arise from consumption of unsafe drinking water, such as cholera, typhoid, and polio (11).</p>
<p>Here&rsquo;s a short video detailing what Clean Water AI does:
<div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;">
<iframe src="https://www.youtube.com/embed/Df1X1Km9riQ" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; border:0;" allowfullscreen title="YouTube Video"></iframe>
</div>
</p>
<br>
<p>Lack of proper waste management is another huge issue for underdeveloped regions. Without systems in place to take care of waste, it has become common for garbage to be thrown out in the surrounding areas or tossed into nearby water sources, where it sometimes becomes a playground for the neighboring children (7). While the establishment and utilization of governmental systems and resources could help manage this waste problem, there are also innovations in the AI sector that could be applied to target the problem. Recycling is an important process for these communities, and a robot designed by engineers from Simon Fraser University could help distinguish waste from recyclable materials (8). Growing company CleanRobotics is also taking steps to aid the waste management process with an autonomous system called TrashBot, which uses “robotics, computer vision and artificial intelligence to detect and separate landfill from recyclables” (12). Establishing automated systems for removing trash build-up could make the process easier in underdeveloped regions that lack the proper systems, and this could be crucial for lowering rates of disease caused by unhygienic environments. Such use of artificial intelligence could also potentially improve financial outlooks for the citizens in these areas through reuse and repurposing of recyclable materials.</p>
<p><img src="assembly_recycle.png" alt="Recycling"></p>
<center style="font-size:15px;">
Credit: Arvinder Singh
</center>
<h2 id="education">Education</h2>
<p>The standard of education and the availability of educational resources also suffer in impoverished regions. Improved educational resources correlates positively with poverty statistics, as better education can benefit a region overall and positively impact its economy; “Education promotes economic growth because it provides skills that increase employment opportunities and income” (13)(14). It is no surprise, then, that poorer regions have less access to proper education and fewer members of the community acquire an education. Lack of nearby schools, teachers, transportation, and time are all contributors to this problem.</p>
<p>Universal education is a popular initiative and there is work being done with the AI field to progress this goal. The rise of the internet has provided opportunities for bringing education into the home with the growing format of online schooling. Having the capability to view pre-taught lessons online is an important development in tackling the aforementioned impediments to education in underdeveloped regions. While there already exist many online resources that provide information on a variety of subjects for anyone to browse, language barriers still persist. The Presentation Translator from Microsoft is one such tool involving AI that is attempting to address language barriers (15). It uses speech recognition and translation to create subtitles of presentations in the desired language, which users can access through the tool’s affiliated app or browser. Google’s translation application can also be used for reading, writing, and speaking translations. There are many other recent developments in the field of natural language processing that can help tackle language barriers, and further expansion of available languages in these applications would be advantageous for poorer regions with lesser-known tongues.</p>
<p><img src="translation.png" alt="Learning"></p>
<center style="font-size:15px;">
Credit: Arvinder Singh
</center>
<h2 id="challenges-to-ai-access">Challenges to AI Access</h2>
<p>There is much more growth happening in the AI field than what has been discussed here, and these technological advancements may be useful for targeting the persisting problems of poverty. But a major obstacle of using these tools to benefit developing countries is that many of these regions do not have the necessary structures in place to even implement such technologies.</p>
<p>If specialists are needed for the establishment and maintenance of these AI applications, it is unlikely there will be someone in these areas who can fulfill that role, especially with the lack of access to education. It could become even more costly to hire outside help for maintaining these applications than it already is just to instate them. It must also be determined who will fund these tools – if the creators of these applications are not providing them for free, who will the responsibility fall upon for payment? The impoverished region presumably cannot bear that burden. Governmental assistance is often what is needed in these situations, but these are developing areas and governmental instability is a common feature, as well as the fact that the developing economy often does not yet supply the financial resources needed to establish such systems. Lack of internet access is another deterrent to providing these AI tools. When the poorer regions of Asia and Africa are the ones more likely to have fewer people using the internet (16), and less than 5% of people are online in the poorest countries (10), this creates difficulty in making use of resources such as online education.</p>
<p>Some initiatives seeking to resolve these obstacles are in the works, but they encounter their own obstacles in the sheer size of the issue and lack of financial resources (like Project Loon, which was attempting to provide worldwide internet access through essential parts of cell towers attached to balloons (10) but has since shut down in January of 2021, stating they “haven’t found a way to get the costs low enough to build a long-term, sustainable business” (17)). The barriers to technological access in underdeveloped areas are widespread and persistent, and it is difficult for one well-meaning company or organization to solve them. These significant concerns will need to be addressed if artificial intelligence is to play a role in reducing poverty in our world.</p>
<h3 id="references">References</h3>
<p>[1]:
<a href="https://lifewater.org/blog/9-world-poverty-statistics-to-know-today/" target="_blank" rel="noopener">World Poverty Statistics via lifewater.org</a></p>
<p>[2]:
<a href="https://www.worldbank.org/en/topic/poverty#:~:text=Today%2C%20less%20than%2010%20percent,less%20than%20%241.90%20a%20day." target="_blank" rel="noopener">World Bank</a></p>
<p>[3]:
<a href="https://ourworldindata.org/water-access" target="_blank" rel="noopener">Water Access Data</a></p>
<p>[4]:
<a href="https://www.cdc.gov/healthywater/global/wash_statistics.html#:~:text=An%20estimated%20790%20million%20people,to%20an%20improved%20water%20supply." target="_blank" rel="noopener">CDC Wash Statistics</a></p>
<p>[5]:
<a href="https://www.who.int/mediacentre/news/releases/2015/uhc-report/en/" target="_blank" rel="noopener">New report shows that 400 million do not have access to essential health services via WHO</a></p>
<p>[6]:
<a href="https://cleanwaterai.com/#intro" target="_blank" rel="noopener">Clean Water AI</a></p>
<p>[7]:
<a href="https://www.pbs.org/newshour/world/in-worlds-poorest-slums-landfills-and-polluted-rivers-become-a-childs-playground" target="_blank" rel="noopener">via PBS</a></p>
<p>[8]:
<a href="https://www.sfu.ca/sfunews/stories/2019/07/artificial-intelligence-robot-reduces-waste-contamination-at-sfu.html" target="_blank" rel="noopener">Artificial intelligence robot reduces waste contamination at SFU</a></p>
<p>[9]:
<a href="https://loon.com/technology/flight-systems/" target="_blank" rel="noopener">Flight systems via Loon</a></p>
<p>[10]:
<a href="https://ourworldindata.org/internet" target="_blank" rel="noopener">Internet Access</a></p>
<p>[11]:
<a href="https://www.who.int/news-room/fact-sheets/detail/drinking-water#:~:text=Contaminated%20water%20can%20transmit%20diseases,000%20diarrhoeal%20deaths%20each%20year" target="_blank" rel="noopener">Contaminated water can transmit diseases</a></p>
<p>[12]:
<a href="https://cleanrobotics.com/trashbot/" target="_blank" rel="noopener">TrashBot via CleanRobotics</a></p>
<p>[13]:
<a href="https://www.globalcitizen.org/en/content/poverty-education-satistics-facts/" target="_blank" rel="noopener">Poverty Education Statistics</a></p>
<p>[14]:
<a href="https://www.un.org/sustainabledevelopment/blog/2017/06/millions-could-escape-poverty-by-finishing-secondary-education-says-un-cultural-agency/" target="_blank" rel="noopener">Millions could escape poverty by finishing secondary education</a></p>
<p>[15]:
<a href="https://www.microsoft.com/en-us/translator/APPS/PRESENTATION-TRANSLATOR/#:~:text=About%20Presentation%20Translator,-Presentation%20Translator%20subtitles&amp;text=As%20you%20speak%2C%20Presentation%20Translator,deaf%20or%20hard%20of%20hearing" target="_blank" rel="noopener">Microsoft Presentation Translator</a></p>
<p>[16]:
<a href="https://www.pewresearch.org/global/2016/02/22/internet-access-growing-worldwide-but-remains-higher-in-advanced-economies/" target="_blank" rel="noopener">Internet access growing worldwide but remains higher in advanced economies via Pew Research</a></p>
<p>[17]:
<a href="https://medium.com/loon-for-all/loon-draft-c3fcebc11f3f" target="_blank" rel="noopener">Loon for all</a></p>
</description>
</item>
<item>
<title>Using Transformers for Vision</title>
<link>https://MSAIL.github.io/talk/image-worth-16x16-words/</link>
<pubDate>Tue, 09 Mar 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/image-worth-16x16-words/</guid>
<description><p><strong>Speaker(s)</strong>: Andrew Awad and Drake Svoboda<br>
<strong>Topic</strong>: Using Transformers for Computer Vision</p>
<p>In recent years we&rsquo;ve seen the rise of transformers in natural language processing research, burgeoning the field to incredible heights. However, these very same transformers were seldom applied to computer vision tasks until recently. Andrew and Drake discussed how transformers have been used in vision tasks in recent years in a presentation covering two papers. The first, An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale (via Google Brain), is the &ldquo;Attention is All You Need&rdquo; of vision. Namely, this paper covers how one can construct a vision architecture devoid of the commonly applied CNN and still achieve comparable or better performance results while possibly cutting down computing resources. The second paper, End-to-End Object Detection with Transformers (via FAIR), formalizes the object detection task in a unique way that affords the usage of transformers.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p><strong>Papers:</strong><br>
<a href="https://arxiv.org/pdf/2010.11929.pdf" target="_blank" rel="noopener">AN IMAGE IS WORTH 16X16 WORDS: TRANSFORMERS FOR IMAGE RECOGNITION AT SCALE</a></p>
<p>
<a href="https://arxiv.org/pdf/2005.12872.pdf" target="_blank" rel="noopener">End-to-End Object Detection with Transformers</a></p>
</description>
</item>
<item>
<title>Proving Theorems with Generative Language Models</title>
<link>https://MSAIL.github.io/talk/generative_language_modeling/</link>
<pubDate>Mon, 01 Mar 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/generative_language_modeling/</guid>
<description><p><strong>Speaker(s)</strong>: Ashwin Sreevatsa<br>
<strong>Topic</strong>: Generative Language Modeling for Automated Theorem Proving Presentation</p>
<p>In the past decade, deep learning and artificial neural networks have been incredibly successful at a variety of tasks such as computer vision, translation, game playing, and robotics among others. However, there have been less examples of deep learning making progress with reasoning related tasks- such as automated theorem proving, the task of proving mathematical theorems using computer programs. This paper explores the use of transformer-based models to automated theorem proving and presents GPT-f, a deep learning-based automated prover and proof assistant.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p><strong>Papers:</strong><br>
<a href="https://arxiv.org/pdf/2009.03393.pdf" target="_blank" rel="noopener">Generative Language Modeling for Automated Theorem Proving Presentation</a></p>
</description>
</item>
<item>
<title>Lightning Round -- Assorted AI Topics</title>
<link>https://MSAIL.github.io/previous_material/lightning/</link>
<pubDate>Sat, 27 Feb 2021 15:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/previous_material/lightning/</guid>
<description><p><strong>Topic</strong>: Lightning Round &ndash; Assorted AI Topics<br>
<strong>Presenter</strong>: Kevin Wang</p>
<p>Here, we talk about a wide range of topics in AI that haven&rsquo;t received their own slide decks &ndash; the list includes reinforcement learning, optimization, adversarial machine learning, meta learning, active learning, multi-agent systems, and more. We hope that showcasing the breadth of AI research inspires you to dig deeper on your own and find what interests you!</p>
<p>
<a href="https://drive.google.com/file/d/169IpCxkST0Fjp7LjQgpdfiDz-Ccs1K-v/view?usp=sharing" target="_blank" rel="noopener">You can view a recording of this lesson here.</a></p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://docs.google.com/presentation/d/1uQzkFpr4LyslagkloUHs5lnCQ3wNmVLfuaa7UsbTaGA/edit?usp=sharing" target="_blank" rel="noopener">Lesson slides</a></p>
</description>
</item>
<item>
<title>Ethics</title>
<link>https://MSAIL.github.io/previous_material/ethics/</link>
<pubDate>Fri, 26 Feb 2021 17:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/previous_material/ethics/</guid>
<description><p><strong>Topic</strong>: Ethics in AI Research<br>
<strong>Presenter</strong>: Kevin Wang</p>
<p>We discuss the various ethical problems AI research presents, including well-known problems like bias and weaponized AI and less publicized problems like interpretability and environmental impact of large machine learning models. We also talk about some of the solutions that researchers are attempting to implement and what we can do to contribute.</p>
<p>
<a href="https://drive.google.com/file/d/1C-bWWrhh_hK6ZwNmLEYK95uLJ6eiCbi1/view?usp=sharing" target="_blank" rel="noopener">You can view a recording of this lesson here.</a></p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://docs.google.com/presentation/d/1KUUqzdz-Te1oNS4AMnxxPqO_mFUpmkDNokr0As9rCHQ/edit?usp=sharing" target="_blank" rel="noopener">Lesson slides</a></p>
</description>
</item>
<item>
<title>Cognitive Load Estimation</title>
<link>https://MSAIL.github.io/talk/cognitive_load_estimation/</link>
<pubDate>Tue, 23 Feb 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/cognitive_load_estimation/</guid>
<description><p><strong>Speaker(s)</strong>: Patrick Morgan<br>
<strong>Topic</strong>: Cognitive Load Estimation</p>
<p>Cognitive load has been shown, over hundreds of studies, to be an important variable for understanding human performance. However, establishing practical, non-contact, automated methods for estimating cognitive loads under real-world conditions is an un-solved problem. In this paper, Fridman et. al. proposes two novel vison-based methods for cognitive-load estimation. These methods address a important and challenging problem that has huge implications and can be used to ensure safety in tasks ranging from driving cars to operating machinery.</p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p><strong>Papers:</strong><br>
<a href="https://www.researchgate.net/profile/Lex-Fridman/publication/324658835_Cognitive_Load_Estimation_in_the_Wild/links/5bf0ba3092851c6b27c74bd1/Cognitive-Load-Estimation-in-the-Wild.pdf" target="_blank" rel="noopener">Cognitive Load Estimation in the Wild</a></p>
</description>
</item>
<item>
<title>Protecting the environment with AI</title>
<link>https://MSAIL.github.io/post/ai_environment/</link>
<pubDate>Mon, 22 Feb 2021 00:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/post/ai_environment/</guid>
<description><p>Employing forest guards to protect endangered species. Organising volunteers for beach cleanups. Encouraging people to lead greener lifestyles. These are just some of the traditional methods that have been used to protect our environment. But, as Alan Turing once said, &lsquo;At some stage,&hellip; we should have to expect the machines to take control&rsquo; [1] and this couldn’t be more true in these conservation efforts. Be it preserving wildlife, cleaning up the environment or reducing green-house gas emissions, AI has started playing an increasingly dominant role as it has become good at numerous tasks such as visually identifying and tracking poachers or designing the most energy efficient buildings.</p>
<p>Google, for example, has used AI to increase the efficiency and significantly reduce the carbon footprint of its data centers. Data centers are massive energy consumers, being turned on 24/7 and requiring significant cooling. In 2016 it was reported that data centers used more electricity than Britain, producing roughly the same carbon footprint as the aviation industry [2]. A google search of the video &ldquo;Despacito&rdquo; activates six to eight of Google&rsquo;s data centers [3]. In line with Google’s effort to stay carbon neutral (which they achieved in 2007 [3]), Google implemented a reinforcement learning algorithm in 2016 to determine what “cooling configurations (in its data centers) would reduce energy consumption” [5]. A reinforcement algorithm is a subset of machine learning in which the environment sends a ‘state’ and ‘reward’ to the ‘agent’ - the reinforcement learning algorithm - which in turn tries to maximise the reward [4]. The data centers using this reinforcement algorithm now consistently use 30% less energy than expected [6].</p>
<p><img src="data-center.jpg" alt="A Google Data Center in Iowa"></p>
<p align="center" style="font-size:15px;">
A Google data center in Iowa (<a href="https://www.technologyreview.com/2018/08/17/140987/google-just-gave-control-over-data-center-cooling-to-an-ai/">MIT Technology Review</a>)
</p>
<p>Big companies are not the only ones that are taking advantage of AI to be more environmentally friendly. Small startups are using AI to tackle environmental problems as well. In a remote reserve in Ecuador, Topher White - founder of Rainforest connection (a startup that aims to combat deforestation) - climbs a tree using a small harness and installs a small box containing an old cell phone and solar cells [7]. These phones recoprd the natural rainforest sounds and use AI to detect logging noises, upon which a notification is sent to a ranger. He had started his firm after learning of the severity of deforestation: the number of trees has fallen by almost 50% since the beginning of human civilisation, and still over 15 billion trees are currently cut down every year [8]. Topher White&rsquo;s first encounter with deforestation came ironically when he was on a trip to the rainforests of Borneo and was shocked to find illegal loggers just a hundred meters from the ranger station. Monitoring forests using AI to identify deforestation on satellite imagery often comes too late as satellite imagery requires some amount of deforestation before it becomes visible. However, the sound, he recalls, was deafening, which gave him the idea to mount these small phones on the treetops to identify logging. The very next day after the first installation, a logger was apprehended, and it is now preventing deforestation in 10 countries [7].</p>
<p><img src="topher-white.jpg" alt="Topher White"></p>
<p align="center" style="font-size:15px;">
Topher White (<a href="https://www.fastcompany.com/90435386/this-network-of-microphones-listens-for-the-chainsaws-of-illegal-loggers-in-the-rainforest">Rolex/Stefan Walter via FastCompany</a>)
</p>
<p>In fact even industries have turned to using AI to reduce costs and also increase their sustainability. One example is in Norway, where AI is being used to increase the efficiency of salmon farms [9]. Telenor Research - the research wing of the Norwegian telecoms company Telenor that is conducting research on the use of AI in fish farms - has come up with a neural network that uses a video feed from underwater cameras to determine when the salmon have finished feeding. The salmon swim in schools which disperse when food is thrown, but when the salmon are full, there are tiny deviations in this behaviour which the neural network picks up with 80% accuracy. Identifying these cues to better feed the right amount of food is beneficial economically (40% of the cost of salmon farms comes from fish food), and also helps prevent low oxygen levels, algae blooms and high nitrate levels which are toxic to fish, among other problems [12].</p>
<p>There are numerous other AI applications in this area: IBM has come up with a machine learning tool named AquaCloud to predict lice outbreaks in Salmon with 70% accuracy using a random forest algorithm [10]. The industries&rsquo; increasingly intensive salmon and rainbow trout fishing encourages lice growth, which in turn makes them unsellable because lice feed on salmon skin [9].</p>
<p><img src="graph.jpg" alt="AquaCloud lice predictions"></p>
<p align="center" style="font-size:15px;">
The results of AquaCloud: the green line shows the lice outbreak predicted two weeks in advance. (<a href="https://www.ibm.com/blogs/cloud-computing/2018/09/17/data-science-norway-fish-farmers/">NCE Seafood Innovation Center</a>)
</p>
<p>The use of AI on fish farms is especially beneficial as fish farms are sustainable and help to reduce the dependency on precious ocean fish populations. Wild salmon are being depleted at an alarming rate, yet Norway’s salmon exports are only rising. Even here, AI is also being used to track the wild salmon population in efforts to sustain its population [9].</p>
<p>These examples are but a small subset of AI-related projects that have been done. A brief search of new competitions regarding environmental solutions (most of which use AI, even if the competition implies only a possible technological solution), confirms the increasing interest in sustainability. The Xprize - a nonprofit that runs public competitions - is currently running a $10 million prize rainforest competition to “develop novel technologies to rapidly and comprehensively survey rainforest biodiversity and use that data to improve our understanding of this complex ecosystem” [11]. Microsoft’s AI for Good grants are given to projects that enhance climate, water, and biodiversity. Prince William recently launched the Earthshot prize - a series of annual one million pound prize competitions in five categories such as reviving the oceans, cleaning the air, and protecting nature. There are countless other competitions and the examples discussed in this article are just a taste of the AI environmental projects to come.</p>
<h3 id="references">References</h3>
<p>[1]:
<a href="https://analyticsindiamag.com/ten-famous-quotes-about-artificial-intelligence/#:~:text=%E2%80%9CArtificial%20intelligence%20will%20reach%20human,%E2%80%93%20a%20billion%2Dfold.%E2%80%9D" target="_blank" rel="noopener">Ten Famous Quotes about Artificial Intelligence</a></p>
<p>[2]:
<a href="https://www.computerworld.com/article/3431148/why-data-centres-are-the-new-frontier-in-the-fight-against-climate-change.html" target="_blank" rel="noopener">Why Data Centres are the New Frontier in the Fight Against Climate Change</a></p>
<p>[3]:
<a href="https://fortune.com/2019/09/18/internet-cloud-server-data-center-energy-consumption-renewable-coal/#:~:text=Data%20centers%20contribute%200.3%25%20to,one%20for%20every%20100%20Americans" target="_blank" rel="noopener">The Internet Cloud has a Dirty Secret</a></p>
<p>[4]:
<a href="https://towardsdatascience.com/introduction-to-various-reinforcement-learning-algorithms-i-q-learning-sarsa-dqn-ddpg-72a5e0cb6287" target="_blank" rel="noopener">Introduction to Various Reinforcement Learning Algorithms</a></p>
<p>[5]:
<a href="https://www.technologyreview.com/2018/08/17/140987/google-just-gave-control-over-data-center-cooling-to-an-ai/#:~:text=Google%20revealed%20today%20that%20it,order%20to%20lower%20power%20consumption" target="_blank" rel="noopener">Google Just Gave Control Over Data Center Cooling to an AI</a></p>
<p>[6]:
<a href="https://services.google.com/fh/files/misc/google_2019-environmental-report.pdf" target="_blank" rel="noopener">Google 2019 Environmental Report</a></p>
<p>[7]:
<a href="https://www.fastcompany.com/90435386/this-network-of-microphones-listens-for-the-chainsaws-of-illegal-loggers-in-the-rainforest" target="_blank" rel="noopener">This Network of Microphones Listens for the Chainsaws of Illegal Loggers in the Rainforest</a></p>
<p>[8]:
<a href="https://www.nature.com/articles/nature14967.epdf?sharing_token=662fd6kwyoW2pWYP7gTtqdRgN0jAjWel9jnR3ZoTv0PVqBqhRh-xvvJTzHFUU9TMfiseqc7XBtw3yJeJCBwHMEd325JNCYv-3DvRroRPJJJkTX95golfBeN0XF1aaW8P59jvn5Sk0G_AU4O4V7AYAm5mOs3rWaxWrsHFRlurXF8zdFAS7FkVY9jYIW5ojMN-nvvGu0eucnWzPgZF2qvs0ca--T3nUj6njgtSI9LJcUU%3D&amp;tracking_referrer=www.nationalgeographic.com" target="_blank" rel="noopener">Crowther et al., Mapping tree density at a global scale</a></p>
<p>[9]:
<a href="https://www.wsj.com/articles/ai-could-help-find-cheaper-and-smarter-ways-to-raise-fish-11601458200?mod=djemfoe" target="_blank" rel="noopener">AI Could Help Find Cheaper and Smarter Ways to Raise Fish</a></p>
<p>[10]:
<a href="https://www.ibm.com/case-studies/the-seafood-innovation-cluster-hybrid-cloud-fish-farming" target="_blank" rel="noopener">The Seafood Innovation Cluster</a></p>
<p>[11]:
<a href="https://rainforest.xprize.org/prizes/rainforest" target="_blank" rel="noopener">Rainforest XPrize</a></p>
<p>[12]:
<a href="https://www.petcoach.co/article/why-overfeeding-fish-is-a-problem-and-how-to-avoid-it/#:~:text=Accumulated%20uneaten%20food%20and%20fish,changes%20in%20the%20water%20chemistry.&amp;text=High%20ammonia%20and%20nitrites%20%2D%20The,are%20extremely%20toxic%20to%20fish" target="_blank" rel="noopener">Why overfeeding fish is a problem and how to avoid it</a></p>
</description>
</item>
<item>
<title>Unsupervised Learning</title>
<link>https://MSAIL.github.io/previous_material/unsupervised/</link>
<pubDate>Sat, 20 Feb 2021 15:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/previous_material/unsupervised/</guid>
<description><p><strong>Topic</strong>: Unsupervised Learning<br>
<strong>Presenter</strong>: Kevin Wang</p>
<p>This lesson went over the unsupervised side of AI, where labels don&rsquo;t exist and models are left on their own to learn useful information. We presented machine learning approaches with and without deep learning that tackle unsupervised problems.</p>
<p>
<a href="https://drive.google.com/file/d/1WXBrrbNDryufUYkzQS1aLwrEcJRbo-xS/view?usp=sharing" target="_blank" rel="noopener">You can view a recording of this lesson here.</a></p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://docs.google.com/presentation/d/1H77BDYebNusyelevFe5-AHZzYCaOB1tid-Vqtmm13oI/edit?usp=sharing" target="_blank" rel="noopener">Lesson slides</a></p>
</description>
</item>
<item>
<title>Natural Language Processing</title>
<link>https://MSAIL.github.io/previous_material/nlp/</link>
<pubDate>Fri, 19 Feb 2021 17:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/previous_material/nlp/</guid>
<description><p><strong>Topic</strong>: Natural Language Processing<br>
<strong>Presenter</strong>: Kevin Wang</p>
<p>This lesson gave a high level overview of NLP (natural language processing) and how AI can be used to work with text and speech data. Points of discussion included recurrent neural networks, LSTMs/GRUs, and GPT-3 and other transformer models.</p>
<p>
<a href="https://drive.google.com/file/d/1DjwaY3p7vb4N4V7DwvZEBQB2qxjs5okS/view?usp=sharing" target="_blank" rel="noopener">You can view a recording of this lesson here.</a></p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://docs.google.com/presentation/d/178FNnk3x8euXO3NHBqQT9VT6-d9FigUVOt56Ru-Lvpo/edit?usp=sharing" target="_blank" rel="noopener">Lesson slides</a></p>
</description>
</item>
<item>
<title>Deep RL for Robotics: A Short Overview</title>
<link>https://MSAIL.github.io/talk/deeprlrobotics_021621/</link>
<pubDate>Tue, 16 Feb 2021 18:00:00 -0400</pubDate>
<guid>https://MSAIL.github.io/talk/deeprlrobotics_021621/</guid>
<description><p><strong>Speaker(s)</strong>: Nikhil Devraj<br>
<strong>Topic</strong>: A Brief Overview of Deep RL in Robotics</p>
<p>Deep reinforcement learning (RL) has emerged as a promising approach for autonomously acquiring complex behaviors from low level sensor observations. Although a large portion of deep RL research has focused on applications in video games and simulated control, which does not connect with the constraints of learning in real environments, deep RL has also demonstrated promise in enabling physical robots to learn complex skills in the real world.<br>
This discussion focused predominantly on the following questions: <br>
(1) What is deep RL and how does it relate to robotics?<br>
(2) What are some examples of studies done with Deep RL in robotics?<br>
(3) What are major challenges faced by researchers who apply deep RL to robotics?</p>
<p>This discussion is heavily inspired by
<a href="https://arxiv.org/pdf/2102.02915.pdf" target="_blank" rel="noopener">Ibarz et al.</a>, although it does not dive into that level of detail.</p>
<p>
<a href="https://drive.google.com/file/d/1gshp58d3yce4LhcLpTymch8IA2cbm4ZO/view?usp=sharing" target="_blank" rel="noopener">You can find the recording of this talk here.</a></p>
<h3 id="supplemental-resources">Supplemental Resources</h3>
<p><strong>Papers:</strong><br>
<a href="https://arxiv.org/pdf/2102.02915.pdf" target="_blank" rel="noopener">How to Train Your Robot with Deep Reinforcement Learning - Lessons We&rsquo;ve Learned</a><br>
<a href="https://arxiv.org/abs/1610.00633" target="_blank" rel="noopener">Deep Reinforcement Learning for Robotic Manipulation with Asynchronous Off-Policy Updates</a><br>
<a href="https://journals.sagepub.com/doi/abs/10.1177/0278364913495721" target="_blank" rel="noopener">Reinforcement learning in robotics: a survey</a></p>
<p><strong>Articles:</strong><br>
<a href="https://medium.com/@vmayoral/reinforcement-learning-in-robotics-d2609702f71b" target="_blank" rel="noopener">Medium: Reinforcement learning in robotics</a></p>
<p><strong>Other</strong>:<br>
<a href="https://ieor8100.github.io/rl/docs/RL%20in%20Robotics.pdf" target="_blank" rel="noopener">Better slides (in our presenter&rsquo;s opinion)</a><br>
<a href="https://www.youtube.com/watch?v=GX_RonOFe1U" target="_blank" rel="noopener">Deep RL Towards Robotics by Shane Gu (Google Brain)</a><br>
<a href="https://www.youtube.com/watch?v=luzOblzznIc" target="_blank" rel="noopener">Deep RL in Robotics with NVIDIA Jetson</a></p>
</description>
</item>
<item>
<title>Computer Vision</title>
<link>https://MSAIL.github.io/previous_material/computer_vision/</link>
<pubDate>Sat, 13 Feb 2021 15:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/previous_material/computer_vision/</guid>
<description><p>
<strong>Topic</strong>: An Overview of Computer Vision<br>
<strong>Presenter</strong>: Kevin Wang</p>
<p>This lesson gave a basic overview of the computer vision problem space. We discussed historically significant developments including convolutional neural networks, AlexNet, ResNet, and more, and we gave a glimpse at ongoing research.</p>
<p>
<a href="https://drive.google.com/file/d/15WxV2hC40Bz4YhcyPVeYqb1gvIViq2Ka/view?usp=sharing" target="_blank" rel="noopener">You can view a recording of this lesson here.</a></p>
<h2 id="supplemental-resources">Supplemental Resources</h2>
<p>
<a href="https://docs.google.com/presentation/d/1MaC9d25kJybNv_pOYQHFv9oNOM1J-65zMkQX2PMlCqg/edit?usp=sharing" target="_blank" rel="noopener">Lesson slides</a></p>
</description>
</item>
<item>
<title>Introduction and Basics of Deep Learning</title>
<link>https://MSAIL.github.io/previous_material/intro_dl_basics/</link>
<pubDate>Fri, 12 Feb 2021 17:00:00 +0000</pubDate>
<guid>https://MSAIL.github.io/previous_material/intro_dl_basics/</guid>
<description><p>
<strong>Topic</strong>: Introduction to AI Research and Basics of Deep Learning<br>
<strong>Presenter</strong>: Kevin Wang </p>
<p>This lesson introduced the format of lessons for the winter 2021 semester, briefly introducing the topics to be presented in the coming weeks. We then gave a high-level overview of neural networks, which form the basis of deep learning and drive much of AI research today. </p>